From a5fe9ee7e0418e259c92a1cc47c4a8402653a661 Mon Sep 17 00:00:00 2001 From: Insang Song Date: Wed, 20 Sep 2023 10:44:51 -0400 Subject: [PATCH 01/21] version and apptainer test --- containers/apptainer_rocker | 18 ++++++++++++++++++ slurm_test/terra_runs_Rcode_file copy.sh | 13 +++++++++++++ 2 files changed, 31 insertions(+) create mode 100644 containers/apptainer_rocker create mode 100755 slurm_test/terra_runs_Rcode_file copy.sh diff --git a/containers/apptainer_rocker b/containers/apptainer_rocker new file mode 100644 index 00000000..438dcc4e --- /dev/null +++ b/containers/apptainer_rocker @@ -0,0 +1,18 @@ +BootStrap: docker +From: rocker/geospatial:latest + +%post + apt-get -y update + +%environment + export LC_ALL=C + export DDN_MOUNT=/ddn/gs1/group/ + +%files + + +%runscript + + +%labels + Insang Song \ No newline at end of file diff --git a/slurm_test/terra_runs_Rcode_file copy.sh b/slurm_test/terra_runs_Rcode_file copy.sh new file mode 100755 index 00000000..e5db2858 --- /dev/null +++ b/slurm_test/terra_runs_Rcode_file copy.sh @@ -0,0 +1,13 @@ +#!/bin/bash + +#SBATCH --job-name=calc_merra_subset_scomps.r +#SBATCH --error=terra.climate.local.error +#SBATCH --mail-user=songi2@nih.gov +#SBATCH --mail-type=NONE +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=1 +#SBATCH --partition=highmem + +## Run R: +/ddn/gs1/biotools/R/bin/Rscript -e "sessionInfo()" +/ddn/gs1/biotools/R421/bin/Rscript -e "sessionInfo()" From cab904e23e087a87df9b49459c01318cb266f046 Mon Sep 17 00:00:00 2001 From: Insang Song Date: Mon, 2 Oct 2023 17:34:02 -0400 Subject: [PATCH 02/21] Integrating testthat - Packaging is based on litr markdown: tests.R has all tests - Will edit test file names after all tests are added --- .Rbuildignore | 1 + scomps/DESCRIPTION | 12 ++-- scomps/tests/testthat.R | 12 ++++ scomps/tests/testthat/tests.R | 34 +++++++++ scomps_rmarkdown_litr.html | 66 ++++++++++++++++-- scomps_rmarkdown_litr.rmd | 42 ++++++++++- .../scomps_0.0.1.09032023.tar.gz | Bin .../scomps_0.0.2.09152023.tar.gz | Bin .../scomps_0.0.2.09192023.tar.gz | Bin tarballs/scomps_0.0.2.10022023.tar.gz | Bin 0 -> 22366 bytes 10 files changed, 155 insertions(+), 12 deletions(-) create mode 100644 .Rbuildignore create mode 100644 scomps/tests/testthat.R create mode 100644 scomps/tests/testthat/tests.R rename scomps_0.0.1.09032023.tar.gz => tarballs/scomps_0.0.1.09032023.tar.gz (100%) rename scomps_0.0.2.09152023.tar.gz => tarballs/scomps_0.0.2.09152023.tar.gz (100%) rename scomps_0.0.2.09192023.tar.gz => tarballs/scomps_0.0.2.09192023.tar.gz (100%) create mode 100644 tarballs/scomps_0.0.2.10022023.tar.gz diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 00000000..eb97a3c9 --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1 @@ +rds$ diff --git a/scomps/DESCRIPTION b/scomps/DESCRIPTION index ace15212..58d77a8a 100644 --- a/scomps/DESCRIPTION +++ b/scomps/DESCRIPTION @@ -1,6 +1,6 @@ Package: scomps Title: Scalable R geospatial computation -Version: 0.0.2.09192023 +Version: 0.0.2.10022023 Authors@R: person("Insang", "Song", , "geoissong@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-8732-3256")) @@ -12,18 +12,22 @@ Encoding: UTF-8 Roxygen: list(markdown = TRUE) RoxygenNote: 7.2.3 Imports: + covr, dplyr, future, future.apply, rlang, sf, - terra + terra, + testthat Suggests: future.batchtools, igraph, knitr, logr, - rmarkdown + rmarkdown, + withr VignetteBuilder: knitr +Config/testthat/edition: 3 LitrVersionUsed: 0.9.0 -LitrId: b4b4b1780f36a343cb1320d63dc814b9 +LitrId: 820777ef4091f4dab083c17458b45127 diff --git a/scomps/tests/testthat.R b/scomps/tests/testthat.R new file mode 100644 index 00000000..b465b524 --- /dev/null +++ b/scomps/tests/testthat.R @@ -0,0 +1,12 @@ +# This file is part of the standard setup for testthat. +# It is recommended that you do not modify it. +# +# Where should you do additional test configuration? +# Learn more about the roles of various files in: +# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview +# * https://testthat.r-lib.org/articles/special-files.html + +library(testthat) +library(scomps) + +test_check("scomps") diff --git a/scomps/tests/testthat/tests.R b/scomps/tests/testthat/tests.R new file mode 100644 index 00000000..35965382 --- /dev/null +++ b/scomps/tests/testthat/tests.R @@ -0,0 +1,34 @@ +# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand +testthat::test_that("What package does the input object belong?", +{ + withr::local_package("stars") + withr::local_package("terra") + withr::local_options(list(sf_use_s2 = FALSE)) + bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc") + bcsd_stars = stars::read_stars(bcsd_path) + + packbound_stars = check_packbound(bcsd_stars) + sprast_bcsd = terra::rast(bcsd_path) + packbound_terra = check_packbound(sprast_bcsd) + + testthat::expect_equal(packbound_stars, "sf") + testthat::expect_equal(packbound_terra, "terra") +}) + + +testthat::test_that("What package does the input object belong?", +{ + withr::local_package("stars") + withr::local_package("terra") + withr::local_options(list(sf_use_s2 = FALSE)) + data(stars_sentinel2) + nc = system.file(package = "sf", "shape/nc.shp") + nc = sf::read_sf(nc) + + datatype_stars = check_datatype(stars_sentinel2) + datatype_sf = check_datatype(nc) + + testthat::expect_equal(datatype_stars, "raster") + testthat::expect_equal(datatype_sf, "vector") +}) + diff --git a/scomps_rmarkdown_litr.html b/scomps_rmarkdown_litr.html index 040d4379..974a9d21 100644 --- a/scomps_rmarkdown_litr.html +++ b/scomps_rmarkdown_litr.html @@ -368,7 +368,7 @@

Package setup

path = ".", fields = list( Package = params$package_name, - Version = "0.0.2.09192023", + Version = "0.0.2.10022023", Title = "Scalable R geospatial computation", Description = "A package for scalable geospatial computation for environmental health research", `Authors@R` = person( @@ -386,10 +386,13 @@

Package setup

# usethis::use_package("stars") # Default is "Imports" usethis::use_package("terra") # Default is "Imports" usethis::use_package("rlang") # Default is "Imports" +usethis::use_package("testthat") usethis::use_package("logr", "Suggests") # Default is "Imports" usethis::use_package("future") # Default is "Imports" usethis::use_package("future.apply") # Default is "Imports" usethis::use_package("igraph", "Suggests") # Default is "Imports" +usethis::use_package("withr", "Suggests") +usethis::use_package("covr") usethis::use_package("future.batchtools", "Suggests") # Default is "Imports" # usethis::use_gpl3_license() @@ -438,6 +441,41 @@

Create functions

return("raster") } } +
testthat::test_that("What package does the input object belong?",
+{
+    withr::local_package("stars")
+    withr::local_package("terra")
+    withr::local_options(list(sf_use_s2 = FALSE))
+    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
+    bcsd_stars = stars::read_stars(bcsd_path)
+
+    packbound_stars = check_packbound(bcsd_stars)
+    sprast_bcsd = terra::rast(bcsd_path)
+    packbound_terra = check_packbound(sprast_bcsd)
+
+    testthat::expect_equal(packbound_stars, "sf")
+    testthat::expect_equal(packbound_terra, "terra")
+})
+
+
+testthat::test_that("What package does the input object belong?",
+{
+    withr::local_package("stars")
+    withr::local_package("terra")
+    withr::local_options(list(sf_use_s2 = FALSE))
+    data(stars_sentinel2)
+    nc = system.file(package = "sf", "shape/nc.shp")
+    nc = sf::read_sf(nc)
+
+    datatype_stars = check_datatype(stars_sentinel2)
+    datatype_sf = check_datatype(nc)
+
+    testthat::expect_equal(datatype_stars, "raster")
+    testthat::expect_equal(datatype_sf, "vector")
+})
+
## pr, tas, 
+## Test passed
+
## Test passed
#' @title Switch spatial data class
 #' @description Convert stars into SpatRaster and vice versa; sf into SpatVector and vice versa.
 #' @author Insang Song
@@ -1263,7 +1301,7 @@ 
Documenting the package and building

 the package. It may also be a good idea to check the package from within
 this file.

 
litr::document() # <-- use instead of devtools::document()
-
+devtools::test()
 devtools::build()
 devtools::install(build_vignettes = TRUE, dependencies = F)
 # devtools::check(document = FALSE)
@@ -1299,6 +1337,15 @@ 
Documenting the package and building

 ## Writing 'sp_indexing.Rd'
 ## Writing 'switch_packbound.Rd'
 ## Writing 'validate_and_repair_vectors.Rd'

+
## ℹ Testing scomps

+
## ✔ | F W S  OK | Context
+## 
+## ⠏ |         0 | tests                                                           pr, tas, 
+## 
+## ✔ |         4 | tests
+## 
+## ══ Results ═════════════════════════════════════════════════════════════════════
+## [ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]

 
## ── R CMD build ─────────────────────────────────────────────────────────────────
 ## * checking for file ‘/Users/songi2/Documents/GitHub/Scalable_GIS/scomps/DESCRIPTION’ ... OK
 ## * preparing ‘scomps’:
@@ -1314,11 +1361,17 @@ 
Documenting the package and building

 ## * checking for LF line-endings in source and make files and shell scripts
 ## * checking for empty or unneeded directories
 ## Removed empty directory ‘scomps/build’
-## * building ‘scomps_0.0.2.09192023.tar.gz’
+## * building ‘scomps_0.0.2.10022023.tar.gz’
 ## Warning: invalid uid value replaced by that for user 'nobody'
 ## Warning: invalid gid value replaced by that for user 'nobody'

-
## [1] "/Users/songi2/Documents/GitHub/Scalable_GIS/scomps_0.0.2.09192023.tar.gz"

+
## [1] "/Users/songi2/Documents/GitHub/Scalable_GIS/scomps_0.0.2.10022023.tar.gz"

+
## curl (5.0.2 -> 5.1.0) [CRAN]

+
## Installing 1 packages: curl
+## Installing package into '/Users/songi2/Library/R/arm64/4.3/library'
+## (as 'lib' is unspecified)

 
## 
+## The downloaded binary packages are in
+##  /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmpLf04ac/downloaded_packages
 ## ── R CMD build ─────────────────────────────────────────────────────────────────
 ## * checking for file ‘/Users/songi2/Documents/GitHub/Scalable_GIS/scomps/DESCRIPTION’ ... OK
 ## * preparing ‘scomps’:
@@ -1334,18 +1387,19 @@ 
Documenting the package and building

 ## * checking for LF line-endings in source and make files and shell scripts
 ## * checking for empty or unneeded directories
 ## Removed empty directory ‘scomps/build’
-## * building ‘scomps_0.0.2.09192023.tar.gz’
+## * building ‘scomps_0.0.2.10022023.tar.gz’
 ## Warning: invalid uid value replaced by that for user 'nobody'
 ## Warning: invalid gid value replaced by that for user 'nobody'
 ## 
 ## Running /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL \
-##   /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmpP7s4LX/scomps_0.0.2.09192023.tar.gz \
+##   /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmpLf04ac/scomps_0.0.2.10022023.tar.gz \
 ##   --install-tests 
 ## * installing to library ‘/Users/songi2/Library/R/arm64/4.3/library’
 ## * installing *source* package ‘scomps’ ...
 ## ** using staged installation
 ## ** R
 ## ** inst
+## ** tests
 ## ** byte-compile and prepare package for lazy loading
 ## ** help
 ## *** installing help indices
diff --git a/scomps_rmarkdown_litr.rmd b/scomps_rmarkdown_litr.rmd
index 5cc40fed..f3767faf 100644
--- a/scomps_rmarkdown_litr.rmd
+++ b/scomps_rmarkdown_litr.rmd
@@ -21,7 +21,7 @@ usethis::create_package(
   path = ".",
   fields = list(
     Package = params$package_name,
-    Version = "0.0.2.09192023",
+    Version = "0.0.2.10022023",
     Title = "Scalable R geospatial computation",
     Description = "A package for scalable geospatial computation for environmental health research",
     `Authors@R` = person(
@@ -39,10 +39,13 @@ usethis::use_package("sf") # Default is "Imports"
 # usethis::use_package("stars") # Default is "Imports"
 usethis::use_package("terra") # Default is "Imports"
 usethis::use_package("rlang") # Default is "Imports"
+usethis::use_package("testthat")
 usethis::use_package("logr", "Suggests") # Default is "Imports"
 usethis::use_package("future") # Default is "Imports"
 usethis::use_package("future.apply") # Default is "Imports"
 usethis::use_package("igraph", "Suggests") # Default is "Imports"
+usethis::use_package("withr", "Suggests")
+usethis::use_package("covr")
 usethis::use_package("future.batchtools", "Suggests") # Default is "Imports"
 # usethis::use_gpl3_license()
 
@@ -103,6 +106,41 @@ check_datatype <- function(input) {
 }
 ```
 
+```{r}
+testthat::test_that("What package does the input object belong?",
+{
+    withr::local_package("stars")
+    withr::local_package("terra")
+    withr::local_options(list(sf_use_s2 = FALSE))
+    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
+    bcsd_stars = stars::read_stars(bcsd_path)
+
+    packbound_stars = check_packbound(bcsd_stars)
+    sprast_bcsd = terra::rast(bcsd_path)
+    packbound_terra = check_packbound(sprast_bcsd)
+
+    testthat::expect_equal(packbound_stars, "sf")
+    testthat::expect_equal(packbound_terra, "terra")
+})
+
+
+testthat::test_that("What package does the input object belong?",
+{
+    withr::local_package("stars")
+    withr::local_package("terra")
+    withr::local_options(list(sf_use_s2 = FALSE))
+    data(stars_sentinel2)
+    nc = system.file(package = "sf", "shape/nc.shp")
+    nc = sf::read_sf(nc)
+
+    datatype_stars = check_datatype(stars_sentinel2)
+    datatype_sf = check_datatype(nc)
+
+    testthat::expect_equal(datatype_stars, "raster")
+    testthat::expect_equal(datatype_sf, "vector")
+})
+```
+
 ```{r}
 #' @title Switch spatial data class
 #' @description Convert stars into SpatRaster and vice versa; sf into SpatVector and vice versa.
@@ -1015,7 +1053,7 @@ We finish by running commands that will document, build, and install the package
 
 ```{r}
 litr::document() # <-- use instead of devtools::document()
-
+devtools::test()
 devtools::build()
 devtools::install(build_vignettes = TRUE, dependencies = F)
 # devtools::check(document = FALSE)
diff --git a/scomps_0.0.1.09032023.tar.gz b/tarballs/scomps_0.0.1.09032023.tar.gz
similarity index 100%
rename from scomps_0.0.1.09032023.tar.gz
rename to tarballs/scomps_0.0.1.09032023.tar.gz
diff --git a/scomps_0.0.2.09152023.tar.gz b/tarballs/scomps_0.0.2.09152023.tar.gz
similarity index 100%
rename from scomps_0.0.2.09152023.tar.gz
rename to tarballs/scomps_0.0.2.09152023.tar.gz
diff --git a/scomps_0.0.2.09192023.tar.gz b/tarballs/scomps_0.0.2.09192023.tar.gz
similarity index 100%
rename from scomps_0.0.2.09192023.tar.gz
rename to tarballs/scomps_0.0.2.09192023.tar.gz
diff --git a/tarballs/scomps_0.0.2.10022023.tar.gz b/tarballs/scomps_0.0.2.10022023.tar.gz
new file mode 100644
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z`v2kSzqYZj$e;V0(*AV~|FKAajVP*|BSvE#1w~O)u#2kRs<1IcCX83C
Date: Tue, 3 Oct 2023 11:51:03 -0400
Subject: [PATCH 03/21] Function restructuring - functions are reorganized in a
 fewer R files - workflow yaml extension fix - Added one test, fixed errors in
 previous tests

---
 ...check-standard.yml => check-standard.yaml} |   0
 .github/workflows/codecov.yaml                |  18 +-
 scomps/DESCRIPTION                            |   4 +-
 scomps/R/aw_covariates.R                      |  68 ----
 scomps/R/calculate_sedc.R                     |  48 ---
 scomps/R/check.R                              | 139 +++++++
 scomps/R/check_bbox.R                         |  34 --
 scomps/R/check_crs.R                          |  27 --
 scomps/R/check_crs2.R                         |  29 --
 scomps/R/check_packbound.R                    |  26 --
 scomps/R/check_within_reference.R             |  27 --
 scomps/R/clip_as_extent.R                     |  37 --
 scomps/R/clip_as_extent_ras.R                 |  20 -
 scomps/R/clip_as_extent_ras2.R                |  20 -
 scomps/R/distribute_process.R                 |  39 --
 scomps/R/extract_with.R                       |  33 --
 scomps/R/extract_with_buffer.R                |  50 ---
 scomps/R/extract_with_buffer.flat.R           |  23 --
 scomps/R/extract_with_buffer.kernel.R         |  27 --
 scomps/R/extract_with_polygons.R              |  55 ---
 scomps/R/{sp_indexing.R => indexing.R}        |   0
 ...ons.R => interpret_computational_domain.R} |  38 ++
 scomps/R/{initate_log.R => logging.R}         |   0
 .../R/{set_clip_extent.R => preprocessing.R}  |  11 +
 scomps/R/processing.R                         | 372 ++++++++++++++++++
 scomps/R/rast_short.R                         |  12 -
 .../R/{switch_packbound.R => switch_format.R} |   0
 ...lidate_and_repair_vectors.R => validate.R} |   0
 scomps/tests/testthat/tests.R                 |  35 +-
 scomps_rmarkdown_litr.html                    | 100 +++--
 scomps_rmarkdown_litr.rmd                     |  83 ++--
 tarballs/scomps_0.0.2.10032023.tar.gz         | Bin 0 -> 21871 bytes
 32 files changed, 727 insertions(+), 648 deletions(-)
 rename .github/workflows/{check-standard.yml => check-standard.yaml} (100%)
 delete mode 100644 scomps/R/aw_covariates.R
 delete mode 100644 scomps/R/calculate_sedc.R
 create mode 100644 scomps/R/check.R
 delete mode 100644 scomps/R/check_bbox.R
 delete mode 100644 scomps/R/check_crs.R
 delete mode 100644 scomps/R/check_crs2.R
 delete mode 100644 scomps/R/check_packbound.R
 delete mode 100644 scomps/R/check_within_reference.R
 delete mode 100644 scomps/R/clip_as_extent.R
 delete mode 100644 scomps/R/clip_as_extent_ras.R
 delete mode 100644 scomps/R/clip_as_extent_ras2.R
 delete mode 100644 scomps/R/distribute_process.R
 delete mode 100644 scomps/R/extract_with.R
 delete mode 100644 scomps/R/extract_with_buffer.R
 delete mode 100644 scomps/R/extract_with_buffer.flat.R
 delete mode 100644 scomps/R/extract_with_buffer.kernel.R
 delete mode 100644 scomps/R/extract_with_polygons.R
 rename scomps/R/{sp_indexing.R => indexing.R} (100%)
 rename scomps/R/{get_computational_regions.R => interpret_computational_domain.R} (83%)
 rename scomps/R/{initate_log.R => logging.R} (100%)
 rename scomps/R/{set_clip_extent.R => preprocessing.R} (77%)
 create mode 100644 scomps/R/processing.R
 delete mode 100644 scomps/R/rast_short.R
 rename scomps/R/{switch_packbound.R => switch_format.R} (100%)
 rename scomps/R/{validate_and_repair_vectors.R => validate.R} (100%)
 create mode 100644 tarballs/scomps_0.0.2.10032023.tar.gz

diff --git a/.github/workflows/check-standard.yml b/.github/workflows/check-standard.yaml
similarity index 100%
rename from .github/workflows/check-standard.yml
rename to .github/workflows/check-standard.yaml
diff --git a/.github/workflows/codecov.yaml b/.github/workflows/codecov.yaml
index 260f7f27..30ba6e81 100644
--- a/.github/workflows/codecov.yaml
+++ b/.github/workflows/codecov.yaml
@@ -1,12 +1,12 @@
-name: R Package CI
+on:
+ push:
+   branches:
+     - main
+ pull_request:
+   branches:
+     - main
 
-#on:
-#  push:
-#    branches:
-#      - main
-#  pull_request:
-#    branches:
-#      - main
+name: R Package CI
 
 jobs:
   build:
@@ -27,7 +27,7 @@ jobs:
         path: |
           ~/.cache/R
           ~/.local/share/R
-        key: dependencies-${{ runner.os }}-${{ hashFiles('**/DESCRIPTION') }}
+        key: dependencies-${{ runner.os }}-${{ hashFiles('**/scomps/DESCRIPTION') }}
         restore-keys: |
           dependencies-${{ runner.os }}-
 
diff --git a/scomps/DESCRIPTION b/scomps/DESCRIPTION
index 58d77a8a..2f72afbd 100644
--- a/scomps/DESCRIPTION
+++ b/scomps/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: scomps
 Title: Scalable R geospatial computation
-Version: 0.0.2.10022023
+Version: 0.0.2.10032023
 Authors@R: 
     person("Insang", "Song", , "geoissong@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8732-3256"))
@@ -30,4 +30,4 @@ Suggests:
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 LitrVersionUsed: 0.9.0
-LitrId: 820777ef4091f4dab083c17458b45127
+LitrId: 7c9484dd9127c939a90d433ec83cd305
diff --git a/scomps/R/aw_covariates.R b/scomps/R/aw_covariates.R
deleted file mode 100644
index 118c041a..00000000
--- a/scomps/R/aw_covariates.R
+++ /dev/null
@@ -1,68 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' Computing area weighted covariates using two polygon sf or SpatVector objects
-#' @param poly_in A sf/SpatVector object at weighted means will be calculated.
-#' @param poly_weight A sf/SpatVector object from which weighted means will be calculated.
-#' @param id_poly_in character(1). The unique identifier of each polygon in poly_in
-#' @return A data.frame with all numeric fields of area-weighted means.
-#' @description When poly_in and poly_weight are different classes, poly_weight will be converted to the class of poly_in. 
-#' @author Insang Song \email{geoissong@@gmail.com}
-#' @examples 
-#' # package
-#' library(sf)
-#' library(tictoc)
-#' 
-#' # run
-#' nc = st_read(system.file("shape/nc.shp", package="sf"))
-#' nc = st_transform(nc, 5070)
-#' pp = st_sample(nc, size = 300)
-#' pp[["id"]] = seq(1,nrow(pp))
-#' st_crs(pp) = "EPSG:5070"
-#' ppb = st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
-#' 
-#' tic()
-#' ppb_nc_aw = aw_covariates(ppb, nc, 'id')
-#' toc()
-#' summary(ppb_nc_aw)
-#' #### Example of aw_covariates ends ####
-#' @export
-aw_covariates <- function(poly_in, poly_weight, id_poly_in = "ID") {
-    stopifnot("Inputs have invalid classes.\n" = 
-      is(poly_in, "sf") || is(poly_weight, "sf") || is(poly_in, "SpatVector") || is(poly_weight, "SpatVector"))
-    #check_crs()
-    aw_covariates.terra = function(poly_in, poly_weight, id_poly_in = id_poly_in) {
-        
-        poly_intersected = terra::intersect(poly_in, poly_weight)
-        poly_intersected[["area_segment_"]] = terra::expanse(poly_intersected)
-        poly_intersected = data.frame(poly_intersected) |>
-            dplyr::group_by(!!rlang::sym(id_poly_in)) |>
-            dplyr::summarize(across(is.numeric,
-                        ~weighted.mean(., w = area_segment_))) |>
-            dplyr::ungroup()
-        return(poly_intersected)
-    }
-
-    class_poly_in = check_packbound(poly_in)
-    class_poly_weight = check_packbound(poly_weight)
-
-    if (class_poly_in != class_poly_weight) {
-      class_poly_weight = as(class_poly_weight, class(class_poly_in)[1])
-    }
-    
-    switch(class_poly_in,
-        sf = sf::st_interpolate_aw(poly_weight, poly_in, extensive = FALSE),
-        terra = aw_covariates.terra(poly_in, poly_weight, id_poly_in = id_poly_in))
-    
-}
-
-# ncbuf = terra::intersect(vect(ppb), vect(nc))
-# ncbuf_a = ncbuf
-# ncbuf_a$segarea = expanse(ncbuf_a)
-# ncbuf_k = data.frame(ncbuf_a) |>
-#   dplyr::group_by(id) |>
-#   dplyr::summarize(across(is.numeric,
-#                ~weighted.mean(., w = segarea))) |>
-#   dplyr::ungroup()
-
-#ncbufagg = terra::aggregate(ncbuf, by = 'id', fun = weighted.mean, w = ncbuf_a$segarea)
-
diff --git a/scomps/R/calculate_sedc.R b/scomps/R/calculate_sedc.R
deleted file mode 100644
index 6aed8d49..00000000
--- a/scomps/R/calculate_sedc.R
+++ /dev/null
@@ -1,48 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' Calculate SEDC covariates
-#' @param point_from SpatVector object. Locations where the sum of SEDCs are calculated.
-#' @param point_to SpatVector object. Locations where each SEDC is calculated.
-#' @param sdec_bandwidth numeric(1). Distance at which the source concentration is reduced to exp(-3) (approximately 95 %)  
-#' @param threshold numeric(1). For computational efficiency, the nearest points in threshold will be selected
-#' @param target_fields character(varying). Field names in characters.
-#' @description NOTE: sf implementation is pending. Only available for terra.
-#' @author Insang Song
-#' @export
-calculate_sedc <- function(point_from, point_to, id, sedc_bandwidth, threshold, target_fields) {
-  # define sources, set SEDC exponential decay range
-  len_point_from = seq_len(nrow(point_from))
-  len_point_to = seq_len(nrow(point_to))
-
-  point_from$from_id = len_point_from
-  # select egrid_v only if closer than 3e5 meters from each aqs
-  point_from_buf = terra::buffer(point_from_buf, threshold = threshold, quadsegs = 90)
-  point_to = point_to[point_from_buf,]
-  point_to$to_id = len_point_to
-
-  # near features with distance argument: only returns integer indices
-  near_from_to = terra::nearby(point_from, point_to, distance = threshold)
-  # attaching actual distance
-  dist_near_to = terra::distance(point_from, point_to)
-  dist_near_to_df = as.vector(dist_near_to)
-  # adding integer indices
-  dist_near_to_tdf = expand.grid(from_id = len_point_from, to_id = len_point_to)
-  dist_near_to_df = cbind(dist_near_to_tdf, dist = dist_near_to_df)
-
-  # summary
-  near_from_to = near_from_to |>
-    as_tibble() |>
-    left_join(data.frame(point_from)) |>
-    left_join(data.frame(point_to)) |>
-    left_join(dist_near_to_df) |>
-    # per the definition in https://mserre.sph.unc.edu/BMElab_web/SEDCtutorial/index.html
-    # exp(-3) is about 0.05
-    mutate(w_sedc = exp((-3 * dist) / sedc_bandwidth)) |>
-    group_by(!!sym(id)) |>
-    summarize(across(all_of(target_fields), list(sedc = ~sum(w_sedc * ., na.rm = TRUE)))) |>
-    ungroup()
-
-  invisible(near_from_to)
-  
-}
-
diff --git a/scomps/R/check.R b/scomps/R/check.R
new file mode 100644
index 00000000..3fed02f7
--- /dev/null
+++ b/scomps/R/check.R
@@ -0,0 +1,139 @@
+# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
+
+#' @title Return the package the input object is based on
+#' @description Detect whether the input object is sf or Spat* object.
+#' @author Insang Song
+#' @param input Spat* in terra or sf object.
+#' @return A character object; one of 'terra' and 'sf'
+#' @export
+check_packbound <- function(input) {
+  # cl_inobj = class(input)[1]
+  stopifnot("Input should be one of sf or Spat* object.\n" = any(is(input, "sf"), is(input, "stars"), is(input, "SpatVector"), is(input, "SpatRaster")))
+  if (is(input, "SpatVector") || is(input, "SpatRaster")) {
+    return("terra")
+  }
+  return("sf")
+}
+
+check_datatype <- function(input) {
+  stopifnot("Input should be one of sf or Spat* object.\n" = any(is(input, "sf"), is(input, "stars"), is(input, "SpatVector"), is(input, "SpatRaster")))
+  if (any(is(input, "SpatVector"), is(input, "sf"))) {
+    return("vector")
+  }
+  if (any(is(input, "SpatRaster"), is(input, "stars"))) {
+    return("raster")
+  }
+}
+
+#' @title check_crs2: Coordinate system checker
+#' @description The input is checked whether its coordinate system is present. If not, it is reprojected to EPSG:5179.
+#' @param input Input object one of sf or terra::Spat* object
+#' @return A (reprojected) sf or SpatVector object.
+#' @export
+check_crs2 <- function(input, crs_standard = "EPSG:4326") {
+  check_crs.sf <- function(input){
+    if (is.na(st_crs(input))){cat('Please check the coordinate system or its EPSG code of your input object.'); return(NULL)}
+    if (sf::st_crs(input)$epsg == crs_standard ) {
+      return(input)
+    } 
+    input_transformed <- sf::st_transform(input, sf::st_crs(crs_standard))
+    return(input_transformed)
+  }
+
+  check_crs.terra <- function(input) {
+    if (terra::crs(input, describe = TRUE)$code == crs_standard) {
+      return(input)
+    }
+    input_transformed = terra::project(input, terra::crs(crs_standard))
+    return(input_transformed)
+  }
+    detected = check_packbound(input)
+    switch(detected,
+          terra = check_crs.terra(input),
+          sf = check_crs.sf(input))
+  }
+
+#' Check if the data extent is inside the reference bounding box
+#' 
+#' @description One of the most common errors in spatial computation is rooted in the entirely or partly incomparable spatial extents of input datasets. This function returns whether your data is inside the target computational extent. It is assumed that you know and have the exact computational region. This function will return TRUE if the reference region completely contains your data's extent and FALSE otherwise.
+#' @param data_query sf*/stars/SpatVector/SpatRaster object.
+#' @param reference sf*/stars/SpatVector/SpatRaster object or a named numeric vector with four names (xmin, ymin, xmax, and ymax).
+#' @param reference_crs Well-known-text-formatted or EPSG code of the reference's coordinate system. Only required when a named numeric vector is passed to reference. 
+#' @return TRUE (the queried data extent is completely within the reference bounding box) or FALSE 
+#' @author Insang Song \email{geoissong@@gmail.com}
+#' 
+#' @export
+check_bbox <- function(
+  data_query, reference, reference_crs = NULL
+) {
+  if (is.numeric(reference) && is.null(reference_crs)) {
+    stop("CRS should be entered when the reference extent is a vector.\n")
+  }
+  if (is.numeric(reference) && !is.null(reference_crs)) {
+    reference = sf::st_as_sfc(sf::st_bbox(reference), crs = reference_crs)
+  }
+  query_crs = check_crs(data_query)
+  ref_crs = check_crs(reference)
+  if (is.na(query_crs) || is.null(query_crs)) {
+    stop("The dataset you queried has no CRS. Please make sure your dataset has the correct CRS.\n")
+  }
+
+  # ...
+
+  check_result
+  return(check_result)
+}
+
+
+
+#' Check Coordinate Reference System
+#' @param x sf/stars/SpatVector/SpatRaster object.
+#' @return A st_crs or crs object.
+#' @description 
+#' @author Insang Song \email{geoissong@@gmail.com}
+#' @examples 
+#' # data
+#' install.packages('spData')
+#' library(spData)
+#' data(us_states)
+#' check_crs(us_states)
+#' 
+#' @export 
+check_crs <- function(x) {
+    stopifnot("Input is invalid.\n" = (is(x, "sf") || is(x, "stars") || is(x, "SpatVector") || is(x, "SpatRaster")))
+    
+    if (is(x, "sf") || is(x, "stars")) {
+        crs_wkt = sf::st_crs(x)
+    } else {
+        crs_wkt = terra::crs(x)
+    }
+
+    stopifnot("No CRS is defined in the input. Please consult the metadata or the data source.\n" = !is.na(crs_wkt) || crs_wkt != "")
+    return(crs_wkt)
+}
+
+#' Check if the boundary of the vector/raster object is inside the reference
+#' @param input_object sf/stars/SpatVector/SpatRaster object.
+#' @param reference sf/stars/SpatVector/SpatRaster object.
+#' @return logical
+#' @author Insang Song \email{geoissong@@gmail.com}
+#' @export 
+check_within_reference <- function(input_object, reference) {
+    stopifnot("Input is invalid.\n" = (is(x, "sf") || is(x, "stars") || is(x, "SpatVector") || is(x, "SpatRaster")))
+    stopifnot("Reference is invalid.\n" = (is(x, "sf") || is(x, "stars") || is(x, "SpatVector") || is(x, "SpatRaster")))
+
+  bbox_input <- input_object
+    sf::st_bbox() |>
+    sf::st_as_sfc()
+  
+  bbox_reference = reference |>
+    sf::st_bbox() |>
+    sf::st_as_sfc()
+
+  iswithin = sf::st_covered_by(bbox_input, bbox_reference)
+  iswithin = length(iswithin[[1]])
+  iswithin = (iswithin == 1)
+  invisible(iswithin)
+}
+
+
diff --git a/scomps/R/check_bbox.R b/scomps/R/check_bbox.R
deleted file mode 100644
index 5f823688..00000000
--- a/scomps/R/check_bbox.R
+++ /dev/null
@@ -1,34 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' Check if the data extent is inside the reference bounding box
-#' 
-#' @description One of the most common errors in spatial computation is rooted in the entirely or partly incomparable spatial extents of input datasets. This function returns whether your data is inside the target computational extent. It is assumed that you know and have the exact computational region. This function will return TRUE if the reference region completely contains your data's extent and FALSE otherwise.
-#' @param data_query sf*/stars/SpatVector/SpatRaster object.
-#' @param reference sf*/stars/SpatVector/SpatRaster object or a named numeric vector with four names (xmin, ymin, xmax, and ymax).
-#' @param reference_crs Well-known-text-formatted or EPSG code of the reference's coordinate system. Only required when a named numeric vector is passed to reference. 
-#' @return TRUE (the queried data extent is completely within the reference bounding box) or FALSE 
-#' @author Insang Song \email{geoissong@@gmail.com}
-#' 
-#' @export
-check_bbox <- function(
-  data_query, reference, reference_crs = NULL
-) {
-  if (is.numeric(reference) && is.null(reference_crs)) {
-    stop("CRS should be entered when the reference extent is a vector.\n")
-  }
-  if (is.numeric(reference) && !is.null(reference_crs)) {
-    reference = sf::st_as_sfc(sf::st_bbox(reference), crs = reference_crs)
-  }
-  query_crs = check_crs(data_query)
-  ref_crs = check_crs(reference)
-  if (is.na(query_crs) || is.null(query_crs)) {
-    stop("The dataset you queried has no CRS. Please make sure your dataset has the correct CRS.\n")
-  }
-
-  # ...
-
-  check_result
-  return(check_result)
-}
-
-
diff --git a/scomps/R/check_crs.R b/scomps/R/check_crs.R
deleted file mode 100644
index 6a31ba76..00000000
--- a/scomps/R/check_crs.R
+++ /dev/null
@@ -1,27 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' Check Coordinate Reference System
-#' @param x sf/stars/SpatVector/SpatRaster object.
-#' @return A st_crs or crs object.
-#' @description 
-#' @author Insang Song \email{geoissong@@gmail.com}
-#' @examples 
-#' # data
-#' install.packages('spData')
-#' library(spData)
-#' data(us_states)
-#' check_crs(us_states)
-#' 
-#' @export 
-check_crs <- function(x) {
-    stopifnot("Input is invalid.\n" = (is(x, "sf") || is(x, "stars") || is(x, "SpatVector") || is(x, "SpatRaster")))
-    
-    if (is(x, "sf") || is(x, "stars")) {
-        crs_wkt = sf::st_crs(x)
-    } else {
-        crs_wkt = terra::crs(x)
-    }
-
-    stopifnot("No CRS is defined in the input. Please consult the metadata or the data source.\n" = !is.na(crs_wkt) || crs_wkt != "")
-    return(crs_wkt)
-}
diff --git a/scomps/R/check_crs2.R b/scomps/R/check_crs2.R
deleted file mode 100644
index 2852796a..00000000
--- a/scomps/R/check_crs2.R
+++ /dev/null
@@ -1,29 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' @title check_crs2: Coordinate system checker
-#' @description The input is checked whether its coordinate system is present. If not, it is reprojected to EPSG:5179.
-#' @param input Input object one of sf or terra::Spat* object
-#' @return A (reprojected) sf or SpatVector object.
-#' @export
-check_crs2 <- function(input, crs_standard = "EPSG:4326") {
-  check_crs.sf <- function(input){
-    if (is.na(st_crs(input))){cat('Please check the coordinate system or its EPSG code of your input object.'); return(NULL)}
-    if (sf::st_crs(input)$epsg == crs_standard ) {
-      return(input)
-    } 
-    input_transformed <- sf::st_transform(input, sf::st_crs(crs_standard))
-    return(input_transformed)
-  }
-
-  check_crs.terra <- function(input) {
-    if (terra::crs(input, describe = TRUE)$code == crs_standard) {
-      return(input)
-    }
-    input_transformed = terra::project(input, terra::crs(crs_standard))
-    return(input_transformed)
-  }
-    detected = check_packbound(input)
-    switch(detected,
-          terra = check_crs.terra(input),
-          sf = check_crs.sf(input))
-  }
diff --git a/scomps/R/check_packbound.R b/scomps/R/check_packbound.R
deleted file mode 100644
index 4de77af7..00000000
--- a/scomps/R/check_packbound.R
+++ /dev/null
@@ -1,26 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' @title Return the package the input object is based on
-#' @description Detect whether the input object is sf or Spat* object.
-#' @author Insang Song
-#' @param input Spat* in terra or sf object.
-#' @return A character object; one of 'terra' and 'sf'
-#' @export
-check_packbound <- function(input) {
-  # cl_inobj = class(input)[1]
-  stopifnot("Input should be one of sf or Spat* object.\n" = any(is(input, "sf"), is(input, "stars"), is(input, "SpatVector"), is(input, "SpatRaster")))
-  if (is(input, "SpatVector") || is(input, "SpatRaster")) {
-    return("terra")
-  }
-  return("sf")
-}
-
-check_datatype <- function(input) {
-  stopifnot("Input should be one of sf or Spat* object.\n" = any(is(input, "sf"), is(input, "stars"), is(input, "SpatVector"), is(input, "SpatRaster")))
-  if (any(is(input, "SpatVector"), is(input, "sf"))) {
-    return("vector")
-  }
-  if (any(is(input, "SpatRaster"), is(input, "stars"))) {
-    return("raster")
-  }
-}
diff --git a/scomps/R/check_within_reference.R b/scomps/R/check_within_reference.R
deleted file mode 100644
index 2df7c63c..00000000
--- a/scomps/R/check_within_reference.R
+++ /dev/null
@@ -1,27 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' Check if the boundary of the vector/raster object is inside the reference
-#' @param input_object sf/stars/SpatVector/SpatRaster object.
-#' @param reference sf/stars/SpatVector/SpatRaster object.
-#' @return logical
-#' @author Insang Song \email{geoissong@@gmail.com}
-#' @export 
-check_within_reference <- function(input_object, reference) {
-    stopifnot("Input is invalid.\n" = (is(x, "sf") || is(x, "stars") || is(x, "SpatVector") || is(x, "SpatRaster")))
-    stopifnot("Reference is invalid.\n" = (is(x, "sf") || is(x, "stars") || is(x, "SpatVector") || is(x, "SpatRaster")))
-
-  bbox_input <- input_object
-    sf::st_bbox() |>
-    sf::st_as_sfc()
-  
-  bbox_reference = reference |>
-    sf::st_bbox() |>
-    sf::st_as_sfc()
-
-  iswithin = sf::st_covered_by(bbox_input, bbox_reference)
-  iswithin = length(iswithin[[1]])
-  iswithin = (iswithin == 1)
-  invisible(iswithin)
-}
-
-
diff --git a/scomps/R/clip_as_extent.R b/scomps/R/clip_as_extent.R
deleted file mode 100644
index 6cea0ca4..00000000
--- a/scomps/R/clip_as_extent.R
+++ /dev/null
@@ -1,37 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' Extent clipping
-#' @description Clip input vector by the expected maximum extent of computation. 
-#' @author Insang Song
-#' @param pnts sf or SpatVector object
-#' @param buffer_r numeric(1). buffer radius. this value will be automatically multiplied by 1.25
-#' @param nqsegs integer(1). the number of points per a quarter circle; SOON TO BE DEPRECATED
-#' @param target_input sf or SpatVector object to be clipped
-#' @return A clipped sf or SpatVector object.
-#' @export
-clip_as_extent <- function(pnts, buffer_r, nqsegs=NULL, target_input){
-  if (any(sapply(list(pnts, buffer_r, target_input), is.null))) {
-    stop("One or more required arguments are NULL. Please check.\n")
-  }
-  detected_pnts = check_packbound(pnts)
-  detected_target = check_packbound(target_input)
-
-  if (detected_pnts != detected_target) {
-    warning("Inputs are not the same class.\n")
-    target_input = switch(detected_target,
-        sf = terra::vect(target_input),
-        terra = sf::st_as_sf(target_input))
-  }
-  
-  ext_input = set_clip_extent(pnts, buffer_r)
-  cat("Clip target features with the input feature extent...\n")
-  if (detected_pnts == "sf") {
-    cae = ext_input |>
-      sf::st_intersection(x = target_input)
-  }
-  if (detected_pnts == "terra") {
-    cae = terra::intersect(target_input, ext_input)
-  }
-   
-  return(cae)
-}
diff --git a/scomps/R/clip_as_extent_ras.R b/scomps/R/clip_as_extent_ras.R
deleted file mode 100644
index 9ad93a61..00000000
--- a/scomps/R/clip_as_extent_ras.R
+++ /dev/null
@@ -1,20 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' @title clip_as_extent_ras: Clip input raster.
-#' @description Clip input raster by the expected maximum extent of computation. 
-#' @author Insang Song
-#' @param pnts sf or SpatVector object
-#' @param buffer_r numeric(1). buffer radius. this value will be automatically multiplied by 1.25
-#' @param nqsegs integer(1). the number of points per a quarter circle
-#' @param ras SpatRaster object to be clipped
-#' @export
-clip_as_extent_ras <- function(pnts, buffer_r, nqsegs = 180, ras){
-  if (any(sapply(list(pnts, buffer_r, ras), is.null))) {
-    stop("Any of required arguments are NULL. Please check.\n")
-  }
-  ext_input = set_clip_extent(pnts, buffer_r) |>
-    terra::ext()
-
-  cae <- terra::crop(ras, ext_input, snap = 'out')
-  return(cae)
-}
diff --git a/scomps/R/clip_as_extent_ras2.R b/scomps/R/clip_as_extent_ras2.R
deleted file mode 100644
index d6c6e2ff..00000000
--- a/scomps/R/clip_as_extent_ras2.R
+++ /dev/null
@@ -1,20 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' @title clip_as_extent_ras2: Clip input raster (version 2).
-#' @description Clip input raster by the expected maximum extent of computation. 
-#' @author Insang Song
-#' @param points_in sf or SpatVector object
-#' @param buffer_r numeric(1). buffer radius. this value will be automatically multiplied by 1.25
-#' @param nqsegs integer(1). the number of points per a quarter circle
-#' @param ras SpatRaster object to be clipped
-#' @export
-clip_as_extent_ras2 <- function(points_in, buffer_r, nqsegs=180, ras){
-  if (any(sapply(list(points_in, buffer_r, ras), is.null))) {
-    stop("Any of required arguments are NULL. Please check.\n")
-  }
-  ext_input = set_clip_extent(points_in, buffer_r) |>
-    terra::ext()
-
-  cae <- terra::crop(ras, ext_input, snap = 'out')
-  return(cae)
-}
diff --git a/scomps/R/distribute_process.R b/scomps/R/distribute_process.R
deleted file mode 100644
index 2fc47eb4..00000000
--- a/scomps/R/distribute_process.R
+++ /dev/null
@@ -1,39 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' @title Process a given function in the entire or partial computational grids (under construction)
-#' 
-#' @description Should 
-#' @param grids sf/SpatVector object. Computational grids.
-#' @param grid_id character(1) or numeric(2). Default is NULL. If NULL, all grid_ids are used. "id_from:id_to" format or c(unique(grid_id)[id_from], unique(grid_id)[id_to])
-#' @param fun function supported in scomps. 
-#' @param ... Arguments passed to fun.
-#' @return a data.frame object with mean value
-#' @author Insang Song \email{geoissong@@gmail.com}
-#' 
-#' @export
-distribute_process <- function(grids, grid_id = NULL, fun, ...) {
-    require(future.apply)
-    
-    # subset using grids and grid_id
-    if (!is.null(grid_id)) {
-        if (is.character(grid_id)) {
-            grid_id_parsed = strsplit(grid_id, ":", fixed = TRUE)[[1]]
-            grid_ids = c(which(unique(grids[["CGRIDID"]]) == grid_id_parsed[1]),
-                         which(unique(grids[["CGRIDID"]]) == grid_id_parsed[2]))
-        }
-        if (is.numeric(grid_id)) {
-            grid_ids = unique(grids[["CGRIDID"]])[grid_id]
-        }
-    }
-    grids_target = grids[grid_ids,]
-    grids_target_list = split(grids_target, grids_target[["CGRIDID"]])
-
-    results_distributed = future.apply::future_lapply(
-        \(x, ...) {
-            fun(...)
-        }, grids_target_list, points_cutslist, SIMPLIFY = FALSE,
-        future.seed = TRUE)
-    results_distributed = do.call(rbind, results_distributed)
-    return(results_distributed)
-}
-
diff --git a/scomps/R/extract_with.R b/scomps/R/extract_with.R
deleted file mode 100644
index c1d4ad95..00000000
--- a/scomps/R/extract_with.R
+++ /dev/null
@@ -1,33 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' Extract raster values with point buffers or polygons
-#' 
-#' @param raster SpatRaster object. 
-#' @param vector SpatVector object.
-#' @param id character(1). Unique identifier of each point.
-#' @param func function taking one numeric vector argument.
-#' @param mode one of "polygon" (generic polygons to extract raster values with) or "buffer" (point with buffer radius)
-#' @param ... various. Passed to extract_with_buffer. See \code{?extract_with_buffer} for details.
-#' @return 
-#' @author Insang Song \email{geoissong@@gmail.com}
-#' @examples 
-#' # data
-#' 
-#' # run
-#' clip_with()
-#' 
-#' @export 
-extract_with <- function(raster, vector, id, func = mean, mode = "polygon", ...) {
-    if (!mode %in% c("polygon", "buffer")) {
-      stop("Argument 'mode' should be one of 'polygon' or 'buffer'.\n")
-    }
-    stopifnot(is.character(id))
-    stopifnot(id %in% names(vector))
-
-    extracted = 
-      switch(mode,
-        polygon = extract_with_polygons(vector, raster, id, func),
-        buffer = extract_with_buffer(vector, raster, id = id, func = func, ...))
-    return(extracted)
-}
-
diff --git a/scomps/R/extract_with_buffer.R b/scomps/R/extract_with_buffer.R
deleted file mode 100644
index 05b79640..00000000
--- a/scomps/R/extract_with_buffer.R
+++ /dev/null
@@ -1,50 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' @title Extract summarized values from raster with points and a buffer radius (to be written)
-#' 
-#' @description For simplicity, it is assumed that the coordinate systems of the points and the raster are the same. Kernel function is not yet implemented. 
-#' @param points SpatVector object. Coordinates where buffers will be generated
-#' @param surf SpatRaster object. A raster of whatnot a summary will be calculated
-#' @param radius numeric(1). Buffer radius. here we assume circular buffers only
-#' @param id character(1). Unique identifier of each point.
-#' @param qsegs integer(1). Number of vertices at a quarter of a circle. Default is 90.
-#' @param func a function taking a numeric vector argument.
-#' @param kernel character(1). Name of a kernel function (yet to be implemented)
-#' @param bandwidth numeric(1). Kernel bandwidth.
-#' @return a data.frame object with mean value
-#' @author Insang Song \email{geoissong@@gmail.com}
-#' 
-#' @export
-extract_with_buffer <- function(
-    points, surf, radius, id, qsegs = 90, func = mean, kernel = NULL, bandwidth = NULL
-    ) {
-    # type check
-    stopifnot("Check class of the input points.\n" = is(points, "SpatVector"))
-    stopifnot("Check class of the input radius.\n" = is.numeric(radius))
-    stopifnot(is.character(id))
-    stopifnot(is.integer(qsegs))
-
-    if (!is.null(kernel)) {
-        extracted = extract_with_buffer.flat(points = points,
-                                      surf = surf,
-                                      radius = radius,
-                                      id = id,
-                                      func = func,
-                                      qsegs = qsegs)
-        return(extracted)
-    }
-
-    extracted = extract_with_buffer.kernel(points = points,
-                                           surf = surf,
-                                           radius = radius,
-                                           id = id,
-                                           func = func,
-                                           qsegs = qsegs,
-                                           kernel = kernel,
-                                           bandwidth = bandwidth)
-    return(extracted)
-
-}
-
-
-
diff --git a/scomps/R/extract_with_buffer.flat.R b/scomps/R/extract_with_buffer.flat.R
deleted file mode 100644
index bcf81c57..00000000
--- a/scomps/R/extract_with_buffer.flat.R
+++ /dev/null
@@ -1,23 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' Subfunction: extract with buffers (flat weight; simple mean)
-#' 
-#' @export 
-extract_with_buffer.flat <- function(
-        points, surf, radius, id, qsegs, func = mean, kernel = NULL, bandwidth = NULL
-    ) {
-    # generate buffers
-    bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
-    # crop raster
-    bufs_extent = terra::ext(bufs)
-    surf_cropped = terra::crop(surf, bufs_extent)
-    name_surf_val = names(surf)
-    # extract raster values
-    surf_at_bufs = terra::extract(surf_cropped, bufs)
-    surf_at_bufs_summary = 
-        surf_at_bufs |> 
-            group_by(ID) |> 
-            summarize(across(all_of(name_surf_val), ~mean, na.rm=T)) |> 
-            ungroup()
-    return(surf_at_bufs_summary)
-}
diff --git a/scomps/R/extract_with_buffer.kernel.R b/scomps/R/extract_with_buffer.kernel.R
deleted file mode 100644
index 3967965f..00000000
--- a/scomps/R/extract_with_buffer.kernel.R
+++ /dev/null
@@ -1,27 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' Subfunction: extract with buffers (kernel weight; weighted mean)
-#'
-#' @export 
-extract_with_buffer.kernel <- function(
-        points, surf, radius, id, qsegs, func = mean, kernel, bandwidth
-    ) {
-        # generate buffers
-        bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
-        # crop raster
-        bufs_extent = terra::ext(bufs)
-        surf_cropped = terra::crop(surf, bufs_extent)
-        name_surf_val = names(surf)
-
-        # TODO: kernel implementation
-
-
-        # extract raster values
-        surf_at_bufs = terra::extract(surf_cropped, bufs)
-        surf_at_bufs_summary = 
-            surf_at_bufs |> 
-                group_by(ID) |> 
-                summarize(across(all_of(name_surf_val), ~mean, na.rm=T)) |> 
-                ungroup()
-        return(surf_at_bufs_summary)
-}
diff --git a/scomps/R/extract_with_polygons.R b/scomps/R/extract_with_polygons.R
deleted file mode 100644
index 4b37763a..00000000
--- a/scomps/R/extract_with_polygons.R
+++ /dev/null
@@ -1,55 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' @title Extract summarized values from raster with generic polygons
-#' 
-#' @description For simplicity, it is assumed that the coordinate systems of the points and the raster are the same. Kernel function is not yet implemented. 
-#' @param polys sf/SpatVector object. Polygons.
-#' @param surf stars/SpatRaster object. A raster of whatnot a summary will be calculated
-#' @param id character(1). Unique identifier of each point.
-#' @param func a function taking one argument. For example, function(x) mean(x, na.rm = TRUE) or \(x) mode(x, na.rm = TRUE)
-#' @param na.rm logical(1). NA values are omitted when summary is calculated.
-#' @return a data.frame object with function value
-#' @author Insang Song \email{geoissong@@gmail.com}
-#' 
-#' @export
-extract_with_polygons <- function(
-    polys, surf, id, func = mean, na.rm = TRUE
-    ) {
-    # type check
-    stopifnot("Check class of the input points.\n" = any(is(polys, "sf"), is(polys, "SpatVector")))
-    stopifnot("Check class of the input raster.\n" = any(is(surf, "stars"), is(surf, "SpatRaster")))
-    stopifnot(is.character(id))
-
-    cls_polys = check_packbound(polys)
-    cls_surf = check_packbound(surf)
-
-    if (cls_polys != cls_surf) {
-      polys = switch_packbound(polys)
-    }
-
-    extract_with_polygons.sf = function(polys, surf, id, func) {
-        extracted = stars::st_extract(x = surf, at = polys, FUN = func)
-        # extracted = extracted |>
-        #   group_by(!!sym(id)) |>
-        #   summarize(across(-!!sym(id), ~func)) |>
-        #   ungroup()
-        return(extracted)
-    }
-
-    extract_with_polygons.terra = function(polys, surf, id, func) {
-        extracted = terra::extract(surf, polys)
-        extracted = extracted |>
-          group_by(!!sym(id)) |>
-          summarize(across(-!!sym(id), ~func)) |>
-          ungroup()
-        return(extracted)
-    }
-
-    extracted_poly = switch(
-        cls_surf,
-        sf = extract_with_polygons.sf(polys = polys, surf = surf, id = id, func = func),
-        terra = extract_with_polygons.terra(polys = polys, surf = surf, id = id, func = func)
-    )
-    return(extracted_poly)
-}
-
diff --git a/scomps/R/sp_indexing.R b/scomps/R/indexing.R
similarity index 100%
rename from scomps/R/sp_indexing.R
rename to scomps/R/indexing.R
diff --git a/scomps/R/get_computational_regions.R b/scomps/R/interpret_computational_domain.R
similarity index 83%
rename from scomps/R/get_computational_regions.R
rename to scomps/R/interpret_computational_domain.R
index bac913a5..757acf37 100644
--- a/scomps/R/get_computational_regions.R
+++ b/scomps/R/interpret_computational_domain.R
@@ -166,3 +166,41 @@ grid_merge <- function(points_in, grid_in, grid_min_features){
 
 
 
+
+#' @title Process a given function in the entire or partial computational grids (under construction)
+#' 
+#' @description Should 
+#' @param grids sf/SpatVector object. Computational grids.
+#' @param grid_id character(1) or numeric(2). Default is NULL. If NULL, all grid_ids are used. "id_from:id_to" format or c(unique(grid_id)[id_from], unique(grid_id)[id_to])
+#' @param fun function supported in scomps. 
+#' @param ... Arguments passed to fun.
+#' @return a data.frame object with mean value
+#' @author Insang Song \email{geoissong@@gmail.com}
+#' 
+#' @export
+distribute_process <- function(grids, grid_id = NULL, fun, ...) {
+    require(future.apply)
+    
+    # subset using grids and grid_id
+    if (!is.null(grid_id)) {
+        if (is.character(grid_id)) {
+            grid_id_parsed = strsplit(grid_id, ":", fixed = TRUE)[[1]]
+            grid_ids = c(which(unique(grids[["CGRIDID"]]) == grid_id_parsed[1]),
+                         which(unique(grids[["CGRIDID"]]) == grid_id_parsed[2]))
+        }
+        if (is.numeric(grid_id)) {
+            grid_ids = unique(grids[["CGRIDID"]])[grid_id]
+        }
+    }
+    grids_target = grids[grid_ids,]
+    grids_target_list = split(grids_target, grids_target[["CGRIDID"]])
+
+    results_distributed = future.apply::future_lapply(
+        \(x, ...) {
+            fun(...)
+        }, grids_target_list, points_cutslist, SIMPLIFY = FALSE,
+        future.seed = TRUE)
+    results_distributed = do.call(rbind, results_distributed)
+    return(results_distributed)
+}
+
diff --git a/scomps/R/initate_log.R b/scomps/R/logging.R
similarity index 100%
rename from scomps/R/initate_log.R
rename to scomps/R/logging.R
diff --git a/scomps/R/set_clip_extent.R b/scomps/R/preprocessing.R
similarity index 77%
rename from scomps/R/set_clip_extent.R
rename to scomps/R/preprocessing.R
index 3a699be8..8f8f6cb8 100644
--- a/scomps/R/set_clip_extent.R
+++ b/scomps/R/preprocessing.R
@@ -22,3 +22,14 @@ set_clip_extent <- function(pnts, buffer_r) {
   }
   return(ext_input)
 }
+
+#' Quick call for SpatRaster with a window
+#' 
+#' @param rasterpath character(1). Path to the raster file.
+#' @param win Named integer vector (4) or terra::ext() results.
+#' @param author Insang Song 
+#' @export 
+rast_short <- function(rasterpath, win) {
+  terra::rast(rasterpath, win = win)
+}
+
diff --git a/scomps/R/processing.R b/scomps/R/processing.R
new file mode 100644
index 00000000..c1c84a03
--- /dev/null
+++ b/scomps/R/processing.R
@@ -0,0 +1,372 @@
+# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
+
+#' Extent clipping
+#' @description Clip input vector by the expected maximum extent of computation. 
+#' @author Insang Song
+#' @param pnts sf or SpatVector object
+#' @param buffer_r numeric(1). buffer radius. this value will be automatically multiplied by 1.25
+#' @param nqsegs integer(1). the number of points per a quarter circle; SOON TO BE DEPRECATED
+#' @param target_input sf or SpatVector object to be clipped
+#' @return A clipped sf or SpatVector object.
+#' @export
+clip_as_extent <- function(pnts, buffer_r, nqsegs=NULL, target_input){
+  if (any(sapply(list(pnts, buffer_r, target_input), is.null))) {
+    stop("One or more required arguments are NULL. Please check.\n")
+  }
+  detected_pnts = check_packbound(pnts)
+  detected_target = check_packbound(target_input)
+
+  if (detected_pnts != detected_target) {
+    warning("Inputs are not the same class.\n")
+    target_input = switch(detected_target,
+        sf = terra::vect(target_input),
+        terra = sf::st_as_sf(target_input))
+  }
+  
+  ext_input = set_clip_extent(pnts, buffer_r)
+  cat("Clip target features with the input feature extent...\n")
+  if (detected_pnts == "sf") {
+    cae = ext_input |>
+      sf::st_intersection(x = target_input)
+  }
+  if (detected_pnts == "terra") {
+    cae = terra::intersect(target_input, ext_input)
+  }
+   
+  return(cae)
+}
+
+#' @title clip_as_extent_ras: Clip input raster.
+#' @description Clip input raster by the expected maximum extent of computation. 
+#' @author Insang Song
+#' @param pnts sf or SpatVector object
+#' @param buffer_r numeric(1). buffer radius. this value will be automatically multiplied by 1.25
+#' @param nqsegs integer(1). the number of points per a quarter circle
+#' @param ras SpatRaster object to be clipped
+#' @export
+clip_as_extent_ras <- function(pnts, buffer_r, nqsegs = 180, ras){
+  if (any(sapply(list(pnts, buffer_r, ras), is.null))) {
+    stop("Any of required arguments are NULL. Please check.\n")
+  }
+  ext_input = set_clip_extent(pnts, buffer_r) |>
+    terra::ext()
+
+  cae <- terra::crop(ras, ext_input, snap = 'out')
+  return(cae)
+}
+
+#' @title clip_as_extent_ras2: Clip input raster (version 2).
+#' @description Clip input raster by the expected maximum extent of computation. 
+#' @author Insang Song
+#' @param points_in sf or SpatVector object
+#' @param buffer_r numeric(1). buffer radius. this value will be automatically multiplied by 1.25
+#' @param nqsegs integer(1). the number of points per a quarter circle
+#' @param ras SpatRaster object to be clipped
+#' @export
+clip_as_extent_ras2 <- function(points_in, buffer_r, nqsegs=180, ras){
+  if (any(sapply(list(points_in, buffer_r, ras), is.null))) {
+    stop("Any of required arguments are NULL. Please check.\n")
+  }
+  ext_input = set_clip_extent(points_in, buffer_r) |>
+    terra::ext()
+
+  cae <- terra::crop(ras, ext_input, snap = 'out')
+  return(cae)
+}
+
+#' @title Extract summarized values from raster with generic polygons
+#' 
+#' @description For simplicity, it is assumed that the coordinate systems of the points and the raster are the same. Kernel function is not yet implemented. 
+#' @param polys sf/SpatVector object. Polygons.
+#' @param surf stars/SpatRaster object. A raster of whatnot a summary will be calculated
+#' @param id character(1). Unique identifier of each point.
+#' @param func a function taking one argument. For example, function(x) mean(x, na.rm = TRUE) or \(x) mode(x, na.rm = TRUE)
+#' @param na.rm logical(1). NA values are omitted when summary is calculated.
+#' @return a data.frame object with function value
+#' @author Insang Song \email{geoissong@@gmail.com}
+#' 
+#' @export
+extract_with_polygons <- function(
+    polys, surf, id, func = mean, na.rm = TRUE
+    ) {
+    # type check
+    stopifnot("Check class of the input points.\n" = any(is(polys, "sf"), is(polys, "SpatVector")))
+    stopifnot("Check class of the input raster.\n" = any(is(surf, "stars"), is(surf, "SpatRaster")))
+    stopifnot(is.character(id))
+
+    cls_polys = check_packbound(polys)
+    cls_surf = check_packbound(surf)
+
+    if (cls_polys != cls_surf) {
+      polys = switch_packbound(polys)
+    }
+
+    extract_with_polygons.sf = function(polys, surf, id, func) {
+        extracted = stars::st_extract(x = surf, at = polys, FUN = func)
+        # extracted = extracted |>
+        #   group_by(!!sym(id)) |>
+        #   summarize(across(-!!sym(id), ~func)) |>
+        #   ungroup()
+        return(extracted)
+    }
+
+    extract_with_polygons.terra = function(polys, surf, id, func) {
+        extracted = terra::extract(surf, polys)
+        extracted = extracted |>
+          group_by(!!sym(id)) |>
+          summarize(across(-!!sym(id), ~func)) |>
+          ungroup()
+        return(extracted)
+    }
+
+    extracted_poly = switch(
+        cls_surf,
+        sf = extract_with_polygons.sf(polys = polys, surf = surf, id = id, func = func),
+        terra = extract_with_polygons.terra(polys = polys, surf = surf, id = id, func = func)
+    )
+    return(extracted_poly)
+}
+
+
+#' Extract raster values with point buffers or polygons
+#' 
+#' @param raster SpatRaster object. 
+#' @param vector SpatVector object.
+#' @param id character(1). Unique identifier of each point.
+#' @param func function taking one numeric vector argument.
+#' @param mode one of "polygon" (generic polygons to extract raster values with) or "buffer" (point with buffer radius)
+#' @param ... various. Passed to extract_with_buffer. See \code{?extract_with_buffer} for details.
+#' @return 
+#' @author Insang Song \email{geoissong@@gmail.com}
+#' @examples 
+#' # data
+#' 
+#' # run
+#' clip_with()
+#' 
+#' @export 
+extract_with <- function(raster, vector, id, func = mean, mode = "polygon", ...) {
+    if (!mode %in% c("polygon", "buffer")) {
+      stop("Argument 'mode' should be one of 'polygon' or 'buffer'.\n")
+    }
+    stopifnot(is.character(id))
+    stopifnot(id %in% names(vector))
+
+    extracted = 
+      switch(mode,
+        polygon = extract_with_polygons(vector, raster, id, func),
+        buffer = extract_with_buffer(vector, raster, id = id, func = func, ...))
+    return(extracted)
+}
+
+
+#' Calculate SEDC covariates
+#' @param point_from SpatVector object. Locations where the sum of SEDCs are calculated.
+#' @param point_to SpatVector object. Locations where each SEDC is calculated.
+#' @param sdec_bandwidth numeric(1). Distance at which the source concentration is reduced to exp(-3) (approximately 95 %)  
+#' @param threshold numeric(1). For computational efficiency, the nearest points in threshold will be selected
+#' @param target_fields character(varying). Field names in characters.
+#' @description NOTE: sf implementation is pending. Only available for terra.
+#' @author Insang Song
+#' @export
+calculate_sedc <- function(point_from, point_to, id, sedc_bandwidth, threshold, target_fields) {
+  # define sources, set SEDC exponential decay range
+  len_point_from = seq_len(nrow(point_from))
+  len_point_to = seq_len(nrow(point_to))
+
+  point_from$from_id = len_point_from
+  # select egrid_v only if closer than 3e5 meters from each aqs
+  point_from_buf = terra::buffer(point_from_buf, threshold = threshold, quadsegs = 90)
+  point_to = point_to[point_from_buf,]
+  point_to$to_id = len_point_to
+
+  # near features with distance argument: only returns integer indices
+  near_from_to = terra::nearby(point_from, point_to, distance = threshold)
+  # attaching actual distance
+  dist_near_to = terra::distance(point_from, point_to)
+  dist_near_to_df = as.vector(dist_near_to)
+  # adding integer indices
+  dist_near_to_tdf = expand.grid(from_id = len_point_from, to_id = len_point_to)
+  dist_near_to_df = cbind(dist_near_to_tdf, dist = dist_near_to_df)
+
+  # summary
+  near_from_to = near_from_to |>
+    as_tibble() |>
+    left_join(data.frame(point_from)) |>
+    left_join(data.frame(point_to)) |>
+    left_join(dist_near_to_df) |>
+    # per the definition in https://mserre.sph.unc.edu/BMElab_web/SEDCtutorial/index.html
+    # exp(-3) is about 0.05
+    mutate(w_sedc = exp((-3 * dist) / sedc_bandwidth)) |>
+    group_by(!!sym(id)) |>
+    summarize(across(all_of(target_fields), list(sedc = ~sum(w_sedc * ., na.rm = TRUE)))) |>
+    ungroup()
+
+  invisible(near_from_to)
+  
+}
+
+
+#' Computing area weighted covariates using two polygon sf or SpatVector objects
+#' @param poly_in A sf/SpatVector object at weighted means will be calculated.
+#' @param poly_weight A sf/SpatVector object from which weighted means will be calculated.
+#' @param id_poly_in character(1). The unique identifier of each polygon in poly_in
+#' @return A data.frame with all numeric fields of area-weighted means.
+#' @description When poly_in and poly_weight are different classes, poly_weight will be converted to the class of poly_in. 
+#' @author Insang Song \email{geoissong@@gmail.com}
+#' @examples 
+#' # package
+#' library(sf)
+#' library(tictoc)
+#' 
+#' # run
+#' nc = st_read(system.file("shape/nc.shp", package="sf"))
+#' nc = st_transform(nc, 5070)
+#' pp = st_sample(nc, size = 300)
+#' pp[["id"]] = seq(1,nrow(pp))
+#' st_crs(pp) = "EPSG:5070"
+#' ppb = st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
+#' 
+#' tic()
+#' ppb_nc_aw = aw_covariates(ppb, nc, 'id')
+#' toc()
+#' summary(ppb_nc_aw)
+#' #### Example of aw_covariates ends ####
+#' @export
+aw_covariates <- function(poly_in, poly_weight, id_poly_in = "ID") {
+    stopifnot("Inputs have invalid classes.\n" = 
+      is(poly_in, "sf") || is(poly_weight, "sf") || is(poly_in, "SpatVector") || is(poly_weight, "SpatVector"))
+    #check_crs()
+    aw_covariates.terra = function(poly_in, poly_weight, id_poly_in = id_poly_in) {
+        
+        poly_intersected = terra::intersect(poly_in, poly_weight)
+        poly_intersected[["area_segment_"]] = terra::expanse(poly_intersected)
+        poly_intersected = data.frame(poly_intersected) |>
+            dplyr::group_by(!!rlang::sym(id_poly_in)) |>
+            dplyr::summarize(across(is.numeric,
+                        ~weighted.mean(., w = area_segment_))) |>
+            dplyr::ungroup()
+        return(poly_intersected)
+    }
+
+    class_poly_in = check_packbound(poly_in)
+    class_poly_weight = check_packbound(poly_weight)
+
+    if (class_poly_in != class_poly_weight) {
+      class_poly_weight = as(class_poly_weight, class(class_poly_in)[1])
+    }
+    
+    switch(class_poly_in,
+        sf = sf::st_interpolate_aw(poly_weight, poly_in, extensive = FALSE),
+        terra = aw_covariates.terra(poly_in, poly_weight, id_poly_in = id_poly_in))
+    
+}
+
+# ncbuf = terra::intersect(vect(ppb), vect(nc))
+# ncbuf_a = ncbuf
+# ncbuf_a$segarea = expanse(ncbuf_a)
+# ncbuf_k = data.frame(ncbuf_a) |>
+#   dplyr::group_by(id) |>
+#   dplyr::summarize(across(is.numeric,
+#                ~weighted.mean(., w = segarea))) |>
+#   dplyr::ungroup()
+
+#ncbufagg = terra::aggregate(ncbuf, by = 'id', fun = weighted.mean, w = ncbuf_a$segarea)
+
+
+#' Subfunction: extract with buffers (flat weight; simple mean)
+#' 
+#' @export 
+extract_with_buffer.flat <- function(
+        points, surf, radius, id, qsegs, func = mean, kernel = NULL, bandwidth = NULL
+    ) {
+    # generate buffers
+    bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
+    # crop raster
+    bufs_extent = terra::ext(bufs)
+    surf_cropped = terra::crop(surf, bufs_extent)
+    name_surf_val = names(surf)
+    # extract raster values
+    surf_at_bufs = terra::extract(surf_cropped, bufs)
+    surf_at_bufs_summary = 
+        surf_at_bufs |> 
+            group_by(ID) |> 
+            summarize(across(all_of(name_surf_val), ~mean, na.rm=T)) |> 
+            ungroup()
+    return(surf_at_bufs_summary)
+}
+
+#' Subfunction: extract with buffers (kernel weight; weighted mean)
+#'
+#' @export 
+extract_with_buffer.kernel <- function(
+        points, surf, radius, id, qsegs, func = mean, kernel, bandwidth
+    ) {
+        # generate buffers
+        bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
+        # crop raster
+        bufs_extent = terra::ext(bufs)
+        surf_cropped = terra::crop(surf, bufs_extent)
+        name_surf_val = names(surf)
+
+        # TODO: kernel implementation
+
+
+        # extract raster values
+        surf_at_bufs = terra::extract(surf_cropped, bufs)
+        surf_at_bufs_summary = 
+            surf_at_bufs |> 
+                group_by(ID) |> 
+                summarize(across(all_of(name_surf_val), ~mean, na.rm=T)) |> 
+                ungroup()
+        return(surf_at_bufs_summary)
+}
+
+#' @title Extract summarized values from raster with points and a buffer radius (to be written)
+#' 
+#' @description For simplicity, it is assumed that the coordinate systems of the points and the raster are the same. Kernel function is not yet implemented. 
+#' @param points SpatVector object. Coordinates where buffers will be generated
+#' @param surf SpatRaster object. A raster of whatnot a summary will be calculated
+#' @param radius numeric(1). Buffer radius. here we assume circular buffers only
+#' @param id character(1). Unique identifier of each point.
+#' @param qsegs integer(1). Number of vertices at a quarter of a circle. Default is 90.
+#' @param func a function taking a numeric vector argument.
+#' @param kernel character(1). Name of a kernel function (yet to be implemented)
+#' @param bandwidth numeric(1). Kernel bandwidth.
+#' @return a data.frame object with mean value
+#' @author Insang Song \email{geoissong@@gmail.com}
+#' 
+#' @export
+extract_with_buffer <- function(
+    points, surf, radius, id, qsegs = 90, func = mean, kernel = NULL, bandwidth = NULL
+    ) {
+    # type check
+    stopifnot("Check class of the input points.\n" = is(points, "SpatVector"))
+    stopifnot("Check class of the input radius.\n" = is.numeric(radius))
+    stopifnot(is.character(id))
+    stopifnot(is.integer(qsegs))
+
+    if (!is.null(kernel)) {
+        extracted = extract_with_buffer.flat(points = points,
+                                      surf = surf,
+                                      radius = radius,
+                                      id = id,
+                                      func = func,
+                                      qsegs = qsegs)
+        return(extracted)
+    }
+
+    extracted = extract_with_buffer.kernel(points = points,
+                                           surf = surf,
+                                           radius = radius,
+                                           id = id,
+                                           func = func,
+                                           qsegs = qsegs,
+                                           kernel = kernel,
+                                           bandwidth = bandwidth)
+    return(extracted)
+
+}
+
+
+
diff --git a/scomps/R/rast_short.R b/scomps/R/rast_short.R
deleted file mode 100644
index 042d12f5..00000000
--- a/scomps/R/rast_short.R
+++ /dev/null
@@ -1,12 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' Quick call for SpatRaster with a window
-#' 
-#' @param rasterpath character(1). Path to the raster file.
-#' @param win Named integer vector (4) or terra::ext() results.
-#' @param author Insang Song 
-#' @export 
-rast_short <- function(rasterpath, win) {
-  terra::rast(rasterpath, win = win)
-}
-
diff --git a/scomps/R/switch_packbound.R b/scomps/R/switch_format.R
similarity index 100%
rename from scomps/R/switch_packbound.R
rename to scomps/R/switch_format.R
diff --git a/scomps/R/validate_and_repair_vectors.R b/scomps/R/validate.R
similarity index 100%
rename from scomps/R/validate_and_repair_vectors.R
rename to scomps/R/validate.R
diff --git a/scomps/tests/testthat/tests.R b/scomps/tests/testthat/tests.R
index 35965382..6efa4142 100644
--- a/scomps/tests/testthat/tests.R
+++ b/scomps/tests/testthat/tests.R
@@ -21,14 +21,45 @@ testthat::test_that("What package does the input object belong?",
     withr::local_package("stars")
     withr::local_package("terra")
     withr::local_options(list(sf_use_s2 = FALSE))
-    data(stars_sentinel2)
+    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
+    bcsd_stars = stars::read_stars(bcsd_path)
+
     nc = system.file(package = "sf", "shape/nc.shp")
     nc = sf::read_sf(nc)
 
-    datatype_stars = check_datatype(stars_sentinel2)
+    datatype_stars = check_datatype(bcsd_stars)
     datatype_sf = check_datatype(nc)
 
     testthat::expect_equal(datatype_stars, "raster")
     testthat::expect_equal(datatype_sf, "vector")
 })
 
+
+testthat::test_that("Format is well converted",
+{
+    withr::local_package("stars")
+    withr::local_package("terra")
+    withr::local_options(list(sf_use_s2 = FALSE))
+
+    # starts from sf/stars
+    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
+    bcsd_stars = stars::read_stars(bcsd_path)
+    nc = system.file(package = "sf", "shape/nc.shp")
+    nc = sf::read_sf(nc)
+
+    stars_bcsd_tr = switch_packbound(bcsd_stars)
+    sf_nc_tr = switch_packbound(nc)
+
+    testthat::expect_equal(check_packbound(stars_bcsd_tr), "terra")
+    testthat::expect_equal(check_packbound(sf_nc_tr), "terra")
+
+    stars_bcsd_trb = switch_packbound(stars_bcsd_tr)
+    sf_nc_trb = switch_packbound(sf_nc_tr)
+
+    testthat::expect_equal(check_packbound(stars_bcsd_trb), "sf")
+    testthat::expect_equal(check_packbound(sf_nc_trb), "sf")
+
+})
+
+
+
diff --git a/scomps_rmarkdown_litr.html b/scomps_rmarkdown_litr.html
index 974a9d21..240b4444 100644
--- a/scomps_rmarkdown_litr.html
+++ b/scomps_rmarkdown_litr.html
@@ -368,7 +368,7 @@ 
Package setup

   path = ".",
   fields = list(
     Package = params$package_name,
-    Version = "0.0.2.10022023",
+    Version = "0.0.2.10032023",
     Title = "Scalable R geospatial computation",
     Description = "A package for scalable geospatial computation for environmental health research",
     `Authors@R` = person(
@@ -463,11 +463,13 @@ 
Create functions

     withr::local_package("stars")
     withr::local_package("terra")
     withr::local_options(list(sf_use_s2 = FALSE))
-    data(stars_sentinel2)
+    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
+    bcsd_stars = stars::read_stars(bcsd_path)
+
     nc = system.file(package = "sf", "shape/nc.shp")
     nc = sf::read_sf(nc)
 
-    datatype_stars = check_datatype(stars_sentinel2)
+    datatype_stars = check_datatype(bcsd_stars)
     datatype_sf = check_datatype(nc)
 
     testthat::expect_equal(datatype_stars, "raster")
@@ -475,7 +477,8 @@ 
Create functions

 })

 
## pr, tas, 
 ## Test passed

-
## Test passed

+
## pr, tas, 
+## Test passed

 
#' @title Switch spatial data class
 #' @description Convert stars into SpatRaster and vice versa; sf into SpatVector and vice versa.
 #' @author Insang Song
@@ -499,6 +502,36 @@ 
Create functions

 
   invisible(switched)
 }

+

+testthat::test_that("Format is well converted",
+{
+    withr::local_package("stars")
+    withr::local_package("terra")
+    withr::local_options(list(sf_use_s2 = FALSE))
+
+    # starts from sf/stars
+    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
+    bcsd_stars = stars::read_stars(bcsd_path)
+    nc = system.file(package = "sf", "shape/nc.shp")
+    nc = sf::read_sf(nc)
+
+    stars_bcsd_tr = switch_packbound(bcsd_stars)
+    sf_nc_tr = switch_packbound(nc)
+
+    testthat::expect_equal(check_packbound(stars_bcsd_tr), "terra")
+    testthat::expect_equal(check_packbound(sf_nc_tr), "terra")
+
+    stars_bcsd_trb = switch_packbound(stars_bcsd_tr)
+    sf_nc_trb = switch_packbound(sf_nc_tr)
+
+    testthat::expect_equal(check_packbound(stars_bcsd_trb), "sf")
+    testthat::expect_equal(check_packbound(sf_nc_trb), "sf")
+
+})
+
+

+
## pr, tas, 
+## Test passed

 
#' @title check_crs2: Coordinate system checker
 #' @description The input is checked whether its coordinate system is present. If not, it is reprojected to EPSG:5179.
 #' @param input Input object one of sf or terra::Spat* object
@@ -1308,44 +1341,47 @@ 
Documenting the package and building

 

 
## ℹ Updating scomps documentation
 ## ℹ Loading scomps

-
## Warning: [check_crs.R:6] @description requires a value

-
## Warning: [extract_with.R:11] @return requires a value

+
## Warning: [check.R:92] @description requires a value

+
## Warning: [processing.R:139] @return requires a value

 
## Writing 'NAMESPACE'
-## Writing 'aw_covariates.Rd'
-## Writing 'calculate_sedc.Rd'
+## Writing 'check_packbound.Rd'
+## Writing 'check_crs2.Rd'
 ## Writing 'check_bbox.Rd'
 ## Writing 'check_crs.Rd'
-## Writing 'check_crs2.Rd'
-## Writing 'check_packbound.Rd'
 ## Writing 'check_within_reference.Rd'
-## Writing 'clip_as_extent.Rd'
-## Writing 'clip_as_extent_ras.Rd'
-## Writing 'clip_as_extent_ras2.Rd'
-## Writing 'distribute_process.Rd'
 ## Writing 'estimate_demands.Rd'
-## Writing 'extract_with.Rd'
-## Writing 'extract_with_buffer.Rd'
-## Writing 'extract_with_buffer.flat.Rd'
-## Writing 'extract_with_buffer.kernel.Rd'
-## Writing 'extract_with_polygons.Rd'
+## Writing 'sp_indexing.Rd'
 ## Writing 'get_computational_regions.Rd'
 ## Writing 'sp_index_grid.Rd'
 ## Writing 'grid_merge.Rd'
+## Writing 'distribute_process.Rd'
 ## Writing 'initate_log.Rd'
-## Writing 'rast_short.Rd'
 ## Writing 'set_clip_extent.Rd'
-## Writing 'sp_indexing.Rd'
+## Writing 'rast_short.Rd'
+## Writing 'clip_as_extent.Rd'
+## Writing 'clip_as_extent_ras.Rd'
+## Writing 'clip_as_extent_ras2.Rd'
+## Writing 'extract_with_polygons.Rd'
+## Writing 'extract_with.Rd'
+## Writing 'calculate_sedc.Rd'
+## Writing 'aw_covariates.Rd'
+## Writing 'extract_with_buffer.flat.Rd'
+## Writing 'extract_with_buffer.kernel.Rd'
+## Writing 'extract_with_buffer.Rd'
 ## Writing 'switch_packbound.Rd'
 ## Writing 'validate_and_repair_vectors.Rd'

 
## ℹ Testing scomps

 
## ✔ | F W S  OK | Context
 ## 
 ## ⠏ |         0 | tests                                                           pr, tas, 
+## pr, tas, 
+## pr, tas, 
 ## 
-## ✔ |         4 | tests
+## ⠼ |         5 | tests                                                           
+## ✔ |         8 | tests
 ## 
 ## ══ Results ═════════════════════════════════════════════════════════════════════
-## [ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]

+## [ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
## ── R CMD build ─────────────────────────────────────────────────────────────────
 ## * checking for file ‘/Users/songi2/Documents/GitHub/Scalable_GIS/scomps/DESCRIPTION’ ... OK
 ## * preparing ‘scomps’:
@@ -1361,18 +1397,12 @@ 
Documenting the package and building

 ## * checking for LF line-endings in source and make files and shell scripts
 ## * checking for empty or unneeded directories
 ## Removed empty directory ‘scomps/build’
-## * building ‘scomps_0.0.2.10022023.tar.gz’
+## * building ‘scomps_0.0.2.10032023.tar.gz’
 ## Warning: invalid uid value replaced by that for user 'nobody'
 ## Warning: invalid gid value replaced by that for user 'nobody'
-
## [1] "/Users/songi2/Documents/GitHub/Scalable_GIS/scomps_0.0.2.10022023.tar.gz"
-
## curl (5.0.2 -> 5.1.0) [CRAN]
-
## Installing 1 packages: curl
-## Installing package into '/Users/songi2/Library/R/arm64/4.3/library'
-## (as 'lib' is unspecified)
-
## 
-## The downloaded binary packages are in
-##  /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmpLf04ac/downloaded_packages
-## ── R CMD build ─────────────────────────────────────────────────────────────────
+
## [1] "/Users/songi2/Documents/GitHub/Scalable_GIS/scomps_0.0.2.10032023.tar.gz"

+
## Skipping 1 packages ahead of CRAN: data.table

+
## ── R CMD build ─────────────────────────────────────────────────────────────────
 ## * checking for file ‘/Users/songi2/Documents/GitHub/Scalable_GIS/scomps/DESCRIPTION’ ... OK
 ## * preparing ‘scomps’:
 ## * checking DESCRIPTION meta-information ... OK
@@ -1387,12 +1417,12 @@ 
Documenting the package and building

 ## * checking for LF line-endings in source and make files and shell scripts
 ## * checking for empty or unneeded directories
 ## Removed empty directory ‘scomps/build’
-## * building ‘scomps_0.0.2.10022023.tar.gz’
+## * building ‘scomps_0.0.2.10032023.tar.gz’
 ## Warning: invalid uid value replaced by that for user 'nobody'
 ## Warning: invalid gid value replaced by that for user 'nobody'
 ## 
 ## Running /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL \
-##   /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmpLf04ac/scomps_0.0.2.10022023.tar.gz \
+##   /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//Rtmp2UqRyZ/scomps_0.0.2.10032023.tar.gz \
 ##   --install-tests 
 ## * installing to library ‘/Users/songi2/Library/R/arm64/4.3/library’
 ## * installing *source* package ‘scomps’ ...
diff --git a/scomps_rmarkdown_litr.rmd b/scomps_rmarkdown_litr.rmd
index f3767faf..e67a1222 100644
--- a/scomps_rmarkdown_litr.rmd
+++ b/scomps_rmarkdown_litr.rmd
@@ -21,7 +21,7 @@ usethis::create_package(
   path = ".",
   fields = list(
     Package = params$package_name,
-    Version = "0.0.2.10022023",
+    Version = "0.0.2.10032023",
     Title = "Scalable R geospatial computation",
     Description = "A package for scalable geospatial computation for environmental health research",
     `Authors@R` = person(
@@ -79,7 +79,7 @@ litr::add_vignettes("../vignettes-sources/01_generate_computational_grid.Rmd")
 # Now to the package itself
 
 ### Create functions
-```{r}
+```{r, send_to = "R/check.R"}
 #' @title Return the package the input object is based on
 #' @description Detect whether the input object is sf or Spat* object.
 #' @author Insang Song
@@ -129,11 +129,13 @@ testthat::test_that("What package does the input object belong?",
     withr::local_package("stars")
     withr::local_package("terra")
     withr::local_options(list(sf_use_s2 = FALSE))
-    data(stars_sentinel2)
+    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
+    bcsd_stars = stars::read_stars(bcsd_path)
+
     nc = system.file(package = "sf", "shape/nc.shp")
     nc = sf::read_sf(nc)
 
-    datatype_stars = check_datatype(stars_sentinel2)
+    datatype_stars = check_datatype(bcsd_stars)
     datatype_sf = check_datatype(nc)
 
     testthat::expect_equal(datatype_stars, "raster")
@@ -141,7 +143,7 @@ testthat::test_that("What package does the input object belong?",
 })
 ```
 
-```{r}
+```{r, send_to = "R/switch_format.R"}
 #' @title Switch spatial data class
 #' @description Convert stars into SpatRaster and vice versa; sf into SpatVector and vice versa.
 #' @author Insang Song
@@ -169,6 +171,37 @@ switch_packbound <- function(input) {
 
 
 ```{r}
+
+testthat::test_that("Format is well converted",
+{
+    withr::local_package("stars")
+    withr::local_package("terra")
+    withr::local_options(list(sf_use_s2 = FALSE))
+
+    # starts from sf/stars
+    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
+    bcsd_stars = stars::read_stars(bcsd_path)
+    nc = system.file(package = "sf", "shape/nc.shp")
+    nc = sf::read_sf(nc)
+
+    stars_bcsd_tr = switch_packbound(bcsd_stars)
+    sf_nc_tr = switch_packbound(nc)
+
+    testthat::expect_equal(check_packbound(stars_bcsd_tr), "terra")
+    testthat::expect_equal(check_packbound(sf_nc_tr), "terra")
+
+    stars_bcsd_trb = switch_packbound(stars_bcsd_tr)
+    sf_nc_trb = switch_packbound(sf_nc_tr)
+
+    testthat::expect_equal(check_packbound(stars_bcsd_trb), "sf")
+    testthat::expect_equal(check_packbound(sf_nc_trb), "sf")
+
+})
+
+
+```
+
+```{r, send_to = "R/check.R"}
 #' @title check_crs2: Coordinate system checker
 #' @description The input is checked whether its coordinate system is present. If not, it is reprojected to EPSG:5179.
 #' @param input Input object one of sf or terra::Spat* object
@@ -198,7 +231,7 @@ check_crs2 <- function(input, crs_standard = "EPSG:4326") {
   }
 ```
 
-```{r}
+```{r, send_to = "R/validate.R"}
 #' Validate and repair input vector data
 #' @description It tries repairing input vector data. Vector validity violation usually appears in polygon data with self-crossing or hole orders. This function will pass the input_vector object to sf::st_make_valid() (if input_vector is sf) or terra::makeValid() (if input_vector is SpatVector). May take some time depending on the geometry complexity.
 #' @author Insang Song
@@ -218,7 +251,7 @@ validate_and_repair_vectors <- function(input_vector) {
 ```
 
 
-```{r}
+```{r, send_to = "R/logging.R"}
 #' Turn on logging
 #' @author Insang Song
 #' @param expr expression. Any function call to be logged.
@@ -239,7 +272,7 @@ initate_log <- function(expr, dolog = FALSE, logpath) {
 
 ```
 
-```{r}
+```{r, send_to = "R/preprocessing.R"}
 #' Setting the clipping extent
 #' @description Return clipping extent with buffer radius. It assumes the input CRS is projected and linear unit is meters.
 #' @author Insang Song
@@ -265,7 +298,7 @@ set_clip_extent <- function(pnts, buffer_r) {
 ```
 
 
-```{r}
+```{r, send_to = "R/processing.R"}
 #' Extent clipping
 #' @description Clip input vector by the expected maximum extent of computation. 
 #' @author Insang Song
@@ -304,7 +337,7 @@ clip_as_extent <- function(pnts, buffer_r, nqsegs=NULL, target_input){
 ```
 
 
-```{r}
+```{r, send_to = "R/processing.R"}
 #' @title clip_as_extent_ras: Clip input raster.
 #' @description Clip input raster by the expected maximum extent of computation. 
 #' @author Insang Song
@@ -326,7 +359,7 @@ clip_as_extent_ras <- function(pnts, buffer_r, nqsegs = 180, ras){
 ```
 
 
-```{r}
+```{r, send_to = "R/processing.R"}
 #' @title clip_as_extent_ras2: Clip input raster (version 2).
 #' @description Clip input raster by the expected maximum extent of computation. 
 #' @author Insang Song
@@ -348,7 +381,7 @@ clip_as_extent_ras2 <- function(points_in, buffer_r, nqsegs=180, ras){
 ```
 
 
-```{r}
+```{r, send_to = "R/indexing.R"}
 #' @title Create integer indices for grid
 #' @description Returns a tibble object that includes x- and y- index by using two inputs ncutsx and ncutsy, which are x- and y-directional splits, respectively.
 #' @author Insang Song
@@ -374,7 +407,7 @@ sp_indexing <- function(points_in, ncutsx, ncutsy){
 }
 ```
 
-```{r}
+```{r, send_to = "R/preprocessing.R"}
 #' Quick call for SpatRaster with a window
 #' 
 #' @param rasterpath character(1). Path to the raster file.
@@ -414,7 +447,7 @@ estimate_demands <- function(
 ```
 
 
-```{r}
+```{r, send_to = "R/interpret_computational_domain.R"}
 #' Get a set of computational regions
 #' 
 #' @param input sf or Spat* object.
@@ -585,7 +618,7 @@ grid_merge <- function(points_in, grid_in, grid_min_features){
 
 
 
-```{r}
+```{r, send_to = "R/check.R"}
 #' Check if the data extent is inside the reference bounding box
 #' 
 #' @description One of the most common errors in spatial computation is rooted in the entirely or partly incomparable spatial extents of input datasets. This function returns whether your data is inside the target computational extent. It is assumed that you know and have the exact computational region. This function will return TRUE if the reference region completely contains your data's extent and FALSE otherwise.
@@ -636,7 +669,7 @@ check_bbox <- function(
 
 ```
 
-```{r}
+```{r, send_to = "R/processing.R"}
 #' @title Extract summarized values from raster with generic polygons
 #' 
 #' @description For simplicity, it is assumed that the coordinate systems of the points and the raster are the same. Kernel function is not yet implemented. 
@@ -692,7 +725,7 @@ extract_with_polygons <- function(
 
 ```
 
-```{r}
+```{r, send_to = "R/processing.R"}
 #' Extract raster values with point buffers or polygons
 #' 
 #' @param raster SpatRaster object. 
@@ -726,7 +759,7 @@ extract_with <- function(raster, vector, id, func = mean, mode = "polygon", ...)
 
 ```
 
-```{r}
+```{r, send_to = "R/check.R"}
 #' Check Coordinate Reference System
 #' @param x sf/stars/SpatVector/SpatRaster object.
 #' @return A st_crs or crs object.
@@ -755,7 +788,7 @@ check_crs <- function(x) {
 ```
 
 
-```{r}
+```{r, send_to = "R/check.R"}
 #' Check if the boundary of the vector/raster object is inside the reference
 #' @param input_object sf/stars/SpatVector/SpatRaster object.
 #' @param reference sf/stars/SpatVector/SpatRaster object.
@@ -784,7 +817,7 @@ check_within_reference <- function(input_object, reference) {
 ```
 
 
-```{r}
+```{r, send_to = "R/processing.R"}
 #' Calculate SEDC covariates
 #' @param point_from SpatVector object. Locations where the sum of SEDCs are calculated.
 #' @param point_to SpatVector object. Locations where each SEDC is calculated.
@@ -833,7 +866,7 @@ calculate_sedc <- function(point_from, point_to, id, sedc_bandwidth, threshold,
 
 ```
 
-```{r}
+```{r, send_to = "R/processing.R"}
 #' Computing area weighted covariates using two polygon sf or SpatVector objects
 #' @param poly_in A sf/SpatVector object at weighted means will be calculated.
 #' @param poly_weight A sf/SpatVector object from which weighted means will be calculated.
@@ -902,7 +935,7 @@ aw_covariates <- function(poly_in, poly_weight, id_poly_in = "ID") {
 
 ```
 
-```{r}
+```{r, send_to = "R/processing.R"}
 #' Subfunction: extract with buffers (flat weight; simple mean)
 #' 
 #' @export 
@@ -926,7 +959,7 @@ extract_with_buffer.flat <- function(
 }
 ```
 
-```{r}
+```{r, send_to = "R/processing.R"}
 #' Subfunction: extract with buffers (kernel weight; weighted mean)
 #'
 #' @export 
@@ -955,7 +988,7 @@ extract_with_buffer.kernel <- function(
 ```
 
 
-```{r}
+```{r, send_to = "R/processing.R"}
 #' @title Extract summarized values from raster with points and a buffer radius (to be written)
 #' 
 #' @description For simplicity, it is assumed that the coordinate systems of the points and the raster are the same. Kernel function is not yet implemented. 
@@ -1007,7 +1040,7 @@ extract_with_buffer <- function(
 ```
 
 
-```{r}
+```{r, send_to = "R/interpret_computational_domain.R"}
 #' @title Process a given function in the entire or partial computational grids (under construction)
 #' 
 #' @description Should 
diff --git a/tarballs/scomps_0.0.2.10032023.tar.gz b/tarballs/scomps_0.0.2.10032023.tar.gz
new file mode 100644
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HcmV?d00001


From 9ca2eae5c6374ff5266257aa249b38bab88be780 Mon Sep 17 00:00:00 2001
From: Insang Song 
Date: Tue, 3 Oct 2023 12:05:22 -0400
Subject: [PATCH 04/21] Directory restructuring - While keeping litr Rmd,
 others were adjusted - codecov edit to find if it works

---
 .github/workflows/codecov.yaml                      |   2 +-
 {containers => tools/containers}/apptainer_rocker   |   0
 .../slurm_test}/merra1h_aero_extract.r              |   0
 .../slurm_test}/merra1h_aero_extract_local.r        |   0
 .../slurm_test}/merra1h_aero_extract_local_stars.r  |   0
 .../slurm_test}/terra_runs_Rcode_file copy.sh       |   0
 .../slurm_test}/terra_runs_Rcode_file.sh            |   0
 .../tarballs}/scomps_0.0.1.09032023.tar.gz          | Bin
 .../tarballs}/scomps_0.0.2.09152023.tar.gz          | Bin
 .../tarballs}/scomps_0.0.2.09192023.tar.gz          | Bin
 .../tarballs}/scomps_0.0.2.10022023.tar.gz          | Bin
 .../tarballs}/scomps_0.0.2.10032023.tar.gz          | Bin
 .../00_good_practice_parallelization.Rmd            |   0
 .../01_generate_computational_grid.Rmd              |   0
 14 files changed, 1 insertion(+), 1 deletion(-)
 rename {containers => tools/containers}/apptainer_rocker (100%)
 rename {slurm_test => tools/slurm_test}/merra1h_aero_extract.r (100%)
 rename {slurm_test => tools/slurm_test}/merra1h_aero_extract_local.r (100%)
 rename {slurm_test => tools/slurm_test}/merra1h_aero_extract_local_stars.r (100%)
 rename {slurm_test => tools/slurm_test}/terra_runs_Rcode_file copy.sh (100%)
 rename {slurm_test => tools/slurm_test}/terra_runs_Rcode_file.sh (100%)
 rename {tarballs => tools/tarballs}/scomps_0.0.1.09032023.tar.gz (100%)
 rename {tarballs => tools/tarballs}/scomps_0.0.2.09152023.tar.gz (100%)
 rename {tarballs => tools/tarballs}/scomps_0.0.2.09192023.tar.gz (100%)
 rename {tarballs => tools/tarballs}/scomps_0.0.2.10022023.tar.gz (100%)
 rename {tarballs => tools/tarballs}/scomps_0.0.2.10032023.tar.gz (100%)
 rename {vignettes-sources => tools/vignettes-sources}/00_good_practice_parallelization.Rmd (100%)
 rename {vignettes-sources => tools/vignettes-sources}/01_generate_computational_grid.Rmd (100%)

diff --git a/.github/workflows/codecov.yaml b/.github/workflows/codecov.yaml
index 30ba6e81..779871b8 100644
--- a/.github/workflows/codecov.yaml
+++ b/.github/workflows/codecov.yaml
@@ -27,7 +27,7 @@ jobs:
         path: |
           ~/.cache/R
           ~/.local/share/R
-        key: dependencies-${{ runner.os }}-${{ hashFiles('**/scomps/DESCRIPTION') }}
+        key: dependencies-${{ runner.os }}-${{ hashFiles('**/**/DESCRIPTION') }}
         restore-keys: |
           dependencies-${{ runner.os }}-
 
diff --git a/containers/apptainer_rocker b/tools/containers/apptainer_rocker
similarity index 100%
rename from containers/apptainer_rocker
rename to tools/containers/apptainer_rocker
diff --git a/slurm_test/merra1h_aero_extract.r b/tools/slurm_test/merra1h_aero_extract.r
similarity index 100%
rename from slurm_test/merra1h_aero_extract.r
rename to tools/slurm_test/merra1h_aero_extract.r
diff --git a/slurm_test/merra1h_aero_extract_local.r b/tools/slurm_test/merra1h_aero_extract_local.r
similarity index 100%
rename from slurm_test/merra1h_aero_extract_local.r
rename to tools/slurm_test/merra1h_aero_extract_local.r
diff --git a/slurm_test/merra1h_aero_extract_local_stars.r b/tools/slurm_test/merra1h_aero_extract_local_stars.r
similarity index 100%
rename from slurm_test/merra1h_aero_extract_local_stars.r
rename to tools/slurm_test/merra1h_aero_extract_local_stars.r
diff --git a/slurm_test/terra_runs_Rcode_file copy.sh b/tools/slurm_test/terra_runs_Rcode_file copy.sh
similarity index 100%
rename from slurm_test/terra_runs_Rcode_file copy.sh
rename to tools/slurm_test/terra_runs_Rcode_file copy.sh
diff --git a/slurm_test/terra_runs_Rcode_file.sh b/tools/slurm_test/terra_runs_Rcode_file.sh
similarity index 100%
rename from slurm_test/terra_runs_Rcode_file.sh
rename to tools/slurm_test/terra_runs_Rcode_file.sh
diff --git a/tarballs/scomps_0.0.1.09032023.tar.gz b/tools/tarballs/scomps_0.0.1.09032023.tar.gz
similarity index 100%
rename from tarballs/scomps_0.0.1.09032023.tar.gz
rename to tools/tarballs/scomps_0.0.1.09032023.tar.gz
diff --git a/tarballs/scomps_0.0.2.09152023.tar.gz b/tools/tarballs/scomps_0.0.2.09152023.tar.gz
similarity index 100%
rename from tarballs/scomps_0.0.2.09152023.tar.gz
rename to tools/tarballs/scomps_0.0.2.09152023.tar.gz
diff --git a/tarballs/scomps_0.0.2.09192023.tar.gz b/tools/tarballs/scomps_0.0.2.09192023.tar.gz
similarity index 100%
rename from tarballs/scomps_0.0.2.09192023.tar.gz
rename to tools/tarballs/scomps_0.0.2.09192023.tar.gz
diff --git a/tarballs/scomps_0.0.2.10022023.tar.gz b/tools/tarballs/scomps_0.0.2.10022023.tar.gz
similarity index 100%
rename from tarballs/scomps_0.0.2.10022023.tar.gz
rename to tools/tarballs/scomps_0.0.2.10022023.tar.gz
diff --git a/tarballs/scomps_0.0.2.10032023.tar.gz b/tools/tarballs/scomps_0.0.2.10032023.tar.gz
similarity index 100%
rename from tarballs/scomps_0.0.2.10032023.tar.gz
rename to tools/tarballs/scomps_0.0.2.10032023.tar.gz
diff --git a/vignettes-sources/00_good_practice_parallelization.Rmd b/tools/vignettes-sources/00_good_practice_parallelization.Rmd
similarity index 100%
rename from vignettes-sources/00_good_practice_parallelization.Rmd
rename to tools/vignettes-sources/00_good_practice_parallelization.Rmd
diff --git a/vignettes-sources/01_generate_computational_grid.Rmd b/tools/vignettes-sources/01_generate_computational_grid.Rmd
similarity index 100%
rename from vignettes-sources/01_generate_computational_grid.Rmd
rename to tools/vignettes-sources/01_generate_computational_grid.Rmd

From 661866aa9f8699e10dd795bcff35421ec0537e16 Mon Sep 17 00:00:00 2001
From: Insang Song 
Date: Tue, 3 Oct 2023 12:53:49 -0400
Subject: [PATCH 05/21] YAML working directory edit

---
 .github/workflows/check-standard.yaml | 1 +
 .github/workflows/codecov.yaml        | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml
index a71ab36e..0e914c84 100644
--- a/.github/workflows/check-standard.yaml
+++ b/.github/workflows/check-standard.yaml
@@ -38,6 +38,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
+          working-directory: "./scomps"
           extra-packages: any::rcmdcheck
           needs: check
 
diff --git a/.github/workflows/codecov.yaml b/.github/workflows/codecov.yaml
index 779871b8..bff599f3 100644
--- a/.github/workflows/codecov.yaml
+++ b/.github/workflows/codecov.yaml
@@ -27,7 +27,7 @@ jobs:
         path: |
           ~/.cache/R
           ~/.local/share/R
-        key: dependencies-${{ runner.os }}-${{ hashFiles('**/**/DESCRIPTION') }}
+        key: dependencies-${{ runner.os }}-${{ hashFiles('**/DESCRIPTION') }}
         restore-keys: |
           dependencies-${{ runner.os }}-
 

From 01d2064aec02d251ce18ecea9da4423ed5ad34da Mon Sep 17 00:00:00 2001
From: Insang Song 
Date: Tue, 3 Oct 2023 13:10:23 -0400
Subject: [PATCH 06/21] Added working-directory in relevant entries

---
 .github/workflows/check-standard.yaml | 1 +
 .github/workflows/codecov.yaml        | 1 +
 .github/workflows/test-coverage.yaml  | 1 +
 3 files changed, 3 insertions(+)

diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml
index 0e914c84..70f743d2 100644
--- a/.github/workflows/check-standard.yaml
+++ b/.github/workflows/check-standard.yaml
@@ -44,4 +44,5 @@ jobs:
 
       - uses: r-lib/actions/check-r-package@v2
         with:
+          working-directory: "./scomps"
           upload-snapshots: true
diff --git a/.github/workflows/codecov.yaml b/.github/workflows/codecov.yaml
index bff599f3..34b8f901 100644
--- a/.github/workflows/codecov.yaml
+++ b/.github/workflows/codecov.yaml
@@ -56,6 +56,7 @@ jobs:
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         coverage_reports: ${{ github.workspace }}/coverage.xml
+        working-directory: "./scomps"
         
     - name: Cleanup
       run: |
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index ad146389..c34f5922 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -26,6 +26,7 @@ jobs:
         with:
           extra-packages: any::covr
           needs: coverage
+          working-directory: "./scomps"
 
       - name: Test coverage
         run: |

From c6946d3977a9cc9212cab701b2dd4802bf2502cd Mon Sep 17 00:00:00 2001
From: Insang Song 
Date: Tue, 3 Oct 2023 13:18:15 -0400
Subject: [PATCH 07/21] package path fix (2)

---
 .github/workflows/codecov.yaml       | 4 ++--
 .github/workflows/test-coverage.yaml | 1 +
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/codecov.yaml b/.github/workflows/codecov.yaml
index 34b8f901..cb8a71b8 100644
--- a/.github/workflows/codecov.yaml
+++ b/.github/workflows/codecov.yaml
@@ -40,7 +40,7 @@ jobs:
     - name: Install dependencies
       run: |
         R -e 'install.packages("remotes")'
-        R -e 'remotes::install_deps()'
+        R -e 'remotes::install_deps(pkgdir = "./scomps")'
 
     - name: Install dependencies for covr and testthat
       run: R -e 'install.packages(c("covr", "testthat"), dependencies = TRUE)'
@@ -48,7 +48,7 @@ jobs:
     - name: Run tests and calculate coverage
       run: |
         echo "Current working directory: $(pwd)"
-        R -e 'library(covr); covr::package_coverage(coverage_file = "coverage.xml")'
+        R -e 'library(covr); covr::package_coverage(path = "./scomps", coverage_file = "coverage.xml")'
 
 
     - name: Upload coverage to Codecov
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index c34f5922..545aea4a 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -31,6 +31,7 @@ jobs:
       - name: Test coverage
         run: |
           covr::codecov(
+            path = "./scomps",
             quiet = FALSE,
             clean = FALSE,
             install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")

From 8f1433058d1c09cc53e8d77b7b3c8bc798cd3764 Mon Sep 17 00:00:00 2001
From: Insang Song 
Date: Tue, 3 Oct 2023 13:27:21 -0400
Subject: [PATCH 08/21] Edited DESCRIPTION - added stars in "Imports"

---
 scomps/DESCRIPTION                          |   3 ++-
 scomps_rmarkdown_litr.html                  |   7 ++++---
 scomps_rmarkdown_litr.rmd                   |   5 +++--
 tools/tarballs/scomps_0.0.2.10032023.tar.gz | Bin 21871 -> 21884 bytes
 4 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/scomps/DESCRIPTION b/scomps/DESCRIPTION
index 2f72afbd..90815873 100644
--- a/scomps/DESCRIPTION
+++ b/scomps/DESCRIPTION
@@ -18,6 +18,7 @@ Imports:
     future.apply,
     rlang,
     sf,
+    stars,
     terra,
     testthat
 Suggests: 
@@ -30,4 +31,4 @@ Suggests:
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 LitrVersionUsed: 0.9.0
-LitrId: 7c9484dd9127c939a90d433ec83cd305
+LitrId: f6481d6de18f4e515f064d81bc8ae4ed
diff --git a/scomps_rmarkdown_litr.html b/scomps_rmarkdown_litr.html
index 240b4444..35f9efea 100644
--- a/scomps_rmarkdown_litr.html
+++ b/scomps_rmarkdown_litr.html
@@ -385,6 +385,7 @@ 
Package setup

 usethis::use_package("sf") # Default is "Imports"
 # usethis::use_package("stars") # Default is "Imports"
 usethis::use_package("terra") # Default is "Imports"
+usethis::use_package("stars")
 usethis::use_package("rlang") # Default is "Imports"
 usethis::use_package("testthat")
 usethis::use_package("logr", "Suggests") # Default is "Imports"
@@ -406,11 +407,11 @@ 
Package setup

 

 

 
Vignettes 1

-
litr::add_vignettes("../vignettes-sources/00_good_practice_parallelization.Rmd")

+
litr::add_vignettes("../tools/vignettes-sources/00_good_practice_parallelization.Rmd")

 

 

 
Vignettes 2

-
litr::add_vignettes("../vignettes-sources/01_generate_computational_grid.Rmd")

+
litr::add_vignettes("../tools/vignettes-sources/01_generate_computational_grid.Rmd")

 

 
 

@@ -1422,7 +1423,7 @@ 
Documenting the package and building

 ## Warning: invalid gid value replaced by that for user 'nobody'
 ## 
 ## Running /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL \
-##   /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//Rtmp2UqRyZ/scomps_0.0.2.10032023.tar.gz \
+##   /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmpfPUv07/scomps_0.0.2.10032023.tar.gz \
 ##   --install-tests 
 ## * installing to library ‘/Users/songi2/Library/R/arm64/4.3/library’
 ## * installing *source* package ‘scomps’ ...
diff --git a/scomps_rmarkdown_litr.rmd b/scomps_rmarkdown_litr.rmd
index e67a1222..d0608b0c 100644
--- a/scomps_rmarkdown_litr.rmd
+++ b/scomps_rmarkdown_litr.rmd
@@ -38,6 +38,7 @@ usethis::use_package("dplyr") # Default is "Imports"
 usethis::use_package("sf") # Default is "Imports"
 # usethis::use_package("stars") # Default is "Imports"
 usethis::use_package("terra") # Default is "Imports"
+usethis::use_package("stars")
 usethis::use_package("rlang") # Default is "Imports"
 usethis::use_package("testthat")
 usethis::use_package("logr", "Suggests") # Default is "Imports"
@@ -66,13 +67,13 @@ usethis::use_package("future.batchtools", "Suggests") # Default is "Imports"
 ### Vignettes 1
 
 ```{r}
-litr::add_vignettes("../vignettes-sources/00_good_practice_parallelization.Rmd")
+litr::add_vignettes("../tools/vignettes-sources/00_good_practice_parallelization.Rmd")
 ```
 
 ### Vignettes 2
 
 ```{r}
-litr::add_vignettes("../vignettes-sources/01_generate_computational_grid.Rmd")
+litr::add_vignettes("../tools/vignettes-sources/01_generate_computational_grid.Rmd")
 ```
 
 
diff --git a/tools/tarballs/scomps_0.0.2.10032023.tar.gz b/tools/tarballs/scomps_0.0.2.10032023.tar.gz
index 9f194ddcd35c000903b9fc653b4d0ac6bdfe2624..6ac28a5d720b22e5a7de6fa4cfc69d66c1ae344e 100644
GIT binary patch
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From dd2151930afaf63bf58c6da4a3dc686706e5c717 Mon Sep 17 00:00:00 2001
From: Insang Song 
Date: Tue, 3 Oct 2023 15:33:01 -0400
Subject: [PATCH 09/21] YAML fix - removed codecov.yaml - dependencies fix -
 codecov path fix

---
 .github/workflows/check-standard.yaml |  5 ++-
 .github/workflows/codecov.yaml        | 63 ---------------------------
 .github/workflows/test-coverage.yaml  |  8 +++-
 3 files changed, 10 insertions(+), 66 deletions(-)
 delete mode 100644 .github/workflows/codecov.yaml

diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml
index 70f743d2..8592acbe 100644
--- a/.github/workflows/check-standard.yaml
+++ b/.github/workflows/check-standard.yaml
@@ -39,7 +39,10 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           working-directory: "./scomps"
-          extra-packages: any::rcmdcheck
+          packages: |
+            any::tictoc
+            any::units
+            any::rcmdcheck
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
diff --git a/.github/workflows/codecov.yaml b/.github/workflows/codecov.yaml
deleted file mode 100644
index cb8a71b8..00000000
--- a/.github/workflows/codecov.yaml
+++ /dev/null
@@ -1,63 +0,0 @@
-on:
- push:
-   branches:
-     - main
- pull_request:
-   branches:
-     - main
-
-name: R Package CI
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-
-    steps:
-    - name: Checkout code
-      uses: actions/checkout@v2
-
-    - name: Set up R
-      uses: r-lib/actions/setup-r@v2
-      with:
-        r-version: 4.1  # You can change this to the R version you need
-
-    - name: Cache C++ and R dependencies
-      uses: actions/cache@v2
-      with:
-        path: |
-          ~/.cache/R
-          ~/.local/share/R
-        key: dependencies-${{ runner.os }}-${{ hashFiles('**/DESCRIPTION') }}
-        restore-keys: |
-          dependencies-${{ runner.os }}-
-
-    - name: Install system dependencies
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y libudunits2-dev libgdal-dev
-
-        
-    - name: Install dependencies
-      run: |
-        R -e 'install.packages("remotes")'
-        R -e 'remotes::install_deps(pkgdir = "./scomps")'
-
-    - name: Install dependencies for covr and testthat
-      run: R -e 'install.packages(c("covr", "testthat"), dependencies = TRUE)'
-
-    - name: Run tests and calculate coverage
-      run: |
-        echo "Current working directory: $(pwd)"
-        R -e 'library(covr); covr::package_coverage(path = "./scomps", coverage_file = "coverage.xml")'
-
-
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-        coverage_reports: ${{ github.workspace }}/coverage.xml
-        working-directory: "./scomps"
-        
-    - name: Cleanup
-      run: |
-        R -e 'remove.packages("remotes")'
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 545aea4a..f99a35d4 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -24,7 +24,11 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          packages: |
+            any::covr
+            any::tictoc
+            any::units
+            any::spData
           needs: coverage
           working-directory: "./scomps"
 
@@ -54,4 +58,4 @@ jobs:
 
       - name: Upload coverage to Codecov # Add this step
         run: |
-          Rscript -e "covr::codecov(token = Sys.getenv('CODECOV_TOKEN'))"
+          Rscript -e "covr::codecov(path = "./scomps", token = Sys.getenv('CODECOV_TOKEN'))"

From 6189b52efbe88f95d6f204f0ebe02cb8980bb4b3 Mon Sep 17 00:00:00 2001
From: Insang Song 
Date: Tue, 3 Oct 2023 15:36:16 -0400
Subject: [PATCH 10/21] knitr error fix

---
 .github/workflows/check-standard.yaml | 3 +++
 .github/workflows/test-coverage.yaml  | 2 ++
 2 files changed, 5 insertions(+)

diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml
index 8592acbe..f2288234 100644
--- a/.github/workflows/check-standard.yaml
+++ b/.github/workflows/check-standard.yaml
@@ -43,6 +43,9 @@ jobs:
             any::tictoc
             any::units
             any::rcmdcheck
+            any::spData
+            any::knitr
+            any::rmarkdown
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index f99a35d4..c2f6f29d 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -29,6 +29,8 @@ jobs:
             any::tictoc
             any::units
             any::spData
+            any::knitr
+            any::rmarkdown
           needs: coverage
           working-directory: "./scomps"
 

From b3e30077a585215b9cecc432299ec81ea43aa524 Mon Sep 17 00:00:00 2001
From: Insang Song 
Date: Tue, 3 Oct 2023 15:49:00 -0400
Subject: [PATCH 11/21] DESCRIPTION patch - linebreak to whitespace

---
 .github/workflows/test-coverage.yaml |  2 +-
 scomps/DESCRIPTION                   | 19 ++-----------------
 2 files changed, 3 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index c2f6f29d..6583f134 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -24,6 +24,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
+          working-directory: "./scomps"
           packages: |
             any::covr
             any::tictoc
@@ -32,7 +33,6 @@ jobs:
             any::knitr
             any::rmarkdown
           needs: coverage
-          working-directory: "./scomps"
 
       - name: Test coverage
         run: |
diff --git a/scomps/DESCRIPTION b/scomps/DESCRIPTION
index 90815873..dfc8ad0e 100644
--- a/scomps/DESCRIPTION
+++ b/scomps/DESCRIPTION
@@ -11,23 +11,8 @@ License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
-Imports: 
-    covr,
-    dplyr,
-    future,
-    future.apply,
-    rlang,
-    sf,
-    stars,
-    terra,
-    testthat
-Suggests: 
-    future.batchtools,
-    igraph,
-    knitr,
-    logr,
-    rmarkdown,
-    withr
+Imports: covr, dplyr, future, future.apply, rlang, sf, stars, terra, testthat
+Suggests: future.batchtools, igraph, knitr, logr, rmarkdown, withr
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 LitrVersionUsed: 0.9.0

From 98b2c8de07a2997c7d5453e7406d338c2745935c Mon Sep 17 00:00:00 2001
From: Insang Song 
Date: Tue, 3 Oct 2023 15:57:34 -0400
Subject: [PATCH 12/21] DESCRIPTION patch (2)

---
 .github/workflows/check-standard.yaml | 2 +-
 .github/workflows/test-coverage.yaml  | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml
index f2288234..076fc94e 100644
--- a/.github/workflows/check-standard.yaml
+++ b/.github/workflows/check-standard.yaml
@@ -39,7 +39,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           working-directory: "./scomps"
-          packages: |
+          extra-packages: |
             any::tictoc
             any::units
             any::rcmdcheck
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 6583f134..d74b4f4d 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -25,8 +25,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           working-directory: "./scomps"
-          packages: |
-            any::covr
+          extra-packages: |
             any::tictoc
             any::units
             any::spData

From ff1956af4f01b7e3ddad188991fe338f2d30f943 Mon Sep 17 00:00:00 2001
From: Insang Song 
Date: Tue, 3 Oct 2023 16:09:04 -0400
Subject: [PATCH 13/21] Redundant dependency fix - tictoc in one of examples
 was removed; system.time() is in place

---
 scomps/DESCRIPTION                          |  21 +++++++++++++++++---
 scomps/R/processing.R                       |   5 +----
 scomps/man/aw_covariates.Rd                 |   5 +----
 scomps_rmarkdown_litr.html                  |   7 ++-----
 scomps_rmarkdown_litr.rmd                   |   5 +----
 tools/tarballs/scomps_0.0.2.10032023.tar.gz | Bin 21884 -> 21874 bytes
 6 files changed, 23 insertions(+), 20 deletions(-)

diff --git a/scomps/DESCRIPTION b/scomps/DESCRIPTION
index dfc8ad0e..f27c2850 100644
--- a/scomps/DESCRIPTION
+++ b/scomps/DESCRIPTION
@@ -11,9 +11,24 @@ License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
-Imports: covr, dplyr, future, future.apply, rlang, sf, stars, terra, testthat
-Suggests: future.batchtools, igraph, knitr, logr, rmarkdown, withr
+Imports: 
+    covr,
+    dplyr,
+    future,
+    future.apply,
+    rlang,
+    sf,
+    stars,
+    terra,
+    testthat
+Suggests: 
+    future.batchtools,
+    igraph,
+    knitr,
+    logr,
+    rmarkdown,
+    withr
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 LitrVersionUsed: 0.9.0
-LitrId: f6481d6de18f4e515f064d81bc8ae4ed
+LitrId: 2567a6b91b5b130f91bd90d6aa1ca518
diff --git a/scomps/R/processing.R b/scomps/R/processing.R
index c1c84a03..b27f3301 100644
--- a/scomps/R/processing.R
+++ b/scomps/R/processing.R
@@ -217,7 +217,6 @@ calculate_sedc <- function(point_from, point_to, id, sedc_bandwidth, threshold,
 #' @examples 
 #' # package
 #' library(sf)
-#' library(tictoc)
 #' 
 #' # run
 #' nc = st_read(system.file("shape/nc.shp", package="sf"))
@@ -227,9 +226,7 @@ calculate_sedc <- function(point_from, point_to, id, sedc_bandwidth, threshold,
 #' st_crs(pp) = "EPSG:5070"
 #' ppb = st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
 #' 
-#' tic()
-#' ppb_nc_aw = aw_covariates(ppb, nc, 'id')
-#' toc()
+#' system.time({ppb_nc_aw = aw_covariates(ppb, nc, 'id')})
 #' summary(ppb_nc_aw)
 #' #### Example of aw_covariates ends ####
 #' @export
diff --git a/scomps/man/aw_covariates.Rd b/scomps/man/aw_covariates.Rd
index fdb5d71e..2cefe0bf 100644
--- a/scomps/man/aw_covariates.Rd
+++ b/scomps/man/aw_covariates.Rd
@@ -22,7 +22,6 @@ When poly_in and poly_weight are different classes, poly_weight will be converte
 \examples{
 # package
 library(sf)
-library(tictoc)
 
 # run
 nc = st_read(system.file("shape/nc.shp", package="sf"))
@@ -32,9 +31,7 @@ pp[["id"]] = seq(1,nrow(pp))
 st_crs(pp) = "EPSG:5070"
 ppb = st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
 
-tic()
-ppb_nc_aw = aw_covariates(ppb, nc, 'id')
-toc()
+system.time({ppb_nc_aw = aw_covariates(ppb, nc, 'id')})
 summary(ppb_nc_aw)
 #### Example of aw_covariates ends ####
 }
diff --git a/scomps_rmarkdown_litr.html b/scomps_rmarkdown_litr.html
index 35f9efea..3e2875de 100644
--- a/scomps_rmarkdown_litr.html
+++ b/scomps_rmarkdown_litr.html
@@ -1141,7 +1141,6 @@ 
Create functions

 #' @examples 
 #' # package
 #' library(sf)
-#' library(tictoc)
 #' 
 #' # run
 #' nc = st_read(system.file("shape/nc.shp", package="sf"))
@@ -1151,9 +1150,7 @@ 
Create functions

 #' st_crs(pp) = "EPSG:5070"
 #' ppb = st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
 #' 
-#' tic()
-#' ppb_nc_aw = aw_covariates(ppb, nc, 'id')
-#' toc()
+#' system.time({ppb_nc_aw = aw_covariates(ppb, nc, 'id')})
 #' summary(ppb_nc_aw)
 #' #### Example of aw_covariates ends ####
 #' @export
@@ -1423,7 +1420,7 @@ 
Documenting the package and building

 ## Warning: invalid gid value replaced by that for user 'nobody'
 ## 
 ## Running /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL \
-##   /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmpfPUv07/scomps_0.0.2.10032023.tar.gz \
+##   /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmpcN1CIt/scomps_0.0.2.10032023.tar.gz \
 ##   --install-tests 
 ## * installing to library ‘/Users/songi2/Library/R/arm64/4.3/library’
 ## * installing *source* package ‘scomps’ ...
diff --git a/scomps_rmarkdown_litr.rmd b/scomps_rmarkdown_litr.rmd
index d0608b0c..353996ee 100644
--- a/scomps_rmarkdown_litr.rmd
+++ b/scomps_rmarkdown_litr.rmd
@@ -878,7 +878,6 @@ calculate_sedc <- function(point_from, point_to, id, sedc_bandwidth, threshold,
 #' @examples 
 #' # package
 #' library(sf)
-#' library(tictoc)
 #' 
 #' # run
 #' nc = st_read(system.file("shape/nc.shp", package="sf"))
@@ -888,9 +887,7 @@ calculate_sedc <- function(point_from, point_to, id, sedc_bandwidth, threshold,
 #' st_crs(pp) = "EPSG:5070"
 #' ppb = st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
 #' 
-#' tic()
-#' ppb_nc_aw = aw_covariates(ppb, nc, 'id')
-#' toc()
+#' system.time({ppb_nc_aw = aw_covariates(ppb, nc, 'id')})
 #' summary(ppb_nc_aw)
 #' #### Example of aw_covariates ends ####
 #' @export
diff --git a/tools/tarballs/scomps_0.0.2.10032023.tar.gz b/tools/tarballs/scomps_0.0.2.10032023.tar.gz
index 6ac28a5d720b22e5a7de6fa4cfc69d66c1ae344e..fd510b70b1b6c3fd01218b7ffb14a1054999830c 100644
GIT binary patch
delta 21217
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From f2e6c736416c84372b38c8a4a22c0a3e3a4f7c63 Mon Sep 17 00:00:00 2001
From: Insang Song 
Date: Tue, 3 Oct 2023 16:41:38 -0400
Subject: [PATCH 14/21] aw_covariates fix - poly_weight will contain
 numeric/integer fields only

---
 scomps/DESCRIPTION                          |   2 +-
 scomps/R/processing.R                       |  13 +++++++++----
 scomps/man/aw_covariates.Rd                 |   3 ++-
 scomps_rmarkdown_litr.html                  |  15 ++++++++++-----
 scomps_rmarkdown_litr.rmd                   |  13 +++++++++----
 tools/tarballs/scomps_0.0.2.10032023.tar.gz | Bin 21874 -> 21939 bytes
 6 files changed, 31 insertions(+), 15 deletions(-)

diff --git a/scomps/DESCRIPTION b/scomps/DESCRIPTION
index f27c2850..b09f16a8 100644
--- a/scomps/DESCRIPTION
+++ b/scomps/DESCRIPTION
@@ -31,4 +31,4 @@ Suggests:
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 LitrVersionUsed: 0.9.0
-LitrId: 2567a6b91b5b130f91bd90d6aa1ca518
+LitrId: e2d777683c377ffccba3c8047709cee6
diff --git a/scomps/R/processing.R b/scomps/R/processing.R
index b27f3301..c02d1ce1 100644
--- a/scomps/R/processing.R
+++ b/scomps/R/processing.R
@@ -222,7 +222,8 @@ calculate_sedc <- function(point_from, point_to, id, sedc_bandwidth, threshold,
 #' nc = st_read(system.file("shape/nc.shp", package="sf"))
 #' nc = st_transform(nc, 5070)
 #' pp = st_sample(nc, size = 300)
-#' pp[["id"]] = seq(1,nrow(pp))
+#' pp = st_as_sf(pp)
+#' pp[["id"]] = seq(1, nrow(pp))
 #' st_crs(pp) = "EPSG:5070"
 #' ppb = st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
 #' 
@@ -234,6 +235,10 @@ aw_covariates <- function(poly_in, poly_weight, id_poly_in = "ID") {
     stopifnot("Inputs have invalid classes.\n" = 
       is(poly_in, "sf") || is(poly_weight, "sf") || is(poly_in, "SpatVector") || is(poly_weight, "SpatVector"))
     #check_crs()
+
+    ## distinguish numeric and nonnumeric columns
+    index_numeric = grep("(integer|numeric)", unlist(sapply(poly_weight, class)))
+    
     aw_covariates.terra = function(poly_in, poly_weight, id_poly_in = id_poly_in) {
         
         poly_intersected = terra::intersect(poly_in, poly_weight)
@@ -250,12 +255,12 @@ aw_covariates <- function(poly_in, poly_weight, id_poly_in = "ID") {
     class_poly_weight = check_packbound(poly_weight)
 
     if (class_poly_in != class_poly_weight) {
-      class_poly_weight = as(class_poly_weight, class(class_poly_in)[1])
+      class_poly_weight = switch_packbound(class_poly_weight)
     }
     
     switch(class_poly_in,
-        sf = sf::st_interpolate_aw(poly_weight, poly_in, extensive = FALSE),
-        terra = aw_covariates.terra(poly_in, poly_weight, id_poly_in = id_poly_in))
+        sf = sf::st_interpolate_aw(poly_weight[,index_numeric], poly_in, extensive = FALSE),
+        terra = aw_covariates.terra(poly_in, poly_weight[,index_numeric], id_poly_in = id_poly_in))
     
 }
 
diff --git a/scomps/man/aw_covariates.Rd b/scomps/man/aw_covariates.Rd
index 2cefe0bf..4604c030 100644
--- a/scomps/man/aw_covariates.Rd
+++ b/scomps/man/aw_covariates.Rd
@@ -27,7 +27,8 @@ library(sf)
 nc = st_read(system.file("shape/nc.shp", package="sf"))
 nc = st_transform(nc, 5070)
 pp = st_sample(nc, size = 300)
-pp[["id"]] = seq(1,nrow(pp))
+pp = st_as_sf(pp)
+pp[["id"]] = seq(1, nrow(pp))
 st_crs(pp) = "EPSG:5070"
 ppb = st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
 
diff --git a/scomps_rmarkdown_litr.html b/scomps_rmarkdown_litr.html
index 3e2875de..a6de8d23 100644
--- a/scomps_rmarkdown_litr.html
+++ b/scomps_rmarkdown_litr.html
@@ -1146,7 +1146,8 @@ 
    Create functions
    
 #' nc = st_read(system.file("shape/nc.shp", package="sf"))
 #' nc = st_transform(nc, 5070)
 #' pp = st_sample(nc, size = 300)
-#' pp[["id"]] = seq(1,nrow(pp))
+#' pp = st_as_sf(pp)
+#' pp[["id"]] = seq(1, nrow(pp))
 #' st_crs(pp) = "EPSG:5070"
 #' ppb = st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
 #' 
@@ -1158,6 +1159,10 @@ 
    Create functions
    
     stopifnot("Inputs have invalid classes.\n" = 
       is(poly_in, "sf") || is(poly_weight, "sf") || is(poly_in, "SpatVector") || is(poly_weight, "SpatVector"))
     #    check_crs()
+
+    ## distinguish numeric and nonnumeric columns
+    index_numeric = grep("(integer|numeric)", unlist(sapply(poly_weight, class)))
+    
     aw_covariates.terra = function(poly_in, poly_weight, id_poly_in = id_poly_in) {
         
         poly_intersected = terra::intersect(poly_in, poly_weight)
@@ -1174,12 +1179,12 @@ 
    Create functions
    
     class_poly_weight = check_packbound(poly_weight)
 
     if (class_poly_in != class_poly_weight) {
-      class_poly_weight = as(class_poly_weight, class(class_poly_in)[1])
+      class_poly_weight = switch_packbound(class_poly_weight)
     }
     
     switch(class_poly_in,
-        sf = sf::st_interpolate_aw(poly_weight, poly_in, extensive = FALSE),
-        terra = aw_covariates.terra(poly_in, poly_weight, id_poly_in = id_poly_in))
+        sf = sf::st_interpolate_aw(poly_weight[,index_numeric], poly_in, extensive = FALSE),
+        terra = aw_covariates.terra(poly_in, poly_weight[,index_numeric], id_poly_in = id_poly_in))
     
 }
 
@@ -1420,7 +1425,7 @@ 
    Documenting the package and building
    
 ## Warning: invalid gid value replaced by that for user 'nobody'
 ## 
 ## Running /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL \
-##   /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmpcN1CIt/scomps_0.0.2.10032023.tar.gz \
+##   /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmpDc71Ig/scomps_0.0.2.10032023.tar.gz \
 ##   --install-tests 
 ## * installing to library ‘/Users/songi2/Library/R/arm64/4.3/library’
 ## * installing *source* package ‘scomps’ ...
diff --git a/scomps_rmarkdown_litr.rmd b/scomps_rmarkdown_litr.rmd
index 353996ee..4b4f8ccb 100644
--- a/scomps_rmarkdown_litr.rmd
+++ b/scomps_rmarkdown_litr.rmd
@@ -883,7 +883,8 @@ calculate_sedc <- function(point_from, point_to, id, sedc_bandwidth, threshold,
 #' nc = st_read(system.file("shape/nc.shp", package="sf"))
 #' nc = st_transform(nc, 5070)
 #' pp = st_sample(nc, size = 300)
-#' pp[["id"]] = seq(1,nrow(pp))
+#' pp = st_as_sf(pp)
+#' pp[["id"]] = seq(1, nrow(pp))
 #' st_crs(pp) = "EPSG:5070"
 #' ppb = st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
 #' 
@@ -895,6 +896,10 @@ aw_covariates <- function(poly_in, poly_weight, id_poly_in = "ID") {
     stopifnot("Inputs have invalid classes.\n" = 
       is(poly_in, "sf") || is(poly_weight, "sf") || is(poly_in, "SpatVector") || is(poly_weight, "SpatVector"))
     #check_crs()
+
+    ## distinguish numeric and nonnumeric columns
+    index_numeric = grep("(integer|numeric)", unlist(sapply(poly_weight, class)))
+    
     aw_covariates.terra = function(poly_in, poly_weight, id_poly_in = id_poly_in) {
         
         poly_intersected = terra::intersect(poly_in, poly_weight)
@@ -911,12 +916,12 @@ aw_covariates <- function(poly_in, poly_weight, id_poly_in = "ID") {
     class_poly_weight = check_packbound(poly_weight)
 
     if (class_poly_in != class_poly_weight) {
-      class_poly_weight = as(class_poly_weight, class(class_poly_in)[1])
+      class_poly_weight = switch_packbound(class_poly_weight)
     }
     
     switch(class_poly_in,
-        sf = sf::st_interpolate_aw(poly_weight, poly_in, extensive = FALSE),
-        terra = aw_covariates.terra(poly_in, poly_weight, id_poly_in = id_poly_in))
+        sf = sf::st_interpolate_aw(poly_weight[,index_numeric], poly_in, extensive = FALSE),
+        terra = aw_covariates.terra(poly_in, poly_weight[,index_numeric], id_poly_in = id_poly_in))
     
 }
 
diff --git a/tools/tarballs/scomps_0.0.2.10032023.tar.gz b/tools/tarballs/scomps_0.0.2.10032023.tar.gz
index fd510b70b1b6c3fd01218b7ffb14a1054999830c..b5395dbcec656415b26985e20b3767f6074b9ad0 100644
GIT binary patch
delta 20437
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From 78fe49ff17685332ab15d65d2007710a23c0f2c9 Mon Sep 17 00:00:00 2001
From: Insang Song 
Date: Tue, 3 Oct 2023 16:49:41 -0400
Subject: [PATCH 15/21] spData dependency removal

---
 .github/workflows/check-standard.yaml |   1 -
 .github/workflows/test-coverage.yaml  |   1 -
 scomps/DESCRIPTION                    |   2 +-
 scomps/R/check.R                      |   8 ++++----
 scomps/man/check_crs.Rd               |   8 ++++----
 scomps_0.0.2.10032023.tar.gz          | Bin 0 -> 21937 bytes
 scomps_rmarkdown_litr.html            |  10 +++++-----
 scomps_rmarkdown_litr.rmd             |   8 ++++----
 8 files changed, 18 insertions(+), 20 deletions(-)
 create mode 100644 scomps_0.0.2.10032023.tar.gz

diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml
index 076fc94e..cb373c74 100644
--- a/.github/workflows/check-standard.yaml
+++ b/.github/workflows/check-standard.yaml
@@ -43,7 +43,6 @@ jobs:
             any::tictoc
             any::units
             any::rcmdcheck
-            any::spData
             any::knitr
             any::rmarkdown
           needs: check
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index d74b4f4d..9a7705b7 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -28,7 +28,6 @@ jobs:
           extra-packages: |
             any::tictoc
             any::units
-            any::spData
             any::knitr
             any::rmarkdown
           needs: coverage
diff --git a/scomps/DESCRIPTION b/scomps/DESCRIPTION
index b09f16a8..a94cfeef 100644
--- a/scomps/DESCRIPTION
+++ b/scomps/DESCRIPTION
@@ -31,4 +31,4 @@ Suggests:
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 LitrVersionUsed: 0.9.0
-LitrId: e2d777683c377ffccba3c8047709cee6
+LitrId: ea0225b0ebfbc140538ec9cfa4fa0628
diff --git a/scomps/R/check.R b/scomps/R/check.R
index 3fed02f7..3e8e20c6 100644
--- a/scomps/R/check.R
+++ b/scomps/R/check.R
@@ -93,10 +93,10 @@ check_bbox <- function(
 #' @author Insang Song \email{geoissong@@gmail.com}
 #' @examples 
 #' # data
-#' install.packages('spData')
-#' library(spData)
-#' data(us_states)
-#' check_crs(us_states)
+#' library(sf)
+#' ncpath = system.file("shape/nc.shp", package = "sf")
+#' nc = read_sf(ncpath)
+#' check_crs(nc)
 #' 
 #' @export 
 check_crs <- function(x) {
diff --git a/scomps/man/check_crs.Rd b/scomps/man/check_crs.Rd
index 2cc3c9d1..ad8edfa3 100644
--- a/scomps/man/check_crs.Rd
+++ b/scomps/man/check_crs.Rd
@@ -17,10 +17,10 @@ Check Coordinate Reference System
 }
 \examples{
 # data
-install.packages('spData')
-library(spData)
-data(us_states)
-check_crs(us_states)
+library(sf)
+ncpath = system.file("shape/nc.shp", package = "sf")
+nc = read_sf(ncpath)
+check_crs(nc)
 
 }
 \author{
diff --git a/scomps_0.0.2.10032023.tar.gz b/scomps_0.0.2.10032023.tar.gz
new file mode 100644
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literal 0
HcmV?d00001

diff --git a/scomps_rmarkdown_litr.html b/scomps_rmarkdown_litr.html
index a6de8d23..5a3b4994 100644
--- a/scomps_rmarkdown_litr.html
+++ b/scomps_rmarkdown_litr.html
@@ -1042,10 +1042,10 @@ 
    Create functions
    
 #' @author Insang Song \email{geoissong@@gmail.com}
 #' @examples 
 #' # data
-#' install.packages('spData')
-#' library(spData)
-#' data(us_states)
-#' check_crs(us_states)
+#' library(sf)
+#' ncpath = system.file("shape/nc.shp", package = "sf")
+#' nc = read_sf(ncpath)
+#' check_crs(nc)
 #' 
 #' @export 
 check_crs <- function(x) {
@@ -1425,7 +1425,7 @@ 
    Documenting the package and building
    
 ## Warning: invalid gid value replaced by that for user 'nobody'
 ## 
 ## Running /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL \
-##   /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmpDc71Ig/scomps_0.0.2.10032023.tar.gz \
+##   /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmpYa4GNv/scomps_0.0.2.10032023.tar.gz \
 ##   --install-tests 
 ## * installing to library ‘/Users/songi2/Library/R/arm64/4.3/library’
 ## * installing *source* package ‘scomps’ ...
diff --git a/scomps_rmarkdown_litr.rmd b/scomps_rmarkdown_litr.rmd
index 4b4f8ccb..f9a54253 100644
--- a/scomps_rmarkdown_litr.rmd
+++ b/scomps_rmarkdown_litr.rmd
@@ -768,10 +768,10 @@ extract_with <- function(raster, vector, id, func = mean, mode = "polygon", ...)
 #' @author Insang Song \email{geoissong@@gmail.com}
 #' @examples 
 #' # data
-#' install.packages('spData')
-#' library(spData)
-#' data(us_states)
-#' check_crs(us_states)
+#' library(sf)
+#' ncpath = system.file("shape/nc.shp", package = "sf")
+#' nc = read_sf(ncpath)
+#' check_crs(nc)
 #' 
 #' @export 
 check_crs <- function(x) {

From 805f41341de908066bd3e98782fedcb66249c125 Mon Sep 17 00:00:00 2001
From: Insang Song 
Date: Tue, 3 Oct 2023 16:55:47 -0400
Subject: [PATCH 16/21] codecov path format fix - path argument in codecov does
 not accept dot as the current directory

---
 .github/workflows/test-coverage.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 9a7705b7..ff55df7e 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -58,4 +58,4 @@ jobs:
 
       - name: Upload coverage to Codecov # Add this step
         run: |
-          Rscript -e "covr::codecov(path = "./scomps", token = Sys.getenv('CODECOV_TOKEN'))"
+          Rscript -e "covr::codecov(path = "scomps", token = Sys.getenv('CODECOV_TOKEN'))"

From bf571061b3276c143b4a330f6a6a6ac42c91261c Mon Sep 17 00:00:00 2001
From: Insang Song 
Date: Tue, 3 Oct 2023 17:30:24 -0400
Subject: [PATCH 17/21] Changed function examples - Deprecated functions were
 removed - Example with implicit dependency is removed - covr.io upload part
 was commented out from YAML

---
 .github/workflows/test-coverage.yaml        |    6 +-
 scomps/DESCRIPTION                          |    2 +-
 scomps/R/interpret_computational_domain.R   |   23 +-
 scomps/R/processing.R                       |    8 +-
 scomps/man/extract_with.Rd                  |    7 -
 scomps/man/grid_merge.Rd                    |   23 +-
 scomps_0.0.2.10032023.tar.gz                |  Bin 21937 -> 0 bytes
 scomps_coverage_report.html                 | 6066 +++++++++++++++++++
 scomps_rmarkdown_litr.html                  |   33 +-
 scomps_rmarkdown_litr.rmd                   |   31 +-
 tools/tarballs/scomps_0.0.2.10032023.tar.gz |  Bin 21939 -> 21945 bytes
 11 files changed, 6122 insertions(+), 77 deletions(-)
 delete mode 100644 scomps_0.0.2.10032023.tar.gz
 create mode 100644 scomps_coverage_report.html

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index ff55df7e..533abab8 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -56,6 +56,6 @@ jobs:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package
 
-      - name: Upload coverage to Codecov # Add this step
-        run: |
-          Rscript -e "covr::codecov(path = "scomps", token = Sys.getenv('CODECOV_TOKEN'))"
+      # - name: Upload coverage to Codecov # Add this step
+      #   run: |
+      #     Rscript -e "covr::codecov(path = "scomps", token = Sys.getenv('CODECOV_TOKEN'))"
diff --git a/scomps/DESCRIPTION b/scomps/DESCRIPTION
index a94cfeef..cbdada5f 100644
--- a/scomps/DESCRIPTION
+++ b/scomps/DESCRIPTION
@@ -31,4 +31,4 @@ Suggests:
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 LitrVersionUsed: 0.9.0
-LitrId: ea0225b0ebfbc140538ec9cfa4fa0628
+LitrId: c9221a987065acea06c724ff541a9119
diff --git a/scomps/R/interpret_computational_domain.R b/scomps/R/interpret_computational_domain.R
index 757acf37..a57ddc33 100644
--- a/scomps/R/interpret_computational_domain.R
+++ b/scomps/R/interpret_computational_domain.R
@@ -76,17 +76,18 @@ sp_index_grid <- function(points_in, ncutsx, ncutsy){
 #' @param grid_min_features integer(1). Threshold to merge adjacent grids.
 #' @return A sf or SpatVector object of computation grids.
 #' @examples
-#' library(sf)
-#' library(igraph)
-#' ligrary(dplyr)
-#' dg = st_as_sfc(st_bbox(c(xmin = 0, ymin = 0, xmax = 8e5, ymax = 6e5)))
-#' st_crs(dg) = 5070
-#' dgs = st_as_sf(st_make_grid(dg, n = c(20, 15)))
-#' dgs$CGRIDID = seq(1, nrow(dgs))
-#' dg_sample = st_sample(dg, kappa = 5e-9, mu = 15, scale = 20000, type = "Thomas")
-#' st_crs(dg_sample) = st_crs(dg)
-#' dg_merged = grid_merge(st_as_sf(sss), dgs, 100)
-#' #### Example End ####
+#' # library(sf)
+#' # library(igraph)
+#' # ligrary(dplyr)
+#' # dg = st_as_sfc(st_bbox(c(xmin = 0, ymin = 0, xmax = 8e5, ymax = 6e5)))
+#' # st_crs(dg) = 5070
+#' # dgs = st_as_sf(st_make_grid(dg, n = c(20, 15)))
+#' # dgs$CGRIDID = seq(1, nrow(dgs))
+#' #
+#' # dg_sample = st_sample(dg, kappa = 5e-9, mu = 15, scale = 20000, type = "Thomas")
+#' # st_crs(dg_sample) = st_crs(dg)
+#' # dg_merged = grid_merge(st_as_sf(sss), dgs, 100)
+#' #### NOT RUN ####
 #' @export
 grid_merge <- function(points_in, grid_in, grid_min_features){
   package_detected = check_packbound(points_in)
diff --git a/scomps/R/processing.R b/scomps/R/processing.R
index c02d1ce1..3b08a05c 100644
--- a/scomps/R/processing.R
+++ b/scomps/R/processing.R
@@ -138,13 +138,7 @@ extract_with_polygons <- function(
 #' @param ... various. Passed to extract_with_buffer. See \code{?extract_with_buffer} for details.
 #' @return 
 #' @author Insang Song \email{geoissong@@gmail.com}
-#' @examples 
-#' # data
-#' 
-#' # run
-#' clip_with()
-#' 
-#' @export 
+#' @export
 extract_with <- function(raster, vector, id, func = mean, mode = "polygon", ...) {
     if (!mode %in% c("polygon", "buffer")) {
       stop("Argument 'mode' should be one of 'polygon' or 'buffer'.\n")
diff --git a/scomps/man/extract_with.Rd b/scomps/man/extract_with.Rd
index eac08536..d95b9bbb 100644
--- a/scomps/man/extract_with.Rd
+++ b/scomps/man/extract_with.Rd
@@ -21,13 +21,6 @@ extract_with(raster, vector, id, func = mean, mode = "polygon", ...)
 }
 \description{
 Extract raster values with point buffers or polygons
-}
-\examples{
-# data
-
-# run
-clip_with()
-
 }
 \author{
 Insang Song \email{geoissong@gmail.com}
diff --git a/scomps/man/grid_merge.Rd b/scomps/man/grid_merge.Rd
index f3b5ac47..614e7ba9 100644
--- a/scomps/man/grid_merge.Rd
+++ b/scomps/man/grid_merge.Rd
@@ -20,17 +20,18 @@ A sf or SpatVector object of computation grids.
 Merge boundary-sharing (in "Rook" contiguity) grids with fewer target features than the threshold. This function strongly assumes that the input is returned from the sp_index_grid, which has 'CGRIDID' as the unique id field.
 }
 \examples{
-library(sf)
-library(igraph)
-ligrary(dplyr)
-dg = st_as_sfc(st_bbox(c(xmin = 0, ymin = 0, xmax = 8e5, ymax = 6e5)))
-st_crs(dg) = 5070
-dgs = st_as_sf(st_make_grid(dg, n = c(20, 15)))
-dgs$CGRIDID = seq(1, nrow(dgs))
-dg_sample = st_sample(dg, kappa = 5e-9, mu = 15, scale = 20000, type = "Thomas")
-st_crs(dg_sample) = st_crs(dg)
-dg_merged = grid_merge(st_as_sf(sss), dgs, 100)
-#### Example End ####
+# library(sf)
+# library(igraph)
+# ligrary(dplyr)
+# dg = st_as_sfc(st_bbox(c(xmin = 0, ymin = 0, xmax = 8e5, ymax = 6e5)))
+# st_crs(dg) = 5070
+# dgs = st_as_sf(st_make_grid(dg, n = c(20, 15)))
+# dgs$CGRIDID = seq(1, nrow(dgs))
+#
+# dg_sample = st_sample(dg, kappa = 5e-9, mu = 15, scale = 20000, type = "Thomas")
+# st_crs(dg_sample) = st_crs(dg)
+# dg_merged = grid_merge(st_as_sf(sss), dgs, 100)
+#### NOT RUN ####
 }
 \author{
 Insang Song
diff --git a/scomps_0.0.2.10032023.tar.gz b/scomps_0.0.2.10032023.tar.gz
deleted file mode 100644
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diff --git a/scomps_coverage_report.html b/scomps_coverage_report.html
new file mode 100644
index 00000000..60117c09
--- /dev/null
+++ b/scomps_coverage_report.html
@@ -0,0 +1,6066 @@
+
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+
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+
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+
    
+  
+  
    
+    
    scomps coverage - 6.75%
    
+    
    
+      
+      
    
+        
    
+          
    
+          
+        
    
+        
    
+          
    
+            
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+            
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+            
+          
    
+        
    
+      
    
+    
    
+  
    
+
    
+
+
diff --git a/scomps_rmarkdown_litr.html b/scomps_rmarkdown_litr.html
index 5a3b4994..bce70b2f 100644
--- a/scomps_rmarkdown_litr.html
+++ b/scomps_rmarkdown_litr.html
@@ -817,17 +817,18 @@ 
    Create functions
    
 #' @param grid_min_features integer(1). Threshold to merge adjacent grids.
 #' @return A sf or SpatVector object of computation grids.
 #' @examples
-#' library(sf)
-#' library(igraph)
-#' ligrary(dplyr)
-#' dg = st_as_sfc(st_bbox(c(xmin = 0, ymin = 0, xmax = 8e5, ymax = 6e5)))
-#' st_crs(dg) = 5070
-#' dgs = st_as_sf(st_make_grid(dg, n = c(20, 15)))
-#' dgs$CGRIDID = seq(1, nrow(dgs))
-#' dg_sample = st_sample(dg, kappa = 5e-9, mu = 15, scale = 20000, type = "Thomas")
-#' st_crs(dg_sample) = st_crs(dg)
-#' dg_merged = grid_merge(st_as_sf(sss), dgs, 100)
-#' #### Example End ####
+#' # library(sf)
+#' # library(igraph)
+#' # ligrary(dplyr)
+#' # dg = st_as_sfc(st_bbox(c(xmin = 0, ymin = 0, xmax = 8e5, ymax = 6e5)))
+#' # st_crs(dg) = 5070
+#' # dgs = st_as_sf(st_make_grid(dg, n = c(20, 15)))
+#' # dgs$CGRIDID = seq(1, nrow(dgs))
+#' #
+#' # dg_sample = st_sample(dg, kappa = 5e-9, mu = 15, scale = 20000, type = "Thomas")
+#' # st_crs(dg_sample) = st_crs(dg)
+#' # dg_merged = grid_merge(st_as_sf(sss), dgs, 100)
+#' #### NOT RUN ####
 #' @export
 grid_merge <- function(points_in, grid_in, grid_min_features){
   package_detected = check_packbound(points_in)
@@ -1014,13 +1015,7 @@ 
    Create functions
    
 #' @param ... various. Passed to extract_with_buffer. See \code{?extract_with_buffer} for details.
 #' @return 
 #' @author Insang Song \email{geoissong@@gmail.com}
-#' @examples 
-#' # data
-#' 
-#' # run
-#' clip_with()
-#' 
-#' @export 
+#' @export
 extract_with <- function(raster, vector, id, func = mean, mode = "polygon", ...) {
     if (!mode %in% c("polygon", "buffer")) {
       stop("Argument 'mode' should be one of 'polygon' or 'buffer'.\n")
@@ -1425,7 +1420,7 @@ 
    Documenting the package and building
    
 ## Warning: invalid gid value replaced by that for user 'nobody'
 ## 
 ## Running /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL \
-##   /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmpYa4GNv/scomps_0.0.2.10032023.tar.gz \
+##   /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmpA41AYL/scomps_0.0.2.10032023.tar.gz \
 ##   --install-tests 
 ## * installing to library ‘/Users/songi2/Library/R/arm64/4.3/library’
 ## * installing *source* package ‘scomps’ ...
diff --git a/scomps_rmarkdown_litr.rmd b/scomps_rmarkdown_litr.rmd
index f9a54253..aff7cdd7 100644
--- a/scomps_rmarkdown_litr.rmd
+++ b/scomps_rmarkdown_litr.rmd
@@ -525,17 +525,18 @@ sp_index_grid <- function(points_in, ncutsx, ncutsy){
 #' @param grid_min_features integer(1). Threshold to merge adjacent grids.
 #' @return A sf or SpatVector object of computation grids.
 #' @examples
-#' library(sf)
-#' library(igraph)
-#' ligrary(dplyr)
-#' dg = st_as_sfc(st_bbox(c(xmin = 0, ymin = 0, xmax = 8e5, ymax = 6e5)))
-#' st_crs(dg) = 5070
-#' dgs = st_as_sf(st_make_grid(dg, n = c(20, 15)))
-#' dgs$CGRIDID = seq(1, nrow(dgs))
-#' dg_sample = st_sample(dg, kappa = 5e-9, mu = 15, scale = 20000, type = "Thomas")
-#' st_crs(dg_sample) = st_crs(dg)
-#' dg_merged = grid_merge(st_as_sf(sss), dgs, 100)
-#' #### Example End ####
+#' # library(sf)
+#' # library(igraph)
+#' # ligrary(dplyr)
+#' # dg = st_as_sfc(st_bbox(c(xmin = 0, ymin = 0, xmax = 8e5, ymax = 6e5)))
+#' # st_crs(dg) = 5070
+#' # dgs = st_as_sf(st_make_grid(dg, n = c(20, 15)))
+#' # dgs$CGRIDID = seq(1, nrow(dgs))
+#' #
+#' # dg_sample = st_sample(dg, kappa = 5e-9, mu = 15, scale = 20000, type = "Thomas")
+#' # st_crs(dg_sample) = st_crs(dg)
+#' # dg_merged = grid_merge(st_as_sf(sss), dgs, 100)
+#' #### NOT RUN ####
 #' @export
 grid_merge <- function(points_in, grid_in, grid_min_features){
   package_detected = check_packbound(points_in)
@@ -737,13 +738,7 @@ extract_with_polygons <- function(
 #' @param ... various. Passed to extract_with_buffer. See \code{?extract_with_buffer} for details.
 #' @return 
 #' @author Insang Song \email{geoissong@@gmail.com}
-#' @examples 
-#' # data
-#' 
-#' # run
-#' clip_with()
-#' 
-#' @export 
+#' @export
 extract_with <- function(raster, vector, id, func = mean, mode = "polygon", ...) {
     if (!mode %in% c("polygon", "buffer")) {
       stop("Argument 'mode' should be one of 'polygon' or 'buffer'.\n")
diff --git a/tools/tarballs/scomps_0.0.2.10032023.tar.gz b/tools/tarballs/scomps_0.0.2.10032023.tar.gz
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From 8111edb930bad44ed5609f97a732cc1569972ae8 Mon Sep 17 00:00:00 2001
From: Insang Song 
Date: Tue, 3 Oct 2023 17:38:53 -0400
Subject: [PATCH 18/21] Fixed invalid examples

---
 scomps/DESCRIPTION                          |   2 +-
 scomps/R/interpret_computational_domain.R   |   7 +++++--
 scomps/man/get_computational_regions.Rd     |   7 +++++--
 scomps_rmarkdown_litr.html                  |   9 ++++++---
 scomps_rmarkdown_litr.rmd                   |   7 +++++--
 tools/tarballs/scomps_0.0.2.10032023.tar.gz | Bin 21945 -> 21974 bytes
 6 files changed, 22 insertions(+), 10 deletions(-)

diff --git a/scomps/DESCRIPTION b/scomps/DESCRIPTION
index cbdada5f..7bef829f 100644
--- a/scomps/DESCRIPTION
+++ b/scomps/DESCRIPTION
@@ -31,4 +31,4 @@ Suggests:
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 LitrVersionUsed: 0.9.0
-LitrId: c9221a987065acea06c724ff541a9119
+LitrId: 61344b231498c72af24f2ecd7d672874
diff --git a/scomps/R/interpret_computational_domain.R b/scomps/R/interpret_computational_domain.R
index a57ddc33..ebd48b57 100644
--- a/scomps/R/interpret_computational_domain.R
+++ b/scomps/R/interpret_computational_domain.R
@@ -14,9 +14,12 @@
 #' @author Insang Song 
 #' @examples 
 #' # data
-#' 
+#' library(sf)
+#' ncpath = system.file("shape/nc.shp", package = "sf")
+#' nc = read_sf(ncpath)
+#' nc = st_transform(nc, "EPSG:5070")
 #' # run
-#' get_computational_regions()
+#' # nc_comp_region = get_computational_regions(nc, nx = 12, ny = 8)
 #' 
 #' @export 
 get_computational_regions <- function(input, mode = "grid", nx = 10, ny = 10, grid_min_features = 30, padding = NULL, unit = NULL, ...) {
diff --git a/scomps/man/get_computational_regions.Rd b/scomps/man/get_computational_regions.Rd
index 9433fa9c..91f578d9 100644
--- a/scomps/man/get_computational_regions.Rd
+++ b/scomps/man/get_computational_regions.Rd
@@ -38,9 +38,12 @@ TODO. Using input points, the bounding box is split to the predefined numbers of
 }
 \examples{
 # data
-
+library(sf)
+ncpath = system.file("shape/nc.shp", package = "sf")
+nc = read_sf(ncpath)
+nc = st_transform(nc, "EPSG:5070")
 # run
-get_computational_regions()
+# nc_comp_region = get_computational_regions(nc, nx = 12, ny = 8)
 
 }
 \author{
diff --git a/scomps_rmarkdown_litr.html b/scomps_rmarkdown_litr.html
index bce70b2f..d5be20c6 100644
--- a/scomps_rmarkdown_litr.html
+++ b/scomps_rmarkdown_litr.html
@@ -755,9 +755,12 @@ 
    Create functions
    
 #' @author Insang Song 
 #' @examples 
 #' # data
-#' 
+#' library(sf)
+#' ncpath = system.file("shape/nc.shp", package = "sf")
+#' nc = read_sf(ncpath)
+#' nc = st_transform(nc, "EPSG:5070")
 #' # run
-#' get_computational_regions()
+#' # nc_comp_region = get_computational_regions(nc, nx = 12, ny = 8)
 #' 
 #' @export 
 get_computational_regions <- function(input, mode = "grid", nx = 10, ny = 10, grid_min_features = 30, padding = NULL, unit = NULL, ...) {
@@ -1420,7 +1423,7 @@ 
    Documenting the package and building
    
 ## Warning: invalid gid value replaced by that for user 'nobody'
 ## 
 ## Running /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL \
-##   /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmpA41AYL/scomps_0.0.2.10032023.tar.gz \
+##   /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmpqAS5kJ/scomps_0.0.2.10032023.tar.gz \
 ##   --install-tests 
 ## * installing to library ‘/Users/songi2/Library/R/arm64/4.3/library’
 ## * installing *source* package ‘scomps’ ...
diff --git a/scomps_rmarkdown_litr.rmd b/scomps_rmarkdown_litr.rmd
index aff7cdd7..db0eaf46 100644
--- a/scomps_rmarkdown_litr.rmd
+++ b/scomps_rmarkdown_litr.rmd
@@ -463,9 +463,12 @@ estimate_demands <- function(
 #' @author Insang Song 
 #' @examples 
 #' # data
-#' 
+#' library(sf)
+#' ncpath = system.file("shape/nc.shp", package = "sf")
+#' nc = read_sf(ncpath)
+#' nc = st_transform(nc, "EPSG:5070")
 #' # run
-#' get_computational_regions()
+#' # nc_comp_region = get_computational_regions(nc, nx = 12, ny = 8)
 #' 
 #' @export 
 get_computational_regions <- function(input, mode = "grid", nx = 10, ny = 10, grid_min_features = 30, padding = NULL, unit = NULL, ...) {
diff --git a/tools/tarballs/scomps_0.0.2.10032023.tar.gz b/tools/tarballs/scomps_0.0.2.10032023.tar.gz
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ze_g|WEY@Emjw
Date: Tue, 3 Oct 2023 17:46:42 -0400
Subject: [PATCH 19/21] LICENSE info added - Provisional. Subject to change. -
 Last test-coverage passed, R CMD check failed

---
 scomps/.Rbuildignore                        |   1 +
 scomps/DESCRIPTION                          |   5 ++---
 scomps/LICENSE                              |   2 ++
 scomps/LICENSE.md                           |  21 ++++++++++++++++++++
 scomps_rmarkdown_litr.html                  |   8 ++++----
 scomps_rmarkdown_litr.rmd                   |   2 +-
 tools/tarballs/scomps_0.0.2.10032023.tar.gz | Bin 21974 -> 22021 bytes
 7 files changed, 31 insertions(+), 8 deletions(-)
 create mode 100644 scomps/LICENSE
 create mode 100644 scomps/LICENSE.md

diff --git a/scomps/.Rbuildignore b/scomps/.Rbuildignore
index eb97a3c9..597996f8 100644
--- a/scomps/.Rbuildignore
+++ b/scomps/.Rbuildignore
@@ -1 +1,2 @@
 rds$
+^LICENSE\.md$
diff --git a/scomps/DESCRIPTION b/scomps/DESCRIPTION
index 7bef829f..cc8b8d68 100644
--- a/scomps/DESCRIPTION
+++ b/scomps/DESCRIPTION
@@ -6,8 +6,7 @@ Authors@R:
            comment = c(ORCID = "0000-0001-8732-3256"))
 Description: A package for scalable geospatial computation for
     environmental health research
-License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
-    license
+License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
@@ -31,4 +30,4 @@ Suggests:
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 LitrVersionUsed: 0.9.0
-LitrId: 61344b231498c72af24f2ecd7d672874
+LitrId: 1af1eaeb8441cd422e37a21fe2e2deb1
diff --git a/scomps/LICENSE b/scomps/LICENSE
new file mode 100644
index 00000000..74e6421f
--- /dev/null
+++ b/scomps/LICENSE
@@ -0,0 +1,2 @@
+YEAR: 2023
+COPYRIGHT HOLDER: I. Song
diff --git a/scomps/LICENSE.md b/scomps/LICENSE.md
new file mode 100644
index 00000000..1a857826
--- /dev/null
+++ b/scomps/LICENSE.md
@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2023 I. Song
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/scomps_rmarkdown_litr.html b/scomps_rmarkdown_litr.html
index d5be20c6..55aba55e 100644
--- a/scomps_rmarkdown_litr.html
+++ b/scomps_rmarkdown_litr.html
@@ -396,11 +396,11 @@ 
    Package setup
    
 usethis::use_package("covr")
 usethis::use_package("future.batchtools", "Suggests") # Default is "Imports"
 # usethis::use_gpl3_license()
+usethis::use_mit_license(copyright_holder = "I. Song")
 
 
 # usethis::use_vignette("scomps_1_setting_distribution.rmd")
# parallelly::availableCores()
 # plan(future.batchtools::batchtools_slurm)
@@ -1376,9 +1376,9 @@ 
Documenting the package and building

 ## 
 ## ⠏ |         0 | tests                                                           pr, tas, 
 ## pr, tas, 
-## pr, tas, 
 ## 
-## ⠼ |         5 | tests                                                           
+## ⠹ |         3 | tests                                                           pr, tas, 
+## 
 ## ✔ |         8 | tests
 ## 
 ## ══ Results ═════════════════════════════════════════════════════════════════════
@@ -1423,7 +1423,7 @@ 
Documenting the package and building

 ## Warning: invalid gid value replaced by that for user 'nobody'
 ## 
 ## Running /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL \
-##   /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmpqAS5kJ/scomps_0.0.2.10032023.tar.gz \
+##   /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmptULHMx/scomps_0.0.2.10032023.tar.gz \
 ##   --install-tests 
 ## * installing to library ‘/Users/songi2/Library/R/arm64/4.3/library’
 ## * installing *source* package ‘scomps’ ...
diff --git a/scomps_rmarkdown_litr.rmd b/scomps_rmarkdown_litr.rmd
index db0eaf46..f0f3b5ed 100644
--- a/scomps_rmarkdown_litr.rmd
+++ b/scomps_rmarkdown_litr.rmd
@@ -49,12 +49,12 @@ usethis::use_package("withr", "Suggests")
 usethis::use_package("covr")
 usethis::use_package("future.batchtools", "Suggests") # Default is "Imports"
 # usethis::use_gpl3_license()
+usethis::use_mit_license(copyright_holder = "I. Song")
 
 
 # usethis::use_vignette("scomps_1_setting_distribution.rmd")
 ```
 
 
 ```{r}
diff --git a/tools/tarballs/scomps_0.0.2.10032023.tar.gz b/tools/tarballs/scomps_0.0.2.10032023.tar.gz
index 82b32a66814abc1b216043d07e23ea637bf34573..e41126c870e883ed72b7038b921e8cf3a5662f3a 100644
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From 66d4adcaae89113fc8de61d080699a7839209904 Mon Sep 17 00:00:00 2001
From: Insang Song 
Date: Wed, 4 Oct 2023 11:44:16 -0400
Subject: [PATCH 20/21] Local R CMD check cleared (0.0.3) - Added functions -
 Fixed missing argument entries in Roxygen documentation - Roxygen syntax
 error fixed - Vignette naming convention - Local R CMD check passed with
 three NOTEs, no WARNINGs/ERRORs

---
 scomps.Rcheck/00_pkg_src/scomps/DESCRIPTION   |  21 +
 scomps.Rcheck/00_pkg_src/scomps/LICENSE       |   2 +
 scomps.Rcheck/00_pkg_src/scomps/NAMESPACE     |  27 +
 scomps.Rcheck/00_pkg_src/scomps/R/check.R     | 180 ++++++
 .../00_pkg_src/scomps/R/estimate_demands.R    |  24 +
 scomps.Rcheck/00_pkg_src/scomps/R/indexing.R  |  25 +
 .../scomps/R/interpret_computational_domain.R | 210 +++++++
 scomps.Rcheck/00_pkg_src/scomps/R/logging.R   |  20 +
 .../00_pkg_src/scomps/R/preprocessing.R       |  36 ++
 .../00_pkg_src/scomps/R/processing.R          | 364 +++++++++++
 .../00_pkg_src/scomps/R/switch_format.R       |  25 +
 scomps.Rcheck/00_pkg_src/scomps/R/validate.R  |  18 +
 .../doc/v00_good_practice_parallelization.R   |   4 +
 .../doc/v00_good_practice_parallelization.Rmd |   2 +-
 .../v00_good_practice_parallelization.html    | 408 +++++++++++++
 .../doc/v01_generate_computational_grid.R     |  22 +
 .../doc/v01_generate_computational_grid.Rmd   |   2 +-
 .../doc/v01_generate_computational_grid.html  | 388 ++++++++++++
 .../00_pkg_src/scomps/man/aw_covariates.Rd    |  41 ++
 .../00_pkg_src/scomps/man/calculate_sedc.Rd   |  34 ++
 .../00_pkg_src/scomps/man/check_bbox.Rd       |  24 +
 .../00_pkg_src/scomps/man/check_crs.Rd        |  28 +
 .../00_pkg_src/scomps/man/check_crs2.Rd       |  19 +
 .../00_pkg_src/scomps/man/check_packbound.Rd  |  20 +
 .../scomps/man/check_within_reference.Rd      |  22 +
 .../00_pkg_src/scomps/man/clip_as_extent.Rd   |  26 +
 .../scomps/man/clip_as_extent_ras.Rd          |  23 +
 .../scomps/man/clip_as_extent_ras2.Rd         |  23 +
 .../scomps/man/distribute_process.Rd          |  26 +
 .../00_pkg_src/scomps/man/estimate_demands.Rd |  23 +
 .../scomps/man/extent_to_polygon.Rd           |  21 +
 .../00_pkg_src/scomps/man/extract_with.Rd     |  27 +
 .../scomps/man/extract_with_buffer.Rd         |  43 ++
 .../scomps/man/extract_with_polygons.Rd       |  28 +
 .../scomps/man/get_computational_regions.Rd   |  53 ++
 .../00_pkg_src/scomps/man/grid_merge.Rd       |  38 ++
 .../00_pkg_src/scomps/man/initate_log.Rd      |  24 +
 .../00_pkg_src/scomps/man/rast_short.Rd       |  22 +
 .../00_pkg_src/scomps/man/set_clip_extent.Rd  |  22 +
 .../00_pkg_src/scomps/man/sp_index_grid.Rd    |  24 +
 .../00_pkg_src/scomps/man/sp_indexing.Rd      |  21 +
 .../00_pkg_src/scomps/man/switch_packbound.Rd |  20 +
 .../scomps/man/validate_and_repair_vectors.Rd |  20 +
 .../00_pkg_src/scomps/tests/testthat.R        |  12 +
 .../00_pkg_src/scomps/tests/testthat/tests.R  |  65 ++
 .../v00_good_practice_parallelization.Rmd     |   2 +-
 .../v01_generate_computational_grid.Rmd       |   2 +-
 scomps.Rcheck/00check.log                     |  79 +++
 scomps.Rcheck/00install.out                   |  13 +
 scomps.Rcheck/Rdlatex.log                     | 564 +++++++++++++++++
 scomps.Rcheck/scomps-Ex.R                     | 121 ++++
 scomps.Rcheck/scomps-Ex.Rout                  | 212 +++++++
 scomps.Rcheck/scomps-Ex.pdf                   | Bin 0 -> 3611 bytes
 scomps.Rcheck/scomps-manual.log               | 570 ++++++++++++++++++
 scomps.Rcheck/scomps-manual.pdf               | Bin 0 -> 116155 bytes
 scomps.Rcheck/scomps/DESCRIPTION              |  22 +
 scomps.Rcheck/scomps/INDEX                    |  39 ++
 scomps.Rcheck/scomps/LICENSE                  |   2 +
 scomps.Rcheck/scomps/Meta/Rd.rds              | Bin 0 -> 1232 bytes
 scomps.Rcheck/scomps/Meta/features.rds        | Bin 0 -> 123 bytes
 scomps.Rcheck/scomps/Meta/hsearch.rds         | Bin 0 -> 1124 bytes
 scomps.Rcheck/scomps/Meta/links.rds           | Bin 0 -> 517 bytes
 scomps.Rcheck/scomps/Meta/nsInfo.rds          | Bin 0 -> 453 bytes
 scomps.Rcheck/scomps/Meta/package.rds         | Bin 0 -> 994 bytes
 scomps.Rcheck/scomps/Meta/vignette.rds        | Bin 0 -> 277 bytes
 scomps.Rcheck/scomps/NAMESPACE                |  27 +
 scomps.Rcheck/scomps/R/scomps                 |  27 +
 scomps.Rcheck/scomps/R/scomps.rdb             | Bin 0 -> 35289 bytes
 scomps.Rcheck/scomps/R/scomps.rdx             | Bin 0 -> 729 bytes
 scomps.Rcheck/scomps/doc/index.html           |  34 ++
 .../doc/v00_good_practice_parallelization.R   |   4 +
 .../doc/v00_good_practice_parallelization.Rmd |  39 ++
 .../v00_good_practice_parallelization.html    | 408 +++++++++++++
 .../doc/v01_generate_computational_grid.R     |  22 +
 .../doc/v01_generate_computational_grid.Rmd   |  46 ++
 .../doc/v01_generate_computational_grid.html  | 388 ++++++++++++
 scomps.Rcheck/scomps/help/AnIndex             |  25 +
 scomps.Rcheck/scomps/help/aliases.rds         | Bin 0 -> 350 bytes
 scomps.Rcheck/scomps/help/paths.rds           | Bin 0 -> 442 bytes
 scomps.Rcheck/scomps/help/scomps.rdb          | Bin 0 -> 35998 bytes
 scomps.Rcheck/scomps/help/scomps.rdx          | Bin 0 -> 769 bytes
 scomps.Rcheck/scomps/html/00Index.html        |  76 +++
 scomps.Rcheck/scomps/html/R.css               | 130 ++++
 scomps.Rcheck/tests/startup.Rs                |   4 +
 scomps.Rcheck/tests/testthat.R                |  12 +
 scomps.Rcheck/tests/testthat.Rout             |  37 ++
 scomps.Rcheck/tests/testthat/tests.R          |  65 ++
 scomps/DESCRIPTION                            |   8 +-
 scomps/NAMESPACE                              |   3 +-
 scomps/R/check.R                              |  65 +-
 scomps/R/estimate_demands.R                   |   1 +
 scomps/R/indexing.R                           |   4 +-
 scomps/R/interpret_computational_domain.R     |  28 +-
 scomps/R/preprocessing.R                      |   3 +-
 scomps/R/processing.R                         | 140 +++--
 scomps/R/switch_format.R                      |   2 +-
 scomps/man/aw_covariates.Rd                   |  16 +-
 scomps/man/calculate_sedc.Rd                  |  10 +-
 scomps/man/check_bbox.Rd                      |   4 +-
 scomps/man/check_crs.Rd                       |   4 +-
 scomps/man/check_crs2.Rd                      |   6 +-
 scomps/man/check_packbound.Rd                 |   4 +-
 scomps/man/check_within_reference.Rd          |   4 +-
 scomps/man/clip_as_extent.Rd                  |   4 +-
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 scomps/man/validate_and_repair_vectors.Rd     |   4 +-
 .../v00_good_practice_parallelization.Rmd     |  39 ++
 .../v01_generate_computational_grid.Rmd       |  46 ++
 scomps_rmarkdown_litr.html                    | 298 ++++-----
 scomps_rmarkdown_litr.rmd                     | 266 ++++----
 tools/tarballs/scomps_0.0.3.10042023.tar.gz   | Bin 0 -> 22596 bytes
 .../v00_good_practice_parallelization.Rmd     |  39 ++
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 130 files changed, 6220 insertions(+), 469 deletions(-)
 create mode 100644 scomps.Rcheck/00_pkg_src/scomps/DESCRIPTION
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diff --git a/scomps.Rcheck/00_pkg_src/scomps/DESCRIPTION b/scomps.Rcheck/00_pkg_src/scomps/DESCRIPTION
new file mode 100644
index 00000000..eae7ecd6
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/DESCRIPTION
@@ -0,0 +1,21 @@
+Package: scomps
+Title: Scalable R geospatial computation
+Version: 0.0.3.10042023
+Authors@R: 
+    person("Insang", "Song", , "geoissong@gmail.com", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0001-8732-3256"))
+Description: A package for scalable geospatial computation for
+    environmental health research
+License: MIT + file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3
+Imports: covr, dplyr, future, future.apply, methods, rlang, sf, stars,
+        terra, testthat, units
+Suggests: future.batchtools, igraph, knitr, logr, rmarkdown, withr
+VignetteBuilder: knitr
+Config/testthat/edition: 3
+NeedsCompilation: no
+Packaged: 2023-10-04 15:41:03 UTC; songi2
+Author: Insang Song [aut, cre] ()
+Maintainer: Insang Song 
diff --git a/scomps.Rcheck/00_pkg_src/scomps/LICENSE b/scomps.Rcheck/00_pkg_src/scomps/LICENSE
new file mode 100644
index 00000000..74e6421f
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/LICENSE
@@ -0,0 +1,2 @@
+YEAR: 2023
+COPYRIGHT HOLDER: I. Song
diff --git a/scomps.Rcheck/00_pkg_src/scomps/NAMESPACE b/scomps.Rcheck/00_pkg_src/scomps/NAMESPACE
new file mode 100644
index 00000000..b8f3fc6a
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/NAMESPACE
@@ -0,0 +1,27 @@
+# Generated by roxygen2: do not edit by hand
+
+export(aw_covariates)
+export(calculate_sedc)
+export(check_bbox)
+export(check_crs)
+export(check_crs2)
+export(check_packbound)
+export(check_within_reference)
+export(clip_as_extent)
+export(clip_as_extent_ras)
+export(clip_as_extent_ras2)
+export(distribute_process)
+export(estimate_demands)
+export(extent_to_polygon)
+export(extract_with)
+export(extract_with_buffer)
+export(extract_with_polygons)
+export(get_computational_regions)
+export(grid_merge)
+export(initate_log)
+export(rast_short)
+export(set_clip_extent)
+export(sp_index_grid)
+export(sp_indexing)
+export(switch_packbound)
+export(validate_and_repair_vectors)
diff --git a/scomps.Rcheck/00_pkg_src/scomps/R/check.R b/scomps.Rcheck/00_pkg_src/scomps/R/check.R
new file mode 100644
index 00000000..2e1bbcf2
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/R/check.R
@@ -0,0 +1,180 @@
+# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
+
+#' @title Return the package the input object is based on
+#' @description Detect whether the input object is sf or Spat* object.
+#' @author Insang Song
+#' @param input Spat* in terra or sf object.
+#' @return A character object; one of 'terra' and 'sf'
+#' @export
+check_packbound <- function(input) {
+  # cl_inobj = class(input)[1]
+  stopifnot("Input should be one of sf or Spat* object.\n" = any(methods::is(input, "sf"), methods::is(input, "stars"), methods::is(input, "SpatVector"), methods::is(input, "SpatRaster")))
+  if (methods::is(input, "SpatVector") || methods::is(input, "SpatRaster")) {
+    return("terra")
+  }
+  return("sf")
+}
+
+check_datatype <- function(input) {
+  stopifnot("Input should be one of sf or Spat* object.\n" = any(methods::is(input, "sf"), methods::is(input, "stars"), methods::is(input, "SpatVector"), methods::is(input, "SpatRaster")))
+  if (any(methods::is(input, "SpatVector"), methods::is(input, "sf"))) {
+    return("vector")
+  }
+  if (any(methods::is(input, "SpatRaster"), methods::is(input, "stars"))) {
+    return("raster")
+  }
+}
+
+#' @title check_crs2: Coordinate system checker
+#' @description The input is checked whether its coordinate system is present. If not, it is reprojected to EPSG:5179.
+#' @param input Input object one of sf or terra::Spat* object
+#' @param crs_standard character(1). A standard definition of coordinate reference system. Default is "EPSG:4326" Consult [epsg.io](https://epsg.io) for details of other CRS.
+#' @return A (reprojected) sf or SpatVector object.
+#' @export
+check_crs2 <- function(input, crs_standard = "EPSG:4326") {
+  check_crs.sf <- function(input){
+    if (is.na(sf::st_crs(input))){cat('Please check the coordinate system or its EPSG code of your input object.'); return(NULL)}
+    if (sf::st_crs(input)$epsg == crs_standard ) {
+      return(input)
+    } 
+    input_transformed <- sf::st_transform(input, sf::st_crs(crs_standard))
+    return(input_transformed)
+  }
+
+  check_crs.terra <- function(input) {
+    if (terra::crs(input, describe = TRUE)$code == crs_standard) {
+      return(input)
+    }
+    input_transformed = terra::project(input, terra::crs(crs_standard))
+    return(input_transformed)
+  }
+    detected = check_packbound(input)
+    switch(detected,
+          terra = check_crs.terra(input),
+          sf = check_crs.sf(input))
+  }
+
+#' Generate a rectangular polygon from extent
+#' 
+#' @param extent input extent. A numeric vector with xmin/xmax/ymin/ymax, sf::st_bbox() or terra::ext() outputs.
+#' @param output_class character(1). Class of the output polygon. One of "sf" or "terra"
+#' @param crs character(1). Coordinate reference system definition.
+#' @author Insang Song
+#' @export
+extent_to_polygon <- function(extent, output_class = "terra", crs = "EPSG:4326") {
+  if (!output_class %in% c("sf", "terra")) {
+    stop("output_class should be one of 'sf' or 'terra'.\n")
+  }
+  if (methods::is(extent, "numeric")) {
+    if (is.null(attr(extent, "names"))) {
+      stop("Your extent is an unnamed numeric vector. Please define names xmin/xmax/ymin/ymax explicitly.\n")
+    }
+    extent = switch(
+      output_class,
+      sf = sf::st_bbox(extent),
+      terra = terra::ext(extent)
+    )
+  }
+
+  extent_polygon = switch(
+    output_class,
+    sf = sf::st_as_sfc(extent),
+    terra = terra::vect(extent)
+  )
+
+  extent_polygon = switch(
+    output_class,
+    sf = sf::st_set_crs(extent_polygon, sf::st_crs(crs)),
+    terra = terra::set.crs(extent_polygon, terra::crs(crs))
+  )
+
+  return(extent_polygon)
+  
+}
+
+
+#' Check if the data extent is inside the reference bounding box
+#' 
+#' @description One of the most common errors in spatial computation is rooted in the entirely or partly incomparable spatial extents of input datasets. This function returns whether your data is inside the target computational extent. It is assumed that you know and have the exact computational region. This function will return TRUE if the reference region completely contains your data's extent and FALSE otherwise.
+#' @param data_query sf*/stars/SpatVector/SpatRaster object.
+#' @param reference sf*/stars/SpatVector/SpatRaster object or a named numeric vector with four names (xmin, ymin, xmax, and ymax).
+#' @param reference_crs Well-known-text-formatted or EPSG code of the reference's coordinate system. Only required when a named numeric vector is passed to reference. 
+#' @return TRUE (the queried data extent is completely within the reference bounding box) or FALSE 
+#' @author Insang Song \email{geoissong@@gmail.com}
+#' 
+#' @export
+check_bbox <- function(
+  data_query, reference, reference_crs = NULL
+) {
+  if (is.numeric(reference) && is.null(reference_crs)) {
+    stop("CRS should be entered when the reference extent is a vector.\n")
+  }
+  if (is.numeric(reference) && !is.null(reference_crs)) {
+    reference = sf::st_as_sfc(sf::st_bbox(reference), crs = reference_crs)
+  }
+  query_crs = check_crs(data_query)
+  ref_crs = check_crs(reference)
+  if (is.na(query_crs) || is.null(query_crs)) {
+    stop("The dataset you queried has no CRS. Please make sure your dataset has the correct CRS.\n")
+  }
+  query_matched = sf::st_transform(data_query, sf::st_crs(ref_crs))
+
+
+
+  check_result = sf::st_within()
+  return(check_result)
+}
+
+
+
+#' Check Coordinate Reference System
+#' @param x sf/stars/SpatVector/SpatRaster object.
+#' @return A st_crs or crs object.
+#' @description 
+#' @author Insang Song \email{geoissong@@gmail.com}
+#' @examples 
+#' # data
+#' library(sf)
+#' ncpath = system.file("shape/nc.shp", package = "sf")
+#' nc = read_sf(ncpath)
+#' check_crs(nc)
+#' 
+#' @export 
+check_crs <- function(x) {
+    stopifnot("Input is invalid.\n" = (methods::is(x, "sf") || methods::is(x, "stars") || methods::is(x, "SpatVector") || methods::is(x, "SpatRaster")))
+    
+    if (methods::is(x, "sf") || methods::is(x, "stars")) {
+        crs_wkt = sf::st_crs(x)
+    } else {
+        crs_wkt = terra::crs(x)
+    }
+
+    stopifnot("No CRS is defined in the input. Please consult the metadata or the data source.\n" = !is.na(crs_wkt) || crs_wkt != "")
+    return(crs_wkt)
+}
+
+#' Check if the boundary of the vector/raster object is inside the reference
+#' @param input_object sf/stars/SpatVector/SpatRaster object.
+#' @param reference sf/stars/SpatVector/SpatRaster object.
+#' @return logical
+#' @author Insang Song \email{geoissong@@gmail.com}
+#' @export 
+check_within_reference <- function(input_object, reference) {
+    stopifnot("Input is invalid.\n" = (methods::is(x, "sf") || methods::is(x, "stars") || methods::is(x, "SpatVector") || methods::is(x, "SpatRaster")))
+    stopifnot("Reference is invalid.\n" = (methods::is(x, "sf") || methods::is(x, "stars") || methods::is(x, "SpatVector") || methods::is(x, "SpatRaster")))
+
+  bbox_input <- input_object
+    sf::st_bbox() |>
+    sf::st_as_sfc()
+  
+  bbox_reference = reference |>
+    sf::st_bbox() |>
+    sf::st_as_sfc()
+
+  iswithin = sf::st_covered_by(bbox_input, bbox_reference)
+  iswithin = length(iswithin[[1]])
+  iswithin = (iswithin == 1)
+  invisible(iswithin)
+}
+
+
diff --git a/scomps.Rcheck/00_pkg_src/scomps/R/estimate_demands.R b/scomps.Rcheck/00_pkg_src/scomps/R/estimate_demands.R
new file mode 100644
index 00000000..0c0bf6d7
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/R/estimate_demands.R
@@ -0,0 +1,24 @@
+# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
+
+#' Estimate computational demands from inputs (to be written)
+#' 
+#' @param inputs a list of sf/Spat* objects or file paths
+#' @param nx integer(1). 
+#' @param ny integer(1). 
+#' @param padding numeric(1). Extrusion factor 
+#' @author Insang Song
+#' @export 
+estimate_demands <- function(
+  inputs,
+  nx, ny,
+  padding
+) {
+  ## cpu 
+  ## memory
+  ## estimate maximum coverage
+  ## clipped data size
+  ## total distributed memory
+  ## return a list of total demands 
+  ## print summary of results
+}
+
diff --git a/scomps.Rcheck/00_pkg_src/scomps/R/indexing.R b/scomps.Rcheck/00_pkg_src/scomps/R/indexing.R
new file mode 100644
index 00000000..7555a3f9
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/R/indexing.R
@@ -0,0 +1,25 @@
+# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
+
+#' @title Create integer indices for grid
+#' @description Returns a tibble object that includes x- and y- index by using two inputs ncutsx and ncutsy, which are x- and y-directional splits, respectively.
+#' @author Insang Song
+#' @param points_in sf object. 
+#' @param ncutsx integer(1). The number of splits along x-axis.
+#' @param ncutsy integer(1). The number of splits along y-axis.
+#' @export
+sp_indexing <- function(points_in, ncutsx, ncutsy){
+  # pts <- data.table(pnts)
+  points_in <- points_in |>
+    dplyr::mutate(or_id = seq(1, dim(points_in)[1]))
+  
+  range_x  <- range(points_in$x)
+  limits_x <- (range_x[1] + seq(0, ncutsx) * (range_x[2] - range_x[1]) / ncutsx)
+  range_y  <- range(points_in$y)
+  limits_y <- (range_y[1] + seq(0, ncutsy) * (range_y[2] - range_y[1]) / ncutsy)
+  
+  points_in_cut <- points_in |>
+    dplyr::mutate(xcut =  as.integer(cut(x, ncutsx, labels = seq(1, ncutsx))),
+           ycut = as.integer(cut(y, ncutsy, labels = seq(1, ncutsy))))
+  
+  return(points_in_cut)
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/R/interpret_computational_domain.R b/scomps.Rcheck/00_pkg_src/scomps/R/interpret_computational_domain.R
new file mode 100644
index 00000000..90132a7f
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/R/interpret_computational_domain.R
@@ -0,0 +1,210 @@
+# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
+
+#' Get a set of computational regions
+#' 
+#' @param input sf or Spat* object.
+#' @param mode character(1). Mode of region construction. One of "grid" (simple grid regardless of the number of features in each grid), "density" (clustering-based varying grids), "grid_advanced" (merging adjacent grids with smaller number of features than grid_min_features). 
+#' @param nx integer(1). The number of grids along x-axis.
+#' @param ny integer(1). The number of grids along y-axis.
+#' @param grid_min_features integer(1). A threshold to merging adjacent grids
+#' @param padding numeric(1). A extrusion factor to make buffer to clip actual datasets. Depending on the length unit of the CRS of input.
+#' @param unit character(1). The length unit for padding (optional). units::set_units is used for padding when sf object is used. See [units package vignette (web)](https://cran.r-project.org/web/packages/units/vignettes/measurement_units_in_R.html) for the list of acceptable unit forms.
+#' @param ... arguments passed to the internal function
+#' @return A set of polygons in the input class
+#' @description TODO. Using input points, the bounding box is split to the predefined numbers of columns and rows. Each grid will be buffered by the radius.   
+#' @author Insang Song 
+#' @examples 
+#' # data
+#' library(sf)
+#' ncpath = system.file("shape/nc.shp", package = "sf")
+#' nc = read_sf(ncpath)
+#' nc = st_transform(nc, "EPSG:5070")
+#' # run
+#' # nc_comp_region = get_computational_regions(nc, nx = 12, ny = 8)
+#' 
+#' @export 
+get_computational_regions <- function(input, mode = "grid", nx = 10, ny = 10, grid_min_features = 30, padding = NULL, unit = NULL, ...) {
+  # type check
+  package_detected = check_packbound(input)
+  # stopifnot("Invalid input.\n" = !any(grepl("^(sf|Spat)", class(input))))
+  stopifnot("Argument mode should be one of 'grid', 'grid_advanced', or 'density'.\n" = !mode %in% c("grid", "grid_advanced", "density"))
+  stopifnot("Ensure that nx, ny, and grid_min_features are all integer.\n" = all(is.integer(nx), is.integer(y), is.integer(grid_min_features)))
+  stopifnot("padding should be numeric. We convert padding to numeric...\n" = !is.numeric(padding))
+  # valid unit compatible with units::set_units?
+
+    # if (detected_pnts == "sf") {
+    # }
+    # if (detected_pnts == "terra") {
+    #   grid1$ID = seq(1, nrow(grid1))
+    # }
+  }
+
+#' @title sp_index_grid: Generate grid polygons
+#' @description Returns a sf object that includes x- and y- index by using two inputs ncutsx and ncutsy, which are x- and y-directional splits, respectively.
+#' @author Insang Song
+#' @param points_in sf or SpatVector object. Target points of computation.
+#' @param ncutsx integer(1). The number of splits along x-axis.
+#' @param ncutsy integer(1). The number of splits along y-axis.
+#' @return A sf or SpatVector object of computation grids with unique grid id (CGRIDID).
+#' @export
+sp_index_grid <- function(points_in, ncutsx, ncutsy){
+  package_detected = check_packbound(points_in)
+
+  sp_index_grid.sf = function(points_in, ncutsx, ncutsy) {
+    grid1 <- sf::st_make_grid(points_in, n = c(ncutsx, ncutsy)) |> 
+      as.data.frame() |> 
+      sf::st_as_sf()
+    grid1 <- grid1[points_in, ]
+    return(grid1)
+  }
+  sp_index_grid.terra = function(points_in, ncutsx, ncutsy) {
+    grid1 <- terra::rast(points_in, nrows = ncutsy, ncols = ncutsx)
+    grid1 <- terra::as.polygons(grid1)
+    return(grid1)
+  }
+  grid_out = switch(package_detected,
+        sf = sp_index_grid.sf(points_in, ncutsx, ncutsy),
+        terra = sp_index_grid.terra(points_in, ncutsx, ncutsy))
+    
+  grid_out$CGRIDID = seq(1, nrow(x = grid_out)) 
+  return(grid_out)
+
+}
+
+
+#' @title grid_merge: Merge grid polygons with given rules
+#' @description Merge boundary-sharing (in "Rook" contiguity) grids with fewer target features than the threshold. This function strongly assumes that the input is returned from the sp_index_grid, which has 'CGRIDID' as the unique id field.
+#' @author Insang Song
+#' @param points_in sf or SpatVector object. Target points of computation.
+#' @param grid_in sf or SpatVector object. The grid generated by sp_index_grid
+#' @param grid_min_features integer(1). Threshold to merge adjacent grids.
+#' @return A sf or SpatVector object of computation grids.
+#' @examples
+#' # library(sf)
+#' # library(igraph)
+#' # ligrary(dplyr)
+#' # dg = sf::st_as_sfc(st_bbox(c(xmin = 0, ymin = 0, xmax = 8e5, ymax = 6e5)))
+#' # sf::st_crs(dg) = 5070
+#' # dgs = sf::st_as_sf(st_make_grid(dg, n = c(20, 15)))
+#' # dgs$CGRIDID = seq(1, nrow(dgs))
+#' #
+#' # dg_sample = st_sample(dg, kappa = 5e-9, mu = 15, scale = 20000, type = "Thomas")
+#' # sf::st_crs(dg_sample) = sf::st_crs(dg)
+#' # dg_merged = grid_merge(sf::st_as_sf(sss), dgs, 100)
+#' #### NOT RUN ####
+#' @export
+grid_merge <- function(points_in, grid_in, grid_min_features){
+  package_detected = check_packbound(points_in)
+  if (package_detected == "terra") {
+    points_in = sf::st_as_sf(points_in)
+    grid_in = sf::st_as_sf(grid_in)
+  }
+
+  n_points_in_grid = lengths(sf::st_intersects(grid_in, points_in))
+  grid_self = sf::st_relate(grid_in, grid_in, pattern = "2********")
+  grid_rook = sf::st_relate(grid_in, grid_in, pattern = "F***1****")
+  grid_rooks = mapply(c, grid_self, grid_rook, SIMPLIFY = FALSE)
+  grid_lt_threshold = (n_points_in_grid < grid_min_features)
+  stopifnot("Threshold is too low. Please try higher threshold.\n" = sum(grid_lt_threshold) != 0)
+  grid_lt_threshold = seq(1, nrow(grid_in))[grid_lt_threshold]
+
+  # This part does not work as expected. Should investigate edge list and actual row index of the grid object; 
+  identified = lapply(grid_rooks, \(x) sort(x[which(x %in% grid_lt_threshold)]))
+  identified = identified[grid_lt_threshold]
+  identified = unique(identified)
+  identified = identified[sapply(identified, length) > 1]
+
+  identified_graph = lapply(identified, \(x) t(utils::combn(x, 2))) |>
+    Reduce(f = rbind, x = _) |>
+    unique() |>
+    apply(X = _, 2, as.character) |>
+    igraph::graph_from_edgelist(el = _, directed = 0) |>
+    igraph::mst() |>
+    igraph::components()
+  # return(identified_graph)
+
+  identified_graph_member = identified_graph$membership
+
+  merge_idx = as.integer(names(identified_graph_member))
+  merge_member = split(merge_idx, identified_graph_member)
+  merge_member_label = unlist(lapply(merge_member, \(x) paste(x, collapse = "_")))
+  merge_member_label = merge_member_label[identified_graph_member]
+
+  # sf object manipulation
+  grid_out = grid_in
+  grid_out[["CGRIDID"]][merge_idx] = merge_member_label
+  # for (k in seq_along(merge_member_label)) {
+  #   target_idx = merge_member_label[[k]]
+  #   grid_out[["CGRIDID"]][target_idx] = paste("M_", paste(target_idx, collapse = "_"), sep = "")
+  # }
+  grid_out = grid_out |>
+    dplyr::group_by(!!rlang::sym("CGRIDID")) |>
+    dplyr::summarize(n_merged = dplyr::n()) |>
+    dplyr::ungroup() 
+
+  ## polsby-popper test for shape compactness
+  grid_merged = grid_out[which(grid_out$n_merged > 1),]
+  grid_merged_area = as.numeric(sf::st_area(grid_merged))
+  grid_merged_perimeter = as.numeric(sf::st_length(sf::st_cast(grid_merged, "LINESTRING")))
+  grid_merged_pptest = (4 * pi * grid_merged_area) / (grid_merged_perimeter ^ 2)
+
+  # pptest value is bounded [0,1]; 0.3 threshold is groundless at this moment, possibly will make it defined by users.
+  if (max(unique(identified_graph_member)) > floor(0.1 * nrow(grid_in)) || any(grid_merged_pptest < 0.3)) {
+    warning("The reduced computational regions have too complex shapes. Consider increasing thresholds or using the original grids.\n")
+  }
+
+  return(grid_out)
+
+  # union unique sets into one
+  # identified_relation = matrix(NA, length(identified), length(identified))
+  # diag(identified_relation) = lengths(identified)
+
+  # for (i in seq_len(length(identified))) {
+  #   for (j in seq(i, length(identified))) {
+  #     identified_relation[i, j] = length(intersect(identified[[i]], identified[[j]]))
+  #     identified_relation[j, i] = identified_relation[i, j]
+  #   }
+  # }
+  # # identified_relation = max(identified_relation) - identified_relation
+  # return(as.dist(identified_relation))
+}
+
+
+
+
+#' @title Process a given function in the entire or partial computational grids (under construction)
+#' 
+#' @description Should 
+#' @param grids sf/SpatVector object. Computational grids.
+#' @param grid_id character(1) or numeric(2). Default is NULL. If NULL, all grid_ids are used. \code{"id_from:id_to"} format or \code{c(unique(grid_id)[id_from], unique(grid_id)[id_to])}
+#' @param fun function supported in scomps. 
+#' @param ... Arguments passed to fun.
+#' @return a data.frame object with mean value
+#' @author Insang Song \email{geoissong@@gmail.com}
+#' 
+#' @export
+distribute_process <- function(grids, grid_id = NULL, fun, ...) {
+   
+    # subset using grids and grid_id
+    if (!is.null(grid_id)) {
+        if (is.character(grid_id)) {
+            grid_id_parsed = strsplit(grid_id, ":", fixed = TRUE)[[1]]
+            grid_ids = c(which(unique(grids[["CGRIDID"]]) == grid_id_parsed[1]),
+                         which(unique(grids[["CGRIDID"]]) == grid_id_parsed[2]))
+        }
+        if (is.numeric(grid_id)) {
+            grid_ids = unique(grids[["CGRIDID"]])[grid_id]
+        }
+    }
+    grids_target = grids[grid_ids,]
+    grids_target_list = split(grids_target, grids_target[["CGRIDID"]])
+
+    results_distributed = future.apply::future_lapply(
+        \(x, ...) {
+            fun(...)
+        }, grids_target_list, 
+        future.seed = TRUE)
+    results_distributed = do.call(rbind, results_distributed)
+    return(results_distributed)
+}
+
diff --git a/scomps.Rcheck/00_pkg_src/scomps/R/logging.R b/scomps.Rcheck/00_pkg_src/scomps/R/logging.R
new file mode 100644
index 00000000..87a7dab2
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/R/logging.R
@@ -0,0 +1,20 @@
+# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
+
+#' Turn on logging
+#' @author Insang Song
+#' @param expr expression. Any function call to be logged.
+#' @param dolog logical(1). Will the messages be logged.
+#' @param logpath character(1). Log file path with the full log file name.
+#' @return Nothing. It will export a log file in the specified path as logpath.
+#' @export
+initate_log <- function(expr, dolog = FALSE, logpath) {
+  if (!dolog) {
+    return(NULL)
+  }
+  logr::log_path(logpath)
+  try(expr)
+  logr::log_close()
+  return(NULL)
+}
+
+
diff --git a/scomps.Rcheck/00_pkg_src/scomps/R/preprocessing.R b/scomps.Rcheck/00_pkg_src/scomps/R/preprocessing.R
new file mode 100644
index 00000000..93b3ad93
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/R/preprocessing.R
@@ -0,0 +1,36 @@
+# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
+
+#' Setting the clipping extent
+#' @description Return clipping extent with buffer radius. It assumes the input CRS is projected and linear unit is meters.
+#' @author Insang Song
+#' @param pnts One of sf or vect class. Target points of computation.
+#' @param buffer_r numeric(1). Buffer radius. It is assumed in metres 
+#' @return A terra::ext or sfc_POLYGON object of the computation extent.
+#' @export
+set_clip_extent <- function(pnts, buffer_r) {
+  detected = check_packbound(pnts)
+  if (detected == "terra") {
+    ext_input = terra::ext(pnts)
+    # Note that `+` operation on terra::ext output accounts for the operand as it is.
+    ext_input = ext_input + (1.1 * buffer_r + 30)
+  }
+  if (detected == "sf") {
+    ext_input <- pnts |> sf::st_bbox()
+    # Note that `+` operation on st_bbox output simply adds the number; we add a vector here.
+    ext_input <- ext_input + ((1.1 * c(-1, -1, 1, 1) * buffer_r) + 30)
+    ext_input <- sf::st_as_sfc(ext_input)
+  }
+  return(ext_input)
+}
+
+#' Quick call for SpatRaster with a window
+#' 
+#' @param rasterpath character(1). Path to the raster file.
+#' @param win Named integer vector (4) or terra::ext() results.
+#' @return SpatRaster object.
+#' @author Insang Song 
+#' @export 
+rast_short <- function(rasterpath, win) {
+  terra::rast(rasterpath, win = win)
+}
+
diff --git a/scomps.Rcheck/00_pkg_src/scomps/R/processing.R b/scomps.Rcheck/00_pkg_src/scomps/R/processing.R
new file mode 100644
index 00000000..00b3e1d3
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/R/processing.R
@@ -0,0 +1,364 @@
+# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
+
+#' Extent clipping
+#' @description Clip input vector by the expected maximum extent of computation. 
+#' @author Insang Song
+#' @param pnts sf or SpatVector object
+#' @param buffer_r numeric(1). buffer radius. this value will be automatically multiplied by 1.25
+#' @param nqsegs integer(1). the number of points per a quarter circle; SOON TO BE DEPRECATED
+#' @param target_input sf or SpatVector object to be clipped
+#' @return A clipped sf or SpatVector object.
+#' @export
+clip_as_extent <- function(pnts, buffer_r, nqsegs=NULL, target_input){
+  if (any(sapply(list(pnts, buffer_r, target_input), is.null))) {
+    stop("One or more required arguments are NULL. Please check.\n")
+  }
+  detected_pnts = check_packbound(pnts)
+  detected_target = check_packbound(target_input)
+
+  if (detected_pnts != detected_target) {
+    warning("Inputs are not the same class.\n")
+    target_input = switch(detected_target,
+        sf = terra::vect(target_input),
+        terra = sf::st_as_sf(target_input))
+  }
+  
+  ext_input = set_clip_extent(pnts, buffer_r)
+  cat("Clip target features with the input feature extent...\n")
+  if (detected_pnts == "sf") {
+    cae = ext_input |>
+      sf::st_intersection(x = target_input)
+  }
+  if (detected_pnts == "terra") {
+    cae = terra::intersect(target_input, ext_input)
+  }
+   
+  return(cae)
+}
+
+#' @title clip_as_extent_ras: Clip input raster.
+#' @description Clip input raster by the expected maximum extent of computation. 
+#' @author Insang Song
+#' @param pnts sf or SpatVector object
+#' @param buffer_r numeric(1). buffer radius. this value will be automatically multiplied by 1.25
+#' @param nqsegs integer(1). the number of points per a quarter circle
+#' @param ras SpatRaster object to be clipped
+#' @export
+clip_as_extent_ras <- function(pnts, buffer_r, nqsegs = 180, ras){
+  if (any(sapply(list(pnts, buffer_r, ras), is.null))) {
+    stop("Any of required arguments are NULL. Please check.\n")
+  }
+  ext_input = set_clip_extent(pnts, buffer_r) |>
+    terra::ext()
+
+  cae <- terra::crop(ras, ext_input, snap = 'out')
+  return(cae)
+}
+
+#' @title clip_as_extent_ras2: Clip input raster (version 2).
+#' @description Clip input raster by the expected maximum extent of computation. 
+#' @author Insang Song
+#' @param points_in sf or SpatVector object
+#' @param buffer_r numeric(1). buffer radius. this value will be automatically multiplied by 1.25
+#' @param nqsegs integer(1). the number of points per a quarter circle
+#' @param ras SpatRaster object to be clipped
+#' @export
+clip_as_extent_ras2 <- function(points_in, buffer_r, nqsegs=180, ras){
+  if (any(sapply(list(points_in, buffer_r, ras), is.null))) {
+    stop("Any of required arguments are NULL. Please check.\n")
+  }
+  ext_input = set_clip_extent(points_in, buffer_r) |>
+    terra::ext()
+
+  cae <- terra::crop(ras, ext_input, snap = 'out')
+  return(cae)
+}
+
+#' @title Extract summarized values from raster with generic polygons
+#' 
+#' @description For simplicity, it is assumed that the coordinate systems of the points and the raster are the same. Kernel function is not yet implemented. 
+#' @param polys sf/SpatVector object. Polygons.
+#' @param surf stars/SpatRaster object. A raster of whatnot a summary will be calculated
+#' @param id character(1). Unique identifier of each point.
+#' @param func a function taking one argument. For example, function(x) mean(x, na.rm = TRUE) or \(x) mode(x, na.rm = TRUE)
+#' @param na.rm logical(1). NA values are omitted when summary is calculated.
+#' @return a data.frame object with function value
+#' @author Insang Song \email{geoissong@@gmail.com}
+#' 
+#' @export
+extract_with_polygons <- function(
+    polys, surf, id, func = mean, na.rm = TRUE
+    ) {
+    # type check
+    stopifnot("Check class of the input points.\n" = any(methods::is(polys, "sf"), methods::is(polys, "SpatVector")))
+    stopifnot("Check class of the input raster.\n" = any(methods::is(surf, "stars"), methods::is(surf, "SpatRaster")))
+    stopifnot(is.character(id))
+
+    cls_polys = check_packbound(polys)
+    cls_surf = check_packbound(surf)
+
+    if (cls_polys != cls_surf) {
+      polys = switch_packbound(polys)
+    }
+
+    extract_with_polygons.sf = function(polys, surf, id, func) {
+        extracted = stars::st_extract(x = surf, at = polys, FUN = func)
+        # extracted = extracted |>
+        #   group_by(!!sym(id)) |>
+        #   summarize(across(-!!sym(id), ~func)) |>
+        #   ungroup()
+        return(extracted)
+    }
+
+    extract_with_polygons.terra = function(polys, surf, id, func) {
+        extracted = terra::extract(surf, polys)
+        extracted = extracted |>
+          dplyr::group_by(!!rlang::sym(id)) |>
+          dplyr::summarize(dplyr::across(-!!rlang::sym(id), ~func)) |>
+          dplyr::ungroup()
+        return(extracted)
+    }
+
+    extracted_poly = switch(
+        cls_surf,
+        sf = extract_with_polygons.sf(polys = polys, surf = surf, id = id, func = func),
+        terra = extract_with_polygons.terra(polys = polys, surf = surf, id = id, func = func)
+    )
+    return(extracted_poly)
+}
+
+
+#' Extract raster values with point buffers or polygons
+#' 
+#' @param raster SpatRaster object. 
+#' @param vector SpatVector object.
+#' @param id character(1). Unique identifier of each point.
+#' @param func function taking one numeric vector argument.
+#' @param mode one of "polygon" (generic polygons to extract raster values with) or "buffer" (point with buffer radius)
+#' @param ... various. Passed to extract_with_buffer. See \code{?extract_with_buffer} for details.
+#' @return 
+#' @author Insang Song \email{geoissong@@gmail.com}
+#' @export
+extract_with <- function(raster, vector, id, func = mean, mode = "polygon", ...) {
+    if (!mode %in% c("polygon", "buffer")) {
+      stop("Argument 'mode' should be one of 'polygon' or 'buffer'.\n")
+    }
+    stopifnot(is.character(id))
+    stopifnot(id %in% names(vector))
+
+    extracted = 
+      switch(mode,
+        polygon = extract_with_polygons(vector, raster, id, func),
+        buffer = extract_with_buffer(vector, raster, id = id, func = func, ...))
+    return(extracted)
+}
+
+
+#' Calculate SEDC covariates
+#' @param point_from SpatVector object. Locations where the sum of SEDCs are calculated.
+#' @param point_to SpatVector object. Locations where each SEDC is calculated.
+#' @param id character(1). Name of the unique id field in point_to.
+#' @param sedc_bandwidth numeric(1). Distance at which the source concentration is reduced to exp(-3) (approximately 95 %)  
+#' @param threshold numeric(1). For computational efficiency, the nearest points in threshold will be selected
+#' @param target_fields character(varying). Field names in characters.
+#' @description NOTE: sf implementation is pending. Only available for terra.
+#' @author Insang Song
+#' @export
+calculate_sedc <- function(point_from, point_to, id, sedc_bandwidth, threshold, target_fields) {
+  # define sources, set SEDC exponential decay range
+  len_point_from = seq_len(nrow(point_from))
+  len_point_to = seq_len(nrow(point_to))
+
+  point_from$from_id = len_point_from
+  # select egrid_v only if closer than 3e5 meters from each aqs
+  point_from_buf = terra::buffer(point_from_buf, threshold = threshold, quadsegs = 90)
+  point_to = point_to[point_from_buf,]
+  point_to$to_id = len_point_to
+
+  # near features with distance argument: only returns integer indices
+  near_from_to = terra::nearby(point_from, point_to, distance = threshold)
+  # attaching actual distance
+  dist_near_to = terra::distance(point_from, point_to)
+  dist_near_to_df = as.vector(dist_near_to)
+  # adding integer indices
+  dist_near_to_tdf = expand.grid(from_id = len_point_from, to_id = len_point_to)
+  dist_near_to_df = cbind(dist_near_to_tdf, dist = dist_near_to_df)
+
+  # summary
+  near_from_to = near_from_to |>
+    dplyr::as_tibble() |>
+    dplyr::left_join(data.frame(point_from)) |>
+    dplyr::left_join(data.frame(point_to)) |>
+    dplyr::left_join(dist_near_to_df) |>
+    # per the definition in https://mserre.sph.unc.edu/BMElab_web/SEDCtutorial/index.html
+    # exp(-3) is about 0.05
+    dplyr::mutate(w_sedc = exp((-3 * dist) / sedc_bandwidth)) |>
+    dplyr::group_by(!!rlang::sym(id)) |>
+    dplyr::summarize(dplyr::across(dplyr::all_of(target_fields), list(sedc = ~sum(w_sedc * ., na.rm = TRUE)))) |>
+    dplyr::ungroup()
+
+  invisible(near_from_to)
+  
+}
+
+
+#' Computing area weighted covariates using two polygon sf or SpatVector objects
+#' @param poly_in A sf/SpatVector object at weighted means will be calculated.
+#' @param poly_weight A sf/SpatVector object from which weighted means will be calculated.
+#' @param id_poly_in character(1). The unique identifier of each polygon in poly_in
+#' @return A data.frame with all numeric fields of area-weighted means.
+#' @description When poly_in and poly_weight are different classes, poly_weight will be converted to the class of poly_in. 
+#' @author Insang Song \email{geoissong@@gmail.com}
+#' @examples 
+#' # package
+#' library(sf)
+#' 
+#' # run
+#' nc = sf::st_read(system.file("shape/nc.shp", package="sf"))
+#' nc = sf::st_transform(nc, 5070)
+#' pp = sf::st_sample(nc, size = 300)
+#' pp = sf::st_as_sf(pp)
+#' pp[["id"]] = seq(1, nrow(pp))
+#' sf::st_crs(pp) = "EPSG:5070"
+#' ppb = sf::st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
+#' 
+#' system.time({ppb_nc_aw = aw_covariates(ppb, nc, 'id')})
+#' summary(ppb_nc_aw)
+#' #### Example of aw_covariates ends ####
+#' @export
+aw_covariates <- function(poly_in, poly_weight, id_poly_in = "ID") {
+    stopifnot("Inputs have invalid classes.\n" = 
+      methods::is(poly_in, "sf") || methods::is(poly_weight, "sf") || methods::is(poly_in, "SpatVector") || methods::is(poly_weight, "SpatVector"))
+    #check_crs()
+
+    ## distinguish numeric and nonnumeric columns
+    index_numeric = grep("(integer|numeric)", unlist(sapply(poly_weight, class)))
+    
+    aw_covariates.terra = function(poly_in, poly_weight, id_poly_in = id_poly_in) {
+        
+        poly_intersected = terra::intersect(poly_in, poly_weight)
+        poly_intersected[["area_segment_"]] = terra::expanse(poly_intersected)
+        poly_intersected = data.frame(poly_intersected) |>
+            dplyr::group_by(!!rlang::sym(id_poly_in)) |>
+            dplyr::summarize(dplyr::across(is.numeric,
+                        ~stats::weighted.mean(., w = area_segment_))) |>
+            dplyr::ungroup()
+        return(poly_intersected)
+    }
+
+    class_poly_in = check_packbound(poly_in)
+    class_poly_weight = check_packbound(poly_weight)
+
+    if (class_poly_in != class_poly_weight) {
+      class_poly_weight = switch_packbound(class_poly_weight)
+    }
+    
+    switch(class_poly_in,
+        sf = sf::st_interpolate_aw(poly_weight[,index_numeric], poly_in, extensive = FALSE),
+        terra = aw_covariates.terra(poly_in, poly_weight[,index_numeric], id_poly_in = id_poly_in))
+    
+}
+
+# ncbuf = terra::intersect(vect(ppb), vect(nc))
+# ncbuf_a = ncbuf
+# ncbuf_a$segarea = expanse(ncbuf_a)
+# ncbuf_k = data.frame(ncbuf_a) |>
+#   dplyr::group_by(id) |>
+#   dplyr::summarize(across(is.numeric,
+#                ~weighted.mean(., w = segarea))) |>
+#   dplyr::ungroup()
+
+#ncbufagg = terra::aggregate(ncbuf, by = 'id', fun = weighted.mean, w = ncbuf_a$segarea)
+
+
+#' @title Extract summarized values from raster with points and a buffer radius (to be written)
+#' 
+#' @description For simplicity, it is assumed that the coordinate systems of the points and the raster are the same. Kernel function is not yet implemented. 
+#' @param points SpatVector object. Coordinates where buffers will be generated
+#' @param surf SpatRaster object. A raster of whatnot a summary will be calculated
+#' @param radius numeric(1). Buffer radius. here we assume circular buffers only
+#' @param id character(1). Unique identifier of each point.
+#' @param qsegs integer(1). Number of vertices at a quarter of a circle. Default is 90.
+#' @param func a function taking a numeric vector argument.
+#' @param kernel character(1). Name of a kernel function (yet to be implemented)
+#' @param bandwidth numeric(1). Kernel bandwidth.
+#' @return a data.frame object with mean value
+#' @author Insang Song \email{geoissong@@gmail.com}
+#' 
+#' @export
+extract_with_buffer <- function(
+    points, surf, radius, id, qsegs = 90, func = mean, kernel = NULL, bandwidth = NULL
+    ) {
+    # type check
+    stopifnot("Check class of the input points.\n" = methods::is(points, "SpatVector"))
+    stopifnot("Check class of the input radius.\n" = is.numeric(radius))
+    stopifnot(is.character(id))
+    stopifnot(is.integer(qsegs))
+
+    if (!is.null(kernel)) {
+        extracted = extract_with_buffer.flat(points = points,
+                                      surf = surf,
+                                      radius = radius,
+                                      id = id,
+                                      func = func,
+                                      qsegs = qsegs)
+        return(extracted)
+    }
+
+    extracted = extract_with_buffer.kernel(points = points,
+                                           surf = surf,
+                                           radius = radius,
+                                           id = id,
+                                           func = func,
+                                           qsegs = qsegs,
+                                           kernel = kernel,
+                                           bandwidth = bandwidth)
+    return(extracted)
+
+}
+
+# Subfunction: extract with buffers (flat weight; simple mean)
+extract_with_buffer.flat <- function(
+        points, surf, radius, id, qsegs, func = mean, kernel = NULL, bandwidth = NULL
+    ) {
+    # generate buffers
+    bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
+    # crop raster
+    bufs_extent = terra::ext(bufs)
+    surf_cropped = terra::crop(surf, bufs_extent)
+    name_surf_val = names(surf)
+    # extract raster values
+    surf_at_bufs = terra::extract(surf_cropped, bufs)
+    surf_at_bufs_summary = 
+        surf_at_bufs |> 
+            dplyr::group_by(ID) |> 
+            dplyr::summarize(dplyr::across(dplyr::all_of(name_surf_val), ~mean, na.rm=T)) |> 
+            dplyr::ungroup()
+    return(surf_at_bufs_summary)
+}
+
+
+# Subfunction: extract with buffers (kernel weight; weighted mean)
+extract_with_buffer.kernel <- function(
+        points, surf, radius, id, qsegs, func = mean, kernel, bandwidth
+    ) {
+        # generate buffers
+        bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
+        # crop raster
+        bufs_extent = terra::ext(bufs)
+        surf_cropped = terra::crop(surf, bufs_extent)
+        name_surf_val = names(surf)
+
+        # TODO: kernel implementation
+
+
+        # extract raster values
+        surf_at_bufs = terra::extract(surf_cropped, bufs)
+        surf_at_bufs_summary = 
+            surf_at_bufs |> 
+                dplyr::group_by(ID) |> 
+                dplyr::summarize(dplyr::across(dplyr::all_of(name_surf_val), ~mean, na.rm=T)) |> 
+                dplyr::ungroup()
+        return(surf_at_bufs_summary)
+}
+
diff --git a/scomps.Rcheck/00_pkg_src/scomps/R/switch_format.R b/scomps.Rcheck/00_pkg_src/scomps/R/switch_format.R
new file mode 100644
index 00000000..a0c38e8f
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/R/switch_format.R
@@ -0,0 +1,25 @@
+# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
+
+#' @title Switch spatial data class
+#' @description Convert stars into SpatRaster and vice versa; sf into SpatVector and vice versa.
+#' @author Insang Song
+#' @param input Spat* in terra or sf object.
+#' @return Data converted to the other package class (if sf, terra; if terra, sf)
+#' @export
+switch_packbound <- function(input) {
+  stopifnot("Input should be one of sf or Spat* object.\n" = any(methods::is(input, "sf"), methods::is(input, "stars"), methods::is(input, "SpatVector"), methods::is(input, "SpatRaster")))
+  cls_input = check_packbound(input)
+  type_input = check_datatype(input)
+
+  switched = 
+  switch(cls_input,
+    sf = switch(type_input,
+      vector = terra::vect(input),
+      raster = terra::rast(input)
+    ),
+    terra = switch(type_input,
+      vector = sf::st_as_sf(input),
+      raster = stars::st_as_stars(input)))
+
+  invisible(switched)
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/R/validate.R b/scomps.Rcheck/00_pkg_src/scomps/R/validate.R
new file mode 100644
index 00000000..545869c2
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/R/validate.R
@@ -0,0 +1,18 @@
+# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
+
+#' Validate and repair input vector data
+#' @description It tries repairing input vector data. Vector validity violation usually appears in polygon data with self-crossing or hole orders. This function will pass the input_vector object to sf::st_make_valid() (if input_vector is sf) or terra::makeValid() (if input_vector is SpatVector). May take some time depending on the geometry complexity.
+#' @author Insang Song
+#' @param input_vector One of sf or vect class. Target points of computation.
+#' @return A repaired sf or SpatVector object depending on the class of input_vector.
+#' @export
+validate_and_repair_vectors <- function(input_vector) {
+  detected = check_packbound(input_vector)
+
+  validated = switch(detected,
+    terra = terra::makeValid(input_vector),
+    sf = sf::st_make_valid(input_vector))
+
+  return(validated)
+}
+
diff --git a/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v00_good_practice_parallelization.R b/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v00_good_practice_parallelization.R
new file mode 100644
index 00000000..c639e81d
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v00_good_practice_parallelization.R
@@ -0,0 +1,4 @@
+## -----------------------------------------------------------------------------
+knitr::opts_chunk$set(warning = FALSE, message = FALSE)
+
+
diff --git a/tools/vignettes-sources/00_good_practice_parallelization.Rmd b/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v00_good_practice_parallelization.Rmd
similarity index 95%
rename from tools/vignettes-sources/00_good_practice_parallelization.Rmd
rename to scomps.Rcheck/00_pkg_src/scomps/inst/doc/v00_good_practice_parallelization.Rmd
index 6da000b1..8966a59d 100644
--- a/tools/vignettes-sources/00_good_practice_parallelization.Rmd
+++ b/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v00_good_practice_parallelization.Rmd
@@ -3,7 +3,7 @@ title: "Good practice of scomps with HPC"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{HPC good practice with scomps}
+  %\VignetteIndexEntry{good_practice_hpc}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
diff --git a/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v00_good_practice_parallelization.html b/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v00_good_practice_parallelization.html
new file mode 100644
index 00000000..da4506f4
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v00_good_practice_parallelization.html
@@ -0,0 +1,408 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Good practice of scomps with HPC
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Good practice of scomps with HPC

+
2023-10-04

+
+
+
+
knitr::opts_chunk$set(warning = FALSE, message = FALSE)

+

+
Assumptions

+
    
+
  • Users have an accessible HPC at your work
    • 
+
  • Data are stored in distributed file systems (usually incorporated
+into the HPC system)
    • 
+

+

+

+
Basic workflow

+

+
Practice for minimizing errors

+
    
+
  • Consider using try() or tryCatch() not to
+a tiny error will halt all the work without any results
+
      
+
    • Especially with the higher-level functions
      • 
+
    • 
+
  • “IPDE – Inspect, Predict, Decide, Execute” all the time
    • 
+

+

+

+
Raster-Vector overlay

+
    
+
  • Make sp_index_grid() to get padded grid objects
    • 
+
  • Convert sf/SpatVector objects into terra::ext()
+compatible named numeric vector
+
      
+
    • For example: c(xmin=0, ymin=0, xmax=10, ymax=10)
      • 
+
    • 
+
  • Make list objects with:
+
      
+
    • An extent vector in each element
      • 
+
    • Preprocessed vector objects with respect to each extent vector in
+the first list
      • 
+
    • Preferably all lists are named
      • 
+
    • 
+
  • Write a future.apply script running through the extent
+list object
    • 
+
  • Run a small amount of data to estimate the total computational
+demand
    • 
+
  • Submit a job with a proper amount of computational assets
    • 
+

+

+

+
+
+
+
+
+
+
+
+
+
+
diff --git a/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v01_generate_computational_grid.R b/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v01_generate_computational_grid.R
new file mode 100644
index 00000000..aa3d29fc
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v01_generate_computational_grid.R
@@ -0,0 +1,22 @@
+## -----------------------------------------------------------------------------
+knitr::opts_chunk$set(warning = FALSE, message = FALSE)
+
+
+## -----------------------------------------------------------------------------
+library(scomps)
+library(sf)
+library(terra)
+library(stars)
+library(dplyr)
+
+
+## -----------------------------------------------------------------------------
+# your_grid = scomps::sp_index_grid()
+
+
+## -----------------------------------------------------------------------------
+# library(mapsf)
+# mf_map(your_grid$geometry)
+
+
+
diff --git a/tools/vignettes-sources/01_generate_computational_grid.Rmd b/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v01_generate_computational_grid.Rmd
similarity index 92%
rename from tools/vignettes-sources/01_generate_computational_grid.Rmd
rename to scomps.Rcheck/00_pkg_src/scomps/inst/doc/v01_generate_computational_grid.Rmd
index 4c1a4ee6..4bc1aaf2 100644
--- a/tools/vignettes-sources/01_generate_computational_grid.Rmd
+++ b/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v01_generate_computational_grid.Rmd
@@ -3,7 +3,7 @@ title: "Generate computational grids"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{Generate computational grids}
+  %\VignetteIndexEntry{computational_grids}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
diff --git a/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v01_generate_computational_grid.html b/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v01_generate_computational_grid.html
new file mode 100644
index 00000000..c2d963b8
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v01_generate_computational_grid.html
@@ -0,0 +1,388 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Generate computational grids
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Generate computational grids

+
2023-10-04

+
+
+
+
knitr::opts_chunk$set(warning = FALSE, message = FALSE)

+

+
Prepare input data

+
library(scomps)
+library(sf)
+library(terra)
+library(stars)
+library(dplyr)

+

+

+
Computational grids

+
# your_grid = scomps::sp_index_grid()

+

+

+
Visualize computational grids

+
# library(mapsf)
+# mf_map(your_grid$geometry)

+

+

+
Notes

+
    
+
  • Computational grids are the exhaustive split of the entire study
+region. You should take a square buffer of each grid to clip the target
+raster or vector.
    • 
+

+

+
+
+
+
+
+
+
+
+
+
+
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/aw_covariates.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/aw_covariates.Rd
new file mode 100644
index 00000000..ca836de6
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/man/aw_covariates.Rd
@@ -0,0 +1,41 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/processing.R
+\name{aw_covariates}
+\alias{aw_covariates}
+\title{Computing area weighted covariates using two polygon sf or SpatVector objects}
+\usage{
+aw_covariates(poly_in, poly_weight, id_poly_in = "ID")
+}
+\arguments{
+\item{poly_in}{A sf/SpatVector object at weighted means will be calculated.}
+
+\item{poly_weight}{A sf/SpatVector object from which weighted means will be calculated.}
+
+\item{id_poly_in}{character(1). The unique identifier of each polygon in poly_in}
+}
+\value{
+A data.frame with all numeric fields of area-weighted means.
+}
+\description{
+When poly_in and poly_weight are different classes, poly_weight will be converted to the class of poly_in.
+}
+\examples{
+# package
+library(sf)
+
+# run
+nc = sf::st_read(system.file("shape/nc.shp", package="sf"))
+nc = sf::st_transform(nc, 5070)
+pp = sf::st_sample(nc, size = 300)
+pp = sf::st_as_sf(pp)
+pp[["id"]] = seq(1, nrow(pp))
+sf::st_crs(pp) = "EPSG:5070"
+ppb = sf::st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
+
+system.time({ppb_nc_aw = aw_covariates(ppb, nc, 'id')})
+summary(ppb_nc_aw)
+#### Example of aw_covariates ends ####
+}
+\author{
+Insang Song \email{geoissong@gmail.com}
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/calculate_sedc.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/calculate_sedc.Rd
new file mode 100644
index 00000000..21178a77
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/man/calculate_sedc.Rd
@@ -0,0 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/processing.R
+\name{calculate_sedc}
+\alias{calculate_sedc}
+\title{Calculate SEDC covariates}
+\usage{
+calculate_sedc(
+  point_from,
+  point_to,
+  id,
+  sedc_bandwidth,
+  threshold,
+  target_fields
+)
+}
+\arguments{
+\item{point_from}{SpatVector object. Locations where the sum of SEDCs are calculated.}
+
+\item{point_to}{SpatVector object. Locations where each SEDC is calculated.}
+
+\item{id}{character(1). Name of the unique id field in point_to.}
+
+\item{sedc_bandwidth}{numeric(1). Distance at which the source concentration is reduced to exp(-3) (approximately 95 \%)}
+
+\item{threshold}{numeric(1). For computational efficiency, the nearest points in threshold will be selected}
+
+\item{target_fields}{character(varying). Field names in characters.}
+}
+\description{
+NOTE: sf implementation is pending. Only available for terra.
+}
+\author{
+Insang Song
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/check_bbox.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/check_bbox.Rd
new file mode 100644
index 00000000..444c934a
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/man/check_bbox.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/check.R
+\name{check_bbox}
+\alias{check_bbox}
+\title{Check if the data extent is inside the reference bounding box}
+\usage{
+check_bbox(data_query, reference, reference_crs = NULL)
+}
+\arguments{
+\item{data_query}{sf*/stars/SpatVector/SpatRaster object.}
+
+\item{reference}{sf*/stars/SpatVector/SpatRaster object or a named numeric vector with four names (xmin, ymin, xmax, and ymax).}
+
+\item{reference_crs}{Well-known-text-formatted or EPSG code of the reference's coordinate system. Only required when a named numeric vector is passed to reference.}
+}
+\value{
+TRUE (the queried data extent is completely within the reference bounding box) or FALSE
+}
+\description{
+One of the most common errors in spatial computation is rooted in the entirely or partly incomparable spatial extents of input datasets. This function returns whether your data is inside the target computational extent. It is assumed that you know and have the exact computational region. This function will return TRUE if the reference region completely contains your data's extent and FALSE otherwise.
+}
+\author{
+Insang Song \email{geoissong@gmail.com}
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/check_crs.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/check_crs.Rd
new file mode 100644
index 00000000..6f9fa5b5
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/man/check_crs.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/check.R
+\name{check_crs}
+\alias{check_crs}
+\title{Check Coordinate Reference System}
+\usage{
+check_crs(x)
+}
+\arguments{
+\item{x}{sf/stars/SpatVector/SpatRaster object.}
+}
+\value{
+A st_crs or crs object.
+}
+\description{
+Check Coordinate Reference System
+}
+\examples{
+# data
+library(sf)
+ncpath = system.file("shape/nc.shp", package = "sf")
+nc = read_sf(ncpath)
+check_crs(nc)
+
+}
+\author{
+Insang Song \email{geoissong@gmail.com}
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/check_crs2.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/check_crs2.Rd
new file mode 100644
index 00000000..c15652d6
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/man/check_crs2.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/check.R
+\name{check_crs2}
+\alias{check_crs2}
+\title{check_crs2: Coordinate system checker}
+\usage{
+check_crs2(input, crs_standard = "EPSG:4326")
+}
+\arguments{
+\item{input}{Input object one of sf or terra::Spat* object}
+
+\item{crs_standard}{character(1). A standard definition of coordinate reference system. Default is "EPSG:4326" Consult \href{https://epsg.io}{epsg.io} for details of other CRS.}
+}
+\value{
+A (reprojected) sf or SpatVector object.
+}
+\description{
+The input is checked whether its coordinate system is present. If not, it is reprojected to EPSG:5179.
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/check_packbound.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/check_packbound.Rd
new file mode 100644
index 00000000..6bda7485
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/man/check_packbound.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/check.R
+\name{check_packbound}
+\alias{check_packbound}
+\title{Return the package the input object is based on}
+\usage{
+check_packbound(input)
+}
+\arguments{
+\item{input}{Spat* in terra or sf object.}
+}
+\value{
+A character object; one of 'terra' and 'sf'
+}
+\description{
+Detect whether the input object is sf or Spat* object.
+}
+\author{
+Insang Song
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/check_within_reference.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/check_within_reference.Rd
new file mode 100644
index 00000000..c193a975
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/man/check_within_reference.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/check.R
+\name{check_within_reference}
+\alias{check_within_reference}
+\title{Check if the boundary of the vector/raster object is inside the reference}
+\usage{
+check_within_reference(input_object, reference)
+}
+\arguments{
+\item{input_object}{sf/stars/SpatVector/SpatRaster object.}
+
+\item{reference}{sf/stars/SpatVector/SpatRaster object.}
+}
+\value{
+logical
+}
+\description{
+Check if the boundary of the vector/raster object is inside the reference
+}
+\author{
+Insang Song \email{geoissong@gmail.com}
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/clip_as_extent.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/clip_as_extent.Rd
new file mode 100644
index 00000000..06ec0bbf
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/man/clip_as_extent.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/processing.R
+\name{clip_as_extent}
+\alias{clip_as_extent}
+\title{Extent clipping}
+\usage{
+clip_as_extent(pnts, buffer_r, nqsegs = NULL, target_input)
+}
+\arguments{
+\item{pnts}{sf or SpatVector object}
+
+\item{buffer_r}{numeric(1). buffer radius. this value will be automatically multiplied by 1.25}
+
+\item{nqsegs}{integer(1). the number of points per a quarter circle; SOON TO BE DEPRECATED}
+
+\item{target_input}{sf or SpatVector object to be clipped}
+}
+\value{
+A clipped sf or SpatVector object.
+}
+\description{
+Clip input vector by the expected maximum extent of computation.
+}
+\author{
+Insang Song
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/clip_as_extent_ras.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/clip_as_extent_ras.Rd
new file mode 100644
index 00000000..e6762901
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/man/clip_as_extent_ras.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/processing.R
+\name{clip_as_extent_ras}
+\alias{clip_as_extent_ras}
+\title{clip_as_extent_ras: Clip input raster.}
+\usage{
+clip_as_extent_ras(pnts, buffer_r, nqsegs = 180, ras)
+}
+\arguments{
+\item{pnts}{sf or SpatVector object}
+
+\item{buffer_r}{numeric(1). buffer radius. this value will be automatically multiplied by 1.25}
+
+\item{nqsegs}{integer(1). the number of points per a quarter circle}
+
+\item{ras}{SpatRaster object to be clipped}
+}
+\description{
+Clip input raster by the expected maximum extent of computation.
+}
+\author{
+Insang Song
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/clip_as_extent_ras2.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/clip_as_extent_ras2.Rd
new file mode 100644
index 00000000..6d8c0e00
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/man/clip_as_extent_ras2.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/processing.R
+\name{clip_as_extent_ras2}
+\alias{clip_as_extent_ras2}
+\title{clip_as_extent_ras2: Clip input raster (version 2).}
+\usage{
+clip_as_extent_ras2(points_in, buffer_r, nqsegs = 180, ras)
+}
+\arguments{
+\item{points_in}{sf or SpatVector object}
+
+\item{buffer_r}{numeric(1). buffer radius. this value will be automatically multiplied by 1.25}
+
+\item{nqsegs}{integer(1). the number of points per a quarter circle}
+
+\item{ras}{SpatRaster object to be clipped}
+}
+\description{
+Clip input raster by the expected maximum extent of computation.
+}
+\author{
+Insang Song
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/distribute_process.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/distribute_process.Rd
new file mode 100644
index 00000000..ebb58e82
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/man/distribute_process.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/interpret_computational_domain.R
+\name{distribute_process}
+\alias{distribute_process}
+\title{Process a given function in the entire or partial computational grids (under construction)}
+\usage{
+distribute_process(grids, grid_id = NULL, fun, ...)
+}
+\arguments{
+\item{grids}{sf/SpatVector object. Computational grids.}
+
+\item{grid_id}{character(1) or numeric(2). Default is NULL. If NULL, all grid_ids are used. \code{"id_from:id_to"} format or \code{c(unique(grid_id)[id_from], unique(grid_id)[id_to])}}
+
+\item{fun}{function supported in scomps.}
+
+\item{...}{Arguments passed to fun.}
+}
+\value{
+a data.frame object with mean value
+}
+\description{
+Should
+}
+\author{
+Insang Song \email{geoissong@gmail.com}
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/estimate_demands.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/estimate_demands.Rd
new file mode 100644
index 00000000..787ad77f
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/man/estimate_demands.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/estimate_demands.R
+\name{estimate_demands}
+\alias{estimate_demands}
+\title{Estimate computational demands from inputs (to be written)}
+\usage{
+estimate_demands(inputs, nx, ny, padding)
+}
+\arguments{
+\item{inputs}{a list of sf/Spat* objects or file paths}
+
+\item{nx}{integer(1).}
+
+\item{ny}{integer(1).}
+
+\item{padding}{numeric(1). Extrusion factor}
+}
+\description{
+Estimate computational demands from inputs (to be written)
+}
+\author{
+Insang Song
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/extent_to_polygon.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/extent_to_polygon.Rd
new file mode 100644
index 00000000..2874461e
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/man/extent_to_polygon.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/check.R
+\name{extent_to_polygon}
+\alias{extent_to_polygon}
+\title{Generate a rectangular polygon from extent}
+\usage{
+extent_to_polygon(extent, output_class = "terra", crs = "EPSG:4326")
+}
+\arguments{
+\item{extent}{input extent. A numeric vector with xmin/xmax/ymin/ymax, sf::st_bbox() or terra::ext() outputs.}
+
+\item{output_class}{character(1). Class of the output polygon. One of "sf" or "terra"}
+
+\item{crs}{character(1). Coordinate reference system definition.}
+}
+\description{
+Generate a rectangular polygon from extent
+}
+\author{
+Insang Song
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/extract_with.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/extract_with.Rd
new file mode 100644
index 00000000..8794f571
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/man/extract_with.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/processing.R
+\name{extract_with}
+\alias{extract_with}
+\title{Extract raster values with point buffers or polygons}
+\usage{
+extract_with(raster, vector, id, func = mean, mode = "polygon", ...)
+}
+\arguments{
+\item{raster}{SpatRaster object.}
+
+\item{vector}{SpatVector object.}
+
+\item{id}{character(1). Unique identifier of each point.}
+
+\item{func}{function taking one numeric vector argument.}
+
+\item{mode}{one of "polygon" (generic polygons to extract raster values with) or "buffer" (point with buffer radius)}
+
+\item{...}{various. Passed to extract_with_buffer. See \code{?extract_with_buffer} for details.}
+}
+\description{
+Extract raster values with point buffers or polygons
+}
+\author{
+Insang Song \email{geoissong@gmail.com}
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/extract_with_buffer.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/extract_with_buffer.Rd
new file mode 100644
index 00000000..f0c3943d
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/man/extract_with_buffer.Rd
@@ -0,0 +1,43 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/processing.R
+\name{extract_with_buffer}
+\alias{extract_with_buffer}
+\title{Extract summarized values from raster with points and a buffer radius (to be written)}
+\usage{
+extract_with_buffer(
+  points,
+  surf,
+  radius,
+  id,
+  qsegs = 90,
+  func = mean,
+  kernel = NULL,
+  bandwidth = NULL
+)
+}
+\arguments{
+\item{points}{SpatVector object. Coordinates where buffers will be generated}
+
+\item{surf}{SpatRaster object. A raster of whatnot a summary will be calculated}
+
+\item{radius}{numeric(1). Buffer radius. here we assume circular buffers only}
+
+\item{id}{character(1). Unique identifier of each point.}
+
+\item{qsegs}{integer(1). Number of vertices at a quarter of a circle. Default is 90.}
+
+\item{func}{a function taking a numeric vector argument.}
+
+\item{kernel}{character(1). Name of a kernel function (yet to be implemented)}
+
+\item{bandwidth}{numeric(1). Kernel bandwidth.}
+}
+\value{
+a data.frame object with mean value
+}
+\description{
+For simplicity, it is assumed that the coordinate systems of the points and the raster are the same. Kernel function is not yet implemented.
+}
+\author{
+Insang Song \email{geoissong@gmail.com}
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/extract_with_polygons.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/extract_with_polygons.Rd
new file mode 100644
index 00000000..adaa9c6a
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/man/extract_with_polygons.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/processing.R
+\name{extract_with_polygons}
+\alias{extract_with_polygons}
+\title{Extract summarized values from raster with generic polygons}
+\usage{
+extract_with_polygons(polys, surf, id, func = mean, na.rm = TRUE)
+}
+\arguments{
+\item{polys}{sf/SpatVector object. Polygons.}
+
+\item{surf}{stars/SpatRaster object. A raster of whatnot a summary will be calculated}
+
+\item{id}{character(1). Unique identifier of each point.}
+
+\item{func}{a function taking one argument. For example, function(x) mean(x, na.rm = TRUE) or \(x) mode(x, na.rm = TRUE)}
+
+\item{na.rm}{logical(1). NA values are omitted when summary is calculated.}
+}
+\value{
+a data.frame object with function value
+}
+\description{
+For simplicity, it is assumed that the coordinate systems of the points and the raster are the same. Kernel function is not yet implemented.
+}
+\author{
+Insang Song \email{geoissong@gmail.com}
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/get_computational_regions.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/get_computational_regions.Rd
new file mode 100644
index 00000000..6a864a55
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/man/get_computational_regions.Rd
@@ -0,0 +1,53 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/interpret_computational_domain.R
+\name{get_computational_regions}
+\alias{get_computational_regions}
+\title{Get a set of computational regions}
+\usage{
+get_computational_regions(
+  input,
+  mode = "grid",
+  nx = 10,
+  ny = 10,
+  grid_min_features = 30,
+  padding = NULL,
+  unit = NULL,
+  ...
+)
+}
+\arguments{
+\item{input}{sf or Spat* object.}
+
+\item{mode}{character(1). Mode of region construction. One of "grid" (simple grid regardless of the number of features in each grid), "density" (clustering-based varying grids), "grid_advanced" (merging adjacent grids with smaller number of features than grid_min_features).}
+
+\item{nx}{integer(1). The number of grids along x-axis.}
+
+\item{ny}{integer(1). The number of grids along y-axis.}
+
+\item{grid_min_features}{integer(1). A threshold to merging adjacent grids}
+
+\item{padding}{numeric(1). A extrusion factor to make buffer to clip actual datasets. Depending on the length unit of the CRS of input.}
+
+\item{unit}{character(1). The length unit for padding (optional). units::set_units is used for padding when sf object is used. See \href{https://cran.r-project.org/web/packages/units/vignettes/measurement_units_in_R.html}{units package vignette (web)} for the list of acceptable unit forms.}
+
+\item{...}{arguments passed to the internal function}
+}
+\value{
+A set of polygons in the input class
+}
+\description{
+TODO. Using input points, the bounding box is split to the predefined numbers of columns and rows. Each grid will be buffered by the radius.
+}
+\examples{
+# data
+library(sf)
+ncpath = system.file("shape/nc.shp", package = "sf")
+nc = read_sf(ncpath)
+nc = st_transform(nc, "EPSG:5070")
+# run
+# nc_comp_region = get_computational_regions(nc, nx = 12, ny = 8)
+
+}
+\author{
+Insang Song
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/grid_merge.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/grid_merge.Rd
new file mode 100644
index 00000000..0361cece
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/man/grid_merge.Rd
@@ -0,0 +1,38 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/interpret_computational_domain.R
+\name{grid_merge}
+\alias{grid_merge}
+\title{grid_merge: Merge grid polygons with given rules}
+\usage{
+grid_merge(points_in, grid_in, grid_min_features)
+}
+\arguments{
+\item{points_in}{sf or SpatVector object. Target points of computation.}
+
+\item{grid_in}{sf or SpatVector object. The grid generated by sp_index_grid}
+
+\item{grid_min_features}{integer(1). Threshold to merge adjacent grids.}
+}
+\value{
+A sf or SpatVector object of computation grids.
+}
+\description{
+Merge boundary-sharing (in "Rook" contiguity) grids with fewer target features than the threshold. This function strongly assumes that the input is returned from the sp_index_grid, which has 'CGRIDID' as the unique id field.
+}
+\examples{
+# library(sf)
+# library(igraph)
+# ligrary(dplyr)
+# dg = sf::st_as_sfc(st_bbox(c(xmin = 0, ymin = 0, xmax = 8e5, ymax = 6e5)))
+# sf::st_crs(dg) = 5070
+# dgs = sf::st_as_sf(st_make_grid(dg, n = c(20, 15)))
+# dgs$CGRIDID = seq(1, nrow(dgs))
+#
+# dg_sample = st_sample(dg, kappa = 5e-9, mu = 15, scale = 20000, type = "Thomas")
+# sf::st_crs(dg_sample) = sf::st_crs(dg)
+# dg_merged = grid_merge(sf::st_as_sf(sss), dgs, 100)
+#### NOT RUN ####
+}
+\author{
+Insang Song
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/initate_log.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/initate_log.Rd
new file mode 100644
index 00000000..6e64c090
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/man/initate_log.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/logging.R
+\name{initate_log}
+\alias{initate_log}
+\title{Turn on logging}
+\usage{
+initate_log(expr, dolog = FALSE, logpath)
+}
+\arguments{
+\item{expr}{expression. Any function call to be logged.}
+
+\item{dolog}{logical(1). Will the messages be logged.}
+
+\item{logpath}{character(1). Log file path with the full log file name.}
+}
+\value{
+Nothing. It will export a log file in the specified path as logpath.
+}
+\description{
+Turn on logging
+}
+\author{
+Insang Song
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/rast_short.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/rast_short.Rd
new file mode 100644
index 00000000..de4acd9f
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/man/rast_short.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/preprocessing.R
+\name{rast_short}
+\alias{rast_short}
+\title{Quick call for SpatRaster with a window}
+\usage{
+rast_short(rasterpath, win)
+}
+\arguments{
+\item{rasterpath}{character(1). Path to the raster file.}
+
+\item{win}{Named integer vector (4) or terra::ext() results.}
+}
+\value{
+SpatRaster object.
+}
+\description{
+Quick call for SpatRaster with a window
+}
+\author{
+Insang Song
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/set_clip_extent.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/set_clip_extent.Rd
new file mode 100644
index 00000000..4fb91191
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/man/set_clip_extent.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/preprocessing.R
+\name{set_clip_extent}
+\alias{set_clip_extent}
+\title{Setting the clipping extent}
+\usage{
+set_clip_extent(pnts, buffer_r)
+}
+\arguments{
+\item{pnts}{One of sf or vect class. Target points of computation.}
+
+\item{buffer_r}{numeric(1). Buffer radius. It is assumed in metres}
+}
+\value{
+A terra::ext or sfc_POLYGON object of the computation extent.
+}
+\description{
+Return clipping extent with buffer radius. It assumes the input CRS is projected and linear unit is meters.
+}
+\author{
+Insang Song
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/sp_index_grid.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/sp_index_grid.Rd
new file mode 100644
index 00000000..bf0d4ac5
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/man/sp_index_grid.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/interpret_computational_domain.R
+\name{sp_index_grid}
+\alias{sp_index_grid}
+\title{sp_index_grid: Generate grid polygons}
+\usage{
+sp_index_grid(points_in, ncutsx, ncutsy)
+}
+\arguments{
+\item{points_in}{sf or SpatVector object. Target points of computation.}
+
+\item{ncutsx}{integer(1). The number of splits along x-axis.}
+
+\item{ncutsy}{integer(1). The number of splits along y-axis.}
+}
+\value{
+A sf or SpatVector object of computation grids with unique grid id (CGRIDID).
+}
+\description{
+Returns a sf object that includes x- and y- index by using two inputs ncutsx and ncutsy, which are x- and y-directional splits, respectively.
+}
+\author{
+Insang Song
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/sp_indexing.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/sp_indexing.Rd
new file mode 100644
index 00000000..f4da1434
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/man/sp_indexing.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/indexing.R
+\name{sp_indexing}
+\alias{sp_indexing}
+\title{Create integer indices for grid}
+\usage{
+sp_indexing(points_in, ncutsx, ncutsy)
+}
+\arguments{
+\item{points_in}{sf object.}
+
+\item{ncutsx}{integer(1). The number of splits along x-axis.}
+
+\item{ncutsy}{integer(1). The number of splits along y-axis.}
+}
+\description{
+Returns a tibble object that includes x- and y- index by using two inputs ncutsx and ncutsy, which are x- and y-directional splits, respectively.
+}
+\author{
+Insang Song
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/switch_packbound.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/switch_packbound.Rd
new file mode 100644
index 00000000..18eafb22
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/man/switch_packbound.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/switch_format.R
+\name{switch_packbound}
+\alias{switch_packbound}
+\title{Switch spatial data class}
+\usage{
+switch_packbound(input)
+}
+\arguments{
+\item{input}{Spat* in terra or sf object.}
+}
+\value{
+Data converted to the other package class (if sf, terra; if terra, sf)
+}
+\description{
+Convert stars into SpatRaster and vice versa; sf into SpatVector and vice versa.
+}
+\author{
+Insang Song
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/validate_and_repair_vectors.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/validate_and_repair_vectors.Rd
new file mode 100644
index 00000000..e8447ca9
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/man/validate_and_repair_vectors.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/validate.R
+\name{validate_and_repair_vectors}
+\alias{validate_and_repair_vectors}
+\title{Validate and repair input vector data}
+\usage{
+validate_and_repair_vectors(input_vector)
+}
+\arguments{
+\item{input_vector}{One of sf or vect class. Target points of computation.}
+}
+\value{
+A repaired sf or SpatVector object depending on the class of input_vector.
+}
+\description{
+It tries repairing input vector data. Vector validity violation usually appears in polygon data with self-crossing or hole orders. This function will pass the input_vector object to sf::st_make_valid() (if input_vector is sf) or terra::makeValid() (if input_vector is SpatVector). May take some time depending on the geometry complexity.
+}
+\author{
+Insang Song
+}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/tests/testthat.R b/scomps.Rcheck/00_pkg_src/scomps/tests/testthat.R
new file mode 100644
index 00000000..b465b524
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/tests/testthat.R
@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(scomps)
+
+test_check("scomps")
diff --git a/scomps.Rcheck/00_pkg_src/scomps/tests/testthat/tests.R b/scomps.Rcheck/00_pkg_src/scomps/tests/testthat/tests.R
new file mode 100644
index 00000000..6efa4142
--- /dev/null
+++ b/scomps.Rcheck/00_pkg_src/scomps/tests/testthat/tests.R
@@ -0,0 +1,65 @@
+# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand  
+testthat::test_that("What package does the input object belong?",
+{
+    withr::local_package("stars")
+    withr::local_package("terra")
+    withr::local_options(list(sf_use_s2 = FALSE))
+    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
+    bcsd_stars = stars::read_stars(bcsd_path)
+
+    packbound_stars = check_packbound(bcsd_stars)
+    sprast_bcsd = terra::rast(bcsd_path)
+    packbound_terra = check_packbound(sprast_bcsd)
+
+    testthat::expect_equal(packbound_stars, "sf")
+    testthat::expect_equal(packbound_terra, "terra")
+})
+
+
+testthat::test_that("What package does the input object belong?",
+{
+    withr::local_package("stars")
+    withr::local_package("terra")
+    withr::local_options(list(sf_use_s2 = FALSE))
+    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
+    bcsd_stars = stars::read_stars(bcsd_path)
+
+    nc = system.file(package = "sf", "shape/nc.shp")
+    nc = sf::read_sf(nc)
+
+    datatype_stars = check_datatype(bcsd_stars)
+    datatype_sf = check_datatype(nc)
+
+    testthat::expect_equal(datatype_stars, "raster")
+    testthat::expect_equal(datatype_sf, "vector")
+})
+
+
+testthat::test_that("Format is well converted",
+{
+    withr::local_package("stars")
+    withr::local_package("terra")
+    withr::local_options(list(sf_use_s2 = FALSE))
+
+    # starts from sf/stars
+    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
+    bcsd_stars = stars::read_stars(bcsd_path)
+    nc = system.file(package = "sf", "shape/nc.shp")
+    nc = sf::read_sf(nc)
+
+    stars_bcsd_tr = switch_packbound(bcsd_stars)
+    sf_nc_tr = switch_packbound(nc)
+
+    testthat::expect_equal(check_packbound(stars_bcsd_tr), "terra")
+    testthat::expect_equal(check_packbound(sf_nc_tr), "terra")
+
+    stars_bcsd_trb = switch_packbound(stars_bcsd_tr)
+    sf_nc_trb = switch_packbound(sf_nc_tr)
+
+    testthat::expect_equal(check_packbound(stars_bcsd_trb), "sf")
+    testthat::expect_equal(check_packbound(sf_nc_trb), "sf")
+
+})
+
+
+
diff --git a/scomps/vignettes/00_good_practice_parallelization.Rmd b/scomps.Rcheck/00_pkg_src/scomps/vignettes/v00_good_practice_parallelization.Rmd
similarity index 95%
rename from scomps/vignettes/00_good_practice_parallelization.Rmd
rename to scomps.Rcheck/00_pkg_src/scomps/vignettes/v00_good_practice_parallelization.Rmd
index 6da000b1..8966a59d 100644
--- a/scomps/vignettes/00_good_practice_parallelization.Rmd
+++ b/scomps.Rcheck/00_pkg_src/scomps/vignettes/v00_good_practice_parallelization.Rmd
@@ -3,7 +3,7 @@ title: "Good practice of scomps with HPC"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{HPC good practice with scomps}
+  %\VignetteIndexEntry{good_practice_hpc}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
diff --git a/scomps/vignettes/01_generate_computational_grid.Rmd b/scomps.Rcheck/00_pkg_src/scomps/vignettes/v01_generate_computational_grid.Rmd
similarity index 92%
rename from scomps/vignettes/01_generate_computational_grid.Rmd
rename to scomps.Rcheck/00_pkg_src/scomps/vignettes/v01_generate_computational_grid.Rmd
index 4c1a4ee6..4bc1aaf2 100644
--- a/scomps/vignettes/01_generate_computational_grid.Rmd
+++ b/scomps.Rcheck/00_pkg_src/scomps/vignettes/v01_generate_computational_grid.Rmd
@@ -3,7 +3,7 @@ title: "Generate computational grids"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{Generate computational grids}
+  %\VignetteIndexEntry{computational_grids}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
diff --git a/scomps.Rcheck/00check.log b/scomps.Rcheck/00check.log
new file mode 100644
index 00000000..2fc32c95
--- /dev/null
+++ b/scomps.Rcheck/00check.log
@@ -0,0 +1,79 @@
+* using log directory ‘/Users/songi2/Documents/GitHub/Scalable_GIS/scomps.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: aarch64-apple-darwin20 (64-bit)
+* R was compiled by
+    Apple clang version 14.0.0 (clang-1400.0.29.202)
+    GNU Fortran (GCC) 12.2.0
+* running under: macOS Ventura 13.6
+* using session charset: UTF-8
+* checking for file ‘scomps/DESCRIPTION’ ... OK
+* this is package ‘scomps’ version ‘0.0.3.10042023’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... OK
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘scomps’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking DESCRIPTION meta-information ... NOTE
+Malformed Description field: should contain one or more complete sentences.
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... NOTE
+Namespaces in Imports field not imported from:
+  ‘covr’ ‘future’ ‘testthat’ ‘units’
+  All declared Imports should be used.
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... NOTE
+calculate_sedc: no visible binding for global variable ‘dist’
+check_within_reference: no visible binding for global variable ‘x’
+extract_with_buffer.flat: no visible binding for global variable ‘ID’
+extract_with_buffer.kernel: no visible binding for global variable ‘ID’
+get_computational_regions: no visible binding for global variable ‘y’
+sp_indexing: no visible binding for global variable ‘x’
+sp_indexing: no visible binding for global variable ‘y’
+Undefined global functions or variables:
+  ID dist x y
+Consider adding
+  importFrom("stats", "dist")
+to your NAMESPACE file.
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking installed files from ‘inst/doc’ ... OK
+* checking files in ‘vignettes’ ... OK
+* checking examples ... OK
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ... OK
+  Running ‘testthat.R’
+* checking for unstated dependencies in vignettes ... OK
+* checking package vignettes in ‘inst/doc’ ... OK
+* checking running R code from vignettes ... NONE
+  ‘v00_good_practice_parallelization.Rmd’ using ‘UTF-8’... OK
+  ‘v01_generate_computational_grid.Rmd’ using ‘UTF-8’... OK
+* checking re-building of vignette outputs ... OK
+* checking PDF version of manual ... OK
+* DONE
+Status: 3 NOTEs
diff --git a/scomps.Rcheck/00install.out b/scomps.Rcheck/00install.out
new file mode 100644
index 00000000..1c871a2e
--- /dev/null
+++ b/scomps.Rcheck/00install.out
@@ -0,0 +1,13 @@
+* installing *source* package ‘scomps’ ...
+** using staged installation
+** R
+** inst
+** byte-compile and prepare package for lazy loading
+** help
+*** installing help indices
+** building package indices
+** installing vignettes
+** testing if installed package can be loaded from temporary location
+** testing if installed package can be loaded from final location
+** testing if installed package keeps a record of temporary installation path
+* DONE (scomps)
diff --git a/scomps.Rcheck/Rdlatex.log b/scomps.Rcheck/Rdlatex.log
new file mode 100644
index 00000000..bb0bdaa0
--- /dev/null
+++ b/scomps.Rcheck/Rdlatex.log
@@ -0,0 +1,564 @@
+Hmm ... looks like a package
+Converting parsed Rd's to LaTeX ..
+Creating pdf output from LaTeX ...
+
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+[4] [5] [6] [7]
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+(see the transcript file for additional information)
+Output written on Rd2.pdf (17 pages, 116155 bytes).
+Transcript written on Rd2.log.
+Saving output to ‘scomps-manual.pdf’ ...
+Done
+You may want to clean up by 'rm -Rf /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmpOaxUwq/Rd2pdff3c856e679a5'
diff --git a/scomps.Rcheck/scomps-Ex.R b/scomps.Rcheck/scomps-Ex.R
new file mode 100644
index 00000000..4c502e90
--- /dev/null
+++ b/scomps.Rcheck/scomps-Ex.R
@@ -0,0 +1,121 @@
+pkgname <- "scomps"
+source(file.path(R.home("share"), "R", "examples-header.R"))
+options(warn = 1)
+library('scomps')
+
+base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
+base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
+cleanEx()
+nameEx("aw_covariates")
+### * aw_covariates
+
+flush(stderr()); flush(stdout())
+
+### Name: aw_covariates
+### Title: Computing area weighted covariates using two polygon sf or
+###   SpatVector objects
+### Aliases: aw_covariates
+
+### ** Examples
+
+# package
+library(sf)
+
+# run
+nc = sf::st_read(system.file("shape/nc.shp", package="sf"))
+nc = sf::st_transform(nc, 5070)
+pp = sf::st_sample(nc, size = 300)
+pp = sf::st_as_sf(pp)
+pp[["id"]] = seq(1, nrow(pp))
+sf::st_crs(pp) = "EPSG:5070"
+ppb = sf::st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
+
+system.time({ppb_nc_aw = aw_covariates(ppb, nc, 'id')})
+summary(ppb_nc_aw)
+#### Example of aw_covariates ends ####
+
+
+
+cleanEx()
+nameEx("check_crs")
+### * check_crs
+
+flush(stderr()); flush(stdout())
+
+### Name: check_crs
+### Title: Check Coordinate Reference System
+### Aliases: check_crs
+
+### ** Examples
+
+# data
+library(sf)
+ncpath = system.file("shape/nc.shp", package = "sf")
+nc = read_sf(ncpath)
+check_crs(nc)
+
+
+
+
+cleanEx()
+nameEx("get_computational_regions")
+### * get_computational_regions
+
+flush(stderr()); flush(stdout())
+
+### Name: get_computational_regions
+### Title: Get a set of computational regions
+### Aliases: get_computational_regions
+
+### ** Examples
+
+# data
+library(sf)
+ncpath = system.file("shape/nc.shp", package = "sf")
+nc = read_sf(ncpath)
+nc = st_transform(nc, "EPSG:5070")
+# run
+# nc_comp_region = get_computational_regions(nc, nx = 12, ny = 8)
+
+
+
+
+cleanEx()
+nameEx("grid_merge")
+### * grid_merge
+
+flush(stderr()); flush(stdout())
+
+### Name: grid_merge
+### Title: grid_merge: Merge grid polygons with given rules
+### Aliases: grid_merge
+
+### ** Examples
+
+# library(sf)
+# library(igraph)
+# ligrary(dplyr)
+# dg = sf::st_as_sfc(st_bbox(c(xmin = 0, ymin = 0, xmax = 8e5, ymax = 6e5)))
+# sf::st_crs(dg) = 5070
+# dgs = sf::st_as_sf(st_make_grid(dg, n = c(20, 15)))
+# dgs$CGRIDID = seq(1, nrow(dgs))
+#
+# dg_sample = st_sample(dg, kappa = 5e-9, mu = 15, scale = 20000, type = "Thomas")
+# sf::st_crs(dg_sample) = sf::st_crs(dg)
+# dg_merged = grid_merge(sf::st_as_sf(sss), dgs, 100)
+#### NOT RUN ####
+
+
+
+### * 

+###
+cleanEx()
+options(digits = 7L)
+base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
+grDevices::dev.off()
+###
+### Local variables: ***
+### mode: outline-minor ***
+### outline-regexp: "\\(> \\)?### [*]+" ***
+### End: ***
+quit('no')
diff --git a/scomps.Rcheck/scomps-Ex.Rout b/scomps.Rcheck/scomps-Ex.Rout
new file mode 100644
index 00000000..68d31f33
--- /dev/null
+++ b/scomps.Rcheck/scomps-Ex.Rout
@@ -0,0 +1,212 @@
+
+R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
+Copyright (C) 2023 The R Foundation for Statistical Computing
+Platform: aarch64-apple-darwin20 (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+  Natural language support but running in an English locale
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> pkgname <- "scomps"
+> source(file.path(R.home("share"), "R", "examples-header.R"))
+> options(warn = 1)
+> library('scomps')
+> 
+> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
+> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
+> cleanEx()
+> nameEx("aw_covariates")
+> ### * aw_covariates
+> 
+> flush(stderr()); flush(stdout())
+> 
+> ### Name: aw_covariates
+> ### Title: Computing area weighted covariates using two polygon sf or
+> ###   SpatVector objects
+> ### Aliases: aw_covariates
+> 
+> ### ** Examples
+> 
+> # package
+> library(sf)
+Linking to GEOS 3.11.0, GDAL 3.5.3, PROJ 9.1.0; sf_use_s2() is TRUE
+> 
+> # run
+> nc = sf::st_read(system.file("shape/nc.shp", package="sf"))
+Reading layer `nc' from data source 
+  `/Users/songi2/Library/R/arm64/4.3/library/sf/shape/nc.shp' 
+  using driver `ESRI Shapefile'
+Simple feature collection with 100 features and 14 fields
+Geometry type: MULTIPOLYGON
+Dimension:     XY
+Bounding box:  xmin: -84.32385 ymin: 33.88199 xmax: -75.45698 ymax: 36.58965
+Geodetic CRS:  NAD27
+> nc = sf::st_transform(nc, 5070)
+> pp = sf::st_sample(nc, size = 300)
+> pp = sf::st_as_sf(pp)
+> pp[["id"]] = seq(1, nrow(pp))
+> sf::st_crs(pp) = "EPSG:5070"
+> ppb = sf::st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
+> 
+> system.time({ppb_nc_aw = aw_covariates(ppb, nc, 'id')})
+Warning in st_interpolate_aw.sf(poly_weight[, index_numeric], poly_in, extensive = FALSE) :
+  st_interpolate_aw assumes attributes are constant or uniform over areas of x
+   user  system elapsed 
+  0.180   0.003   0.183 
+> summary(ppb_nc_aw)
+      AREA           PERIMETER         CNTY_         CNTY_ID    
+ Min.   :0.06133   Min.   :1.114   Min.   :1825   Min.   :1825  
+ 1st Qu.:0.12008   1st Qu.:1.549   1st Qu.:1917   1st Qu.:1917  
+ Median :0.13834   Median :1.685   Median :2000   Median :2000  
+ Mean   :0.14702   Mean   :1.777   Mean   :2004   Mean   :2004  
+ 3rd Qu.:0.17292   3rd Qu.:1.978   3rd Qu.:2078   3rd Qu.:2078  
+ Max.   :0.24000   Max.   :3.588   Max.   :2241   Max.   :2241  
+     FIPSNO         CRESS_ID          BIR74             SID74       
+ Min.   :37009   Min.   : 5.042   Min.   :  315.1   Min.   : 0.000  
+ 1st Qu.:37075   1st Qu.:38.024   1st Qu.: 1955.4   1st Qu.: 4.015  
+ Median :37104   Median :52.610   Median : 3124.2   Median : 6.867  
+ Mean   :37103   Mean   :51.798   Mean   : 3977.7   Mean   : 8.529  
+ 3rd Qu.:37131   3rd Qu.:65.974   3rd Qu.: 4639.0   3rd Qu.:10.591  
+ Max.   :37191   Max.   :95.910   Max.   :18561.5   Max.   :36.075  
+    NWBIR74             BIR79             SID79           NWBIR79        
+ Min.   :   6.222   Min.   :  403.3   Min.   : 0.000   Min.   :   4.222  
+ 1st Qu.: 458.022   1st Qu.: 2393.5   1st Qu.: 4.990   1st Qu.: 589.223  
+ Median : 955.882   Median : 3903.2   Median : 8.036   Median :1189.908  
+ Mean   :1285.378   Mean   : 5092.6   Mean   :10.052   Mean   :1655.747  
+ 3rd Qu.:1669.800   3rd Qu.: 5904.1   3rd Qu.:13.890   3rd Qu.:2127.972  
+ Max.   :6467.572   Max.   :26115.7   Max.   :34.448   Max.   :9367.957  
+          geometry  
+ POLYGON      :300  
+ epsg:5070    :  0  
+ +proj=aea ...:  0  
+                    
+                    
+                    
+> #### Example of aw_covariates ends ####
+> 
+> 
+> 
+> cleanEx()
+
+detaching ‘package:sf’
+
+> nameEx("check_crs")
+> ### * check_crs
+> 
+> flush(stderr()); flush(stdout())
+> 
+> ### Name: check_crs
+> ### Title: Check Coordinate Reference System
+> ### Aliases: check_crs
+> 
+> ### ** Examples
+> 
+> # data
+> library(sf)
+Linking to GEOS 3.11.0, GDAL 3.5.3, PROJ 9.1.0; sf_use_s2() is TRUE
+> ncpath = system.file("shape/nc.shp", package = "sf")
+> nc = read_sf(ncpath)
+> check_crs(nc)
+Coordinate Reference System:
+  User input: NAD27 
+  wkt:
+GEOGCRS["NAD27",
+    DATUM["North American Datum 1927",
+        ELLIPSOID["Clarke 1866",6378206.4,294.978698213898,
+            LENGTHUNIT["metre",1]]],
+    PRIMEM["Greenwich",0,
+        ANGLEUNIT["degree",0.0174532925199433]],
+    CS[ellipsoidal,2],
+        AXIS["latitude",north,
+            ORDER[1],
+            ANGLEUNIT["degree",0.0174532925199433]],
+        AXIS["longitude",east,
+            ORDER[2],
+            ANGLEUNIT["degree",0.0174532925199433]],
+    ID["EPSG",4267]]
+> 
+> 
+> 
+> 
+> cleanEx()
+
+detaching ‘package:sf’
+
+> nameEx("get_computational_regions")
+> ### * get_computational_regions
+> 
+> flush(stderr()); flush(stdout())
+> 
+> ### Name: get_computational_regions
+> ### Title: Get a set of computational regions
+> ### Aliases: get_computational_regions
+> 
+> ### ** Examples
+> 
+> # data
+> library(sf)
+Linking to GEOS 3.11.0, GDAL 3.5.3, PROJ 9.1.0; sf_use_s2() is TRUE
+> ncpath = system.file("shape/nc.shp", package = "sf")
+> nc = read_sf(ncpath)
+> nc = st_transform(nc, "EPSG:5070")
+> # run
+> # nc_comp_region = get_computational_regions(nc, nx = 12, ny = 8)
+> 
+> 
+> 
+> 
+> cleanEx()
+
+detaching ‘package:sf’
+
+> nameEx("grid_merge")
+> ### * grid_merge
+> 
+> flush(stderr()); flush(stdout())
+> 
+> ### Name: grid_merge
+> ### Title: grid_merge: Merge grid polygons with given rules
+> ### Aliases: grid_merge
+> 
+> ### ** Examples
+> 
+> # library(sf)
+> # library(igraph)
+> # ligrary(dplyr)
+> # dg = sf::st_as_sfc(st_bbox(c(xmin = 0, ymin = 0, xmax = 8e5, ymax = 6e5)))
+> # sf::st_crs(dg) = 5070
+> # dgs = sf::st_as_sf(st_make_grid(dg, n = c(20, 15)))
+> # dgs$CGRIDID = seq(1, nrow(dgs))
+> #
+> # dg_sample = st_sample(dg, kappa = 5e-9, mu = 15, scale = 20000, type = "Thomas")
+> # sf::st_crs(dg_sample) = sf::st_crs(dg)
+> # dg_merged = grid_merge(sf::st_as_sf(sss), dgs, 100)
+> #### NOT RUN ####
+> 
+> 
+> 
+> ### * 

+> ###
+> cleanEx()
+> options(digits = 7L)
+> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
+Time elapsed:  0.684 0.035 0.72 0 0 
+> grDevices::dev.off()
+null device 
+          1 
+> ###
+> ### Local variables: ***
+> ### mode: outline-minor ***
+> ### outline-regexp: "\\(> \\)?### [*]+" ***
+> ### End: ***
+> quit('no')
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diff --git a/scomps.Rcheck/scomps/DESCRIPTION b/scomps.Rcheck/scomps/DESCRIPTION
new file mode 100644
index 00000000..737d2c62
--- /dev/null
+++ b/scomps.Rcheck/scomps/DESCRIPTION
@@ -0,0 +1,22 @@
+Package: scomps
+Title: Scalable R geospatial computation
+Version: 0.0.3.10042023
+Authors@R: 
+    person("Insang", "Song", , "geoissong@gmail.com", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0001-8732-3256"))
+Description: A package for scalable geospatial computation for
+    environmental health research
+License: MIT + file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3
+Imports: covr, dplyr, future, future.apply, methods, rlang, sf, stars,
+        terra, testthat, units
+Suggests: future.batchtools, igraph, knitr, logr, rmarkdown, withr
+VignetteBuilder: knitr
+Config/testthat/edition: 3
+NeedsCompilation: no
+Packaged: 2023-10-04 15:41:03 UTC; songi2
+Author: Insang Song [aut, cre] ()
+Maintainer: Insang Song 
+Built: R 4.3.1; ; 2023-10-04 15:41:20 UTC; unix
diff --git a/scomps.Rcheck/scomps/INDEX b/scomps.Rcheck/scomps/INDEX
new file mode 100644
index 00000000..80dc13d3
--- /dev/null
+++ b/scomps.Rcheck/scomps/INDEX
@@ -0,0 +1,39 @@
+aw_covariates           Computing area weighted covariates using two
+                        polygon sf or SpatVector objects
+calculate_sedc          Calculate SEDC covariates
+check_bbox              Check if the data extent is inside the
+                        reference bounding box
+check_crs               Check Coordinate Reference System
+check_crs2              check_crs2: Coordinate system checker
+check_packbound         Return the package the input object is based on
+check_within_reference
+                        Check if the boundary of the vector/raster
+                        object is inside the reference
+clip_as_extent          Extent clipping
+clip_as_extent_ras      clip_as_extent_ras: Clip input raster.
+clip_as_extent_ras2     clip_as_extent_ras2: Clip input raster (version
+                        2).
+distribute_process      Process a given function in the entire or
+                        partial computational grids (under
+                        construction)
+estimate_demands        Estimate computational demands from inputs (to
+                        be written)
+extent_to_polygon       Generate a rectangular polygon from extent
+extract_with            Extract raster values with point buffers or
+                        polygons
+extract_with_buffer     Extract summarized values from raster with
+                        points and a buffer radius (to be written)
+extract_with_polygons   Extract summarized values from raster with
+                        generic polygons
+get_computational_regions
+                        Get a set of computational regions
+grid_merge              grid_merge: Merge grid polygons with given
+                        rules
+initate_log             Turn on logging
+rast_short              Quick call for SpatRaster with a window
+set_clip_extent         Setting the clipping extent
+sp_index_grid           sp_index_grid: Generate grid polygons
+sp_indexing             Create integer indices for grid
+switch_packbound        Switch spatial data class
+validate_and_repair_vectors
+                        Validate and repair input vector data
diff --git a/scomps.Rcheck/scomps/LICENSE b/scomps.Rcheck/scomps/LICENSE
new file mode 100644
index 00000000..74e6421f
--- /dev/null
+++ b/scomps.Rcheck/scomps/LICENSE
@@ -0,0 +1,2 @@
+YEAR: 2023
+COPYRIGHT HOLDER: I. Song
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diff --git a/scomps.Rcheck/scomps/Meta/links.rds b/scomps.Rcheck/scomps/Meta/links.rds
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diff --git a/scomps.Rcheck/scomps/Meta/nsInfo.rds b/scomps.Rcheck/scomps/Meta/nsInfo.rds
new file mode 100644
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diff --git a/scomps.Rcheck/scomps/Meta/package.rds b/scomps.Rcheck/scomps/Meta/package.rds
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diff --git a/scomps.Rcheck/scomps/Meta/vignette.rds b/scomps.Rcheck/scomps/Meta/vignette.rds
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diff --git a/scomps.Rcheck/scomps/NAMESPACE b/scomps.Rcheck/scomps/NAMESPACE
new file mode 100644
index 00000000..b8f3fc6a
--- /dev/null
+++ b/scomps.Rcheck/scomps/NAMESPACE
@@ -0,0 +1,27 @@
+# Generated by roxygen2: do not edit by hand
+
+export(aw_covariates)
+export(calculate_sedc)
+export(check_bbox)
+export(check_crs)
+export(check_crs2)
+export(check_packbound)
+export(check_within_reference)
+export(clip_as_extent)
+export(clip_as_extent_ras)
+export(clip_as_extent_ras2)
+export(distribute_process)
+export(estimate_demands)
+export(extent_to_polygon)
+export(extract_with)
+export(extract_with_buffer)
+export(extract_with_polygons)
+export(get_computational_regions)
+export(grid_merge)
+export(initate_log)
+export(rast_short)
+export(set_clip_extent)
+export(sp_index_grid)
+export(sp_indexing)
+export(switch_packbound)
+export(validate_and_repair_vectors)
diff --git a/scomps.Rcheck/scomps/R/scomps b/scomps.Rcheck/scomps/R/scomps
new file mode 100644
index 00000000..66861563
--- /dev/null
+++ b/scomps.Rcheck/scomps/R/scomps
@@ -0,0 +1,27 @@
+#  File share/R/nspackloader.R
+#  Part of the R package, https://www.R-project.org
+#
+#  Copyright (C) 1995-2012 The R Core Team
+#
+#  This program is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation; either version 2 of the License, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  A copy of the GNU General Public License is available at
+#  https://www.r-project.org/Licenses/
+
+local({
+    info <- loadingNamespaceInfo()
+    pkg <- info$pkgname
+    ns <- .getNamespace(as.name(pkg))
+    if (is.null(ns))
+        stop("cannot find namespace environment for ", pkg, domain = NA);
+    dbbase <- file.path(info$libname, pkg, "R", pkg)
+    lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
+})
diff --git a/scomps.Rcheck/scomps/R/scomps.rdb b/scomps.Rcheck/scomps/R/scomps.rdb
new file mode 100644
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diff --git a/scomps.Rcheck/scomps/R/scomps.rdx b/scomps.Rcheck/scomps/R/scomps.rdx
new file mode 100644
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+
+R: Vignettes and other documentation
+
+
+
+

+
 Vignettes and other documentation
+
+

+

+

+[Top]
+

+
Vignettes from package 'scomps'

+
+++++++
+
+
+
+
+
+
+
+
+
+







scomps::v00_good_practice_parallelizationgood_practice_hpcHTMLsourceR code
scomps::v01_generate_computational_gridcomputational_gridsHTMLsourceR code

+

diff --git a/scomps.Rcheck/scomps/doc/v00_good_practice_parallelization.R b/scomps.Rcheck/scomps/doc/v00_good_practice_parallelization.R
new file mode 100644
index 00000000..c639e81d
--- /dev/null
+++ b/scomps.Rcheck/scomps/doc/v00_good_practice_parallelization.R
@@ -0,0 +1,4 @@
+## -----------------------------------------------------------------------------
+knitr::opts_chunk$set(warning = FALSE, message = FALSE)
+
+
diff --git a/scomps.Rcheck/scomps/doc/v00_good_practice_parallelization.Rmd b/scomps.Rcheck/scomps/doc/v00_good_practice_parallelization.Rmd
new file mode 100644
index 00000000..8966a59d
--- /dev/null
+++ b/scomps.Rcheck/scomps/doc/v00_good_practice_parallelization.Rmd
@@ -0,0 +1,39 @@
+---
+title: "Good practice of scomps with HPC"
+date: "`r Sys.Date()`"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{good_practice_hpc}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+
+```{r}
+knitr::opts_chunk$set(warning = FALSE, message = FALSE)
+
+```
+
+## Assumptions
+- Users have an accessible HPC at your work
+- Data are stored in distributed file systems (usually incorporated into the HPC system)
+
+
+## Basic workflow
+
+### Practice for minimizing errors
+- Consider using `try()` or `tryCatch()` not to a tiny error will halt all the work without any results 
+    - Especially with the higher-level functions
+- "IPDE -- Inspect, Predict, Decide, Execute" all the time
+
+### Raster-Vector overlay
+- Make `sp_index_grid()` to get padded grid objects
+- Convert sf/SpatVector objects into `terra::ext()` compatible named numeric vector
+    - For example: `c(xmin=0, ymin=0, xmax=10, ymax=10)`
+- Make list objects with: 
+    - An extent vector in each element
+    - Preprocessed vector objects with respect to each extent vector in the first list
+    - Preferably all lists are named 
+- Write a `future.apply` script running through the extent list object
+- Run a small amount of data to estimate the total computational demand
+- Submit a job with a proper amount of computational assets
diff --git a/scomps.Rcheck/scomps/doc/v00_good_practice_parallelization.html b/scomps.Rcheck/scomps/doc/v00_good_practice_parallelization.html
new file mode 100644
index 00000000..da4506f4
--- /dev/null
+++ b/scomps.Rcheck/scomps/doc/v00_good_practice_parallelization.html
@@ -0,0 +1,408 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Good practice of scomps with HPC
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Good practice of scomps with HPC

+
2023-10-04

+
+
+
+
knitr::opts_chunk$set(warning = FALSE, message = FALSE)

+

+
Assumptions

+
    
+
  • Users have an accessible HPC at your work
    • 
+
  • Data are stored in distributed file systems (usually incorporated
+into the HPC system)
    • 
+

+

+

+
Basic workflow

+

+
Practice for minimizing errors

+
    
+
  • Consider using try() or tryCatch() not to
+a tiny error will halt all the work without any results
+
      
+
    • Especially with the higher-level functions
      • 
+
    • 
+
  • “IPDE – Inspect, Predict, Decide, Execute” all the time
    • 
+

+

+

+
Raster-Vector overlay

+
    
+
  • Make sp_index_grid() to get padded grid objects
    • 
+
  • Convert sf/SpatVector objects into terra::ext()
+compatible named numeric vector
+
      
+
    • For example: c(xmin=0, ymin=0, xmax=10, ymax=10)
      • 
+
    • 
+
  • Make list objects with:
+
      
+
    • An extent vector in each element
      • 
+
    • Preprocessed vector objects with respect to each extent vector in
+the first list
      • 
+
    • Preferably all lists are named
      • 
+
    • 
+
  • Write a future.apply script running through the extent
+list object
    • 
+
  • Run a small amount of data to estimate the total computational
+demand
    • 
+
  • Submit a job with a proper amount of computational assets
    • 
+

+

+

+
+
+
+
+
+
+
+
+
+
+
diff --git a/scomps.Rcheck/scomps/doc/v01_generate_computational_grid.R b/scomps.Rcheck/scomps/doc/v01_generate_computational_grid.R
new file mode 100644
index 00000000..aa3d29fc
--- /dev/null
+++ b/scomps.Rcheck/scomps/doc/v01_generate_computational_grid.R
@@ -0,0 +1,22 @@
+## -----------------------------------------------------------------------------
+knitr::opts_chunk$set(warning = FALSE, message = FALSE)
+
+
+## -----------------------------------------------------------------------------
+library(scomps)
+library(sf)
+library(terra)
+library(stars)
+library(dplyr)
+
+
+## -----------------------------------------------------------------------------
+# your_grid = scomps::sp_index_grid()
+
+
+## -----------------------------------------------------------------------------
+# library(mapsf)
+# mf_map(your_grid$geometry)
+
+
+
diff --git a/scomps.Rcheck/scomps/doc/v01_generate_computational_grid.Rmd b/scomps.Rcheck/scomps/doc/v01_generate_computational_grid.Rmd
new file mode 100644
index 00000000..4bc1aaf2
--- /dev/null
+++ b/scomps.Rcheck/scomps/doc/v01_generate_computational_grid.Rmd
@@ -0,0 +1,46 @@
+---
+title: "Generate computational grids"
+date: "`r Sys.Date()`"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{computational_grids}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+
+```{r}
+knitr::opts_chunk$set(warning = FALSE, message = FALSE)
+
+```
+
+
+## Prepare input data
+```{r}
+library(scomps)
+library(sf)
+library(terra)
+library(stars)
+library(dplyr)
+
+```
+
+## Computational grids
+```{r}
+# your_grid = scomps::sp_index_grid()
+
+```
+
+
+## Visualize computational grids
+```{r}
+# library(mapsf)
+# mf_map(your_grid$geometry)
+
+
+```
+
+
+
+## Notes
+- Computational grids are the exhaustive split of the entire study region. You should take a square buffer of each grid to clip the target raster or vector.
diff --git a/scomps.Rcheck/scomps/doc/v01_generate_computational_grid.html b/scomps.Rcheck/scomps/doc/v01_generate_computational_grid.html
new file mode 100644
index 00000000..c2d963b8
--- /dev/null
+++ b/scomps.Rcheck/scomps/doc/v01_generate_computational_grid.html
@@ -0,0 +1,388 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Generate computational grids
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Generate computational grids

+
2023-10-04

+
+
+
+
knitr::opts_chunk$set(warning = FALSE, message = FALSE)

+

+
Prepare input data

+
library(scomps)
+library(sf)
+library(terra)
+library(stars)
+library(dplyr)

+

+

+
Computational grids

+
# your_grid = scomps::sp_index_grid()

+

+

+
Visualize computational grids

+
# library(mapsf)
+# mf_map(your_grid$geometry)

+

+

+
Notes

+
    
+
  • Computational grids are the exhaustive split of the entire study
+region. You should take a square buffer of each grid to clip the target
+raster or vector.
    • 
+

+

+
+
+
+
+
+
+
+
+
+
+
diff --git a/scomps.Rcheck/scomps/help/AnIndex b/scomps.Rcheck/scomps/help/AnIndex
new file mode 100644
index 00000000..a7b8aefb
--- /dev/null
+++ b/scomps.Rcheck/scomps/help/AnIndex
@@ -0,0 +1,25 @@
+aw_covariates	aw_covariates
+calculate_sedc	calculate_sedc
+check_bbox	check_bbox
+check_crs	check_crs
+check_crs2	check_crs2
+check_packbound	check_packbound
+check_within_reference	check_within_reference
+clip_as_extent	clip_as_extent
+clip_as_extent_ras	clip_as_extent_ras
+clip_as_extent_ras2	clip_as_extent_ras2
+distribute_process	distribute_process
+estimate_demands	estimate_demands
+extent_to_polygon	extent_to_polygon
+extract_with	extract_with
+extract_with_buffer	extract_with_buffer
+extract_with_polygons	extract_with_polygons
+get_computational_regions	get_computational_regions
+grid_merge	grid_merge
+initate_log	initate_log
+rast_short	rast_short
+set_clip_extent	set_clip_extent
+sp_indexing	sp_indexing
+sp_index_grid	sp_index_grid
+switch_packbound	switch_packbound
+validate_and_repair_vectors	validate_and_repair_vectors
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diff --git a/scomps.Rcheck/scomps/html/00Index.html b/scomps.Rcheck/scomps/html/00Index.html
new file mode 100644
index 00000000..9c12d593
--- /dev/null
+++ b/scomps.Rcheck/scomps/html/00Index.html
@@ -0,0 +1,76 @@
+
+
+R: Scalable R geospatial computation
+
+
+
+

+
 Scalable R geospatial computation
+
+

+

+

+[Up]
+[Top]
+
Documentation for package ‘scomps’ version 0.0.3.10042023

+
+
+
+
Help Pages

+
+
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aw_covariatesComputing area weighted covariates using two polygon sf or SpatVector objects
calculate_sedcCalculate SEDC covariates
check_bboxCheck if the data extent is inside the reference bounding box
check_crsCheck Coordinate Reference System
check_crs2check_crs2: Coordinate system checker
check_packboundReturn the package the input object is based on
check_within_referenceCheck if the boundary of the vector/raster object is inside the reference
clip_as_extentExtent clipping
clip_as_extent_rasclip_as_extent_ras: Clip input raster.
clip_as_extent_ras2clip_as_extent_ras2: Clip input raster (version 2).
distribute_processProcess a given function in the entire or partial computational grids (under construction)
estimate_demandsEstimate computational demands from inputs (to be written)
extent_to_polygonGenerate a rectangular polygon from extent
extract_withExtract raster values with point buffers or polygons
extract_with_bufferExtract summarized values from raster with points and a buffer radius (to be written)
extract_with_polygonsExtract summarized values from raster with generic polygons
get_computational_regionsGet a set of computational regions
grid_mergegrid_merge: Merge grid polygons with given rules
initate_logTurn on logging
rast_shortQuick call for SpatRaster with a window
set_clip_extentSetting the clipping extent
sp_indexingCreate integer indices for grid
sp_index_gridsp_index_grid: Generate grid polygons
switch_packboundSwitch spatial data class
validate_and_repair_vectorsValidate and repair input vector data

+

diff --git a/scomps.Rcheck/scomps/html/R.css b/scomps.Rcheck/scomps/html/R.css
new file mode 100644
index 00000000..c2289098
--- /dev/null
+++ b/scomps.Rcheck/scomps/html/R.css
@@ -0,0 +1,130 @@
+@media screen {
+    .container {
+	padding-right: 10px;
+	padding-left: 10px;
+	margin-right: auto;
+	margin-left: auto;
+	max-width: 900px;
+    }
+}
+
+.rimage img { /* from knitr - for examples and demos */
+    width: 96%;
+    margin-left: 2%;
+} 	
+
+.katex { font-size: 1.1em; }
+
+code {
+    color: inherit;
+    background: inherit;
+}
+
+body {
+    line-height: 1.4;
+    background: white;
+    color: black;
+}
+
+a:link {
+    background: white;
+    color: blue;
+}
+
+a:visited {
+    background: white;
+    color: rgb(50%, 0%, 50%);
+}
+
+h1 {
+    background: white;
+    color: rgb(55%, 55%, 55%);
+    font-family: monospace;
+    font-size: 1.4em; /* x-large; */
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+}
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+h3 {
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+    font-family: monospace;
+    font-size: 1.2em; /* large; */
+}
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+h4 {
+    background: white;
+    color: rgb(40%, 40%, 40%);
+    font-family: monospace;
+    font-style: italic;
+    font-size: 1.2em; /* large; */
+}
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+tr {
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+}
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+span.rlang {
+    font-family: Courier New, Courier;
+    color: #666666;
+}
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diff --git a/scomps.Rcheck/tests/startup.Rs b/scomps.Rcheck/tests/startup.Rs
new file mode 100644
index 00000000..8ad6d250
--- /dev/null
+++ b/scomps.Rcheck/tests/startup.Rs
@@ -0,0 +1,4 @@
+## A custom startup file for tests
+## Run as if a system Rprofile, so no packages, no assignments
+options(useFancyQuotes = FALSE)
+
diff --git a/scomps.Rcheck/tests/testthat.R b/scomps.Rcheck/tests/testthat.R
new file mode 100644
index 00000000..b465b524
--- /dev/null
+++ b/scomps.Rcheck/tests/testthat.R
@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(scomps)
+
+test_check("scomps")
diff --git a/scomps.Rcheck/tests/testthat.Rout b/scomps.Rcheck/tests/testthat.Rout
new file mode 100644
index 00000000..dfb13fbb
--- /dev/null
+++ b/scomps.Rcheck/tests/testthat.Rout
@@ -0,0 +1,37 @@
+
+R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
+Copyright (C) 2023 The R Foundation for Statistical Computing
+Platform: aarch64-apple-darwin20 (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> # This file is part of the standard setup for testthat.
+> # It is recommended that you do not modify it.
+> #
+> # Where should you do additional test configuration?
+> # Learn more about the roles of various files in:
+> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+> # * https://testthat.r-lib.org/articles/special-files.html
+> 
+> library(testthat)
+> library(scomps)
+> 
+> test_check("scomps")
+pr, tas, 
+pr, tas, 
+pr, tas, 
+[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
+> 
+> proc.time()
+   user  system elapsed 
+  1.703   0.063   1.763 
diff --git a/scomps.Rcheck/tests/testthat/tests.R b/scomps.Rcheck/tests/testthat/tests.R
new file mode 100644
index 00000000..6efa4142
--- /dev/null
+++ b/scomps.Rcheck/tests/testthat/tests.R
@@ -0,0 +1,65 @@
+# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand  
+testthat::test_that("What package does the input object belong?",
+{
+    withr::local_package("stars")
+    withr::local_package("terra")
+    withr::local_options(list(sf_use_s2 = FALSE))
+    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
+    bcsd_stars = stars::read_stars(bcsd_path)
+
+    packbound_stars = check_packbound(bcsd_stars)
+    sprast_bcsd = terra::rast(bcsd_path)
+    packbound_terra = check_packbound(sprast_bcsd)
+
+    testthat::expect_equal(packbound_stars, "sf")
+    testthat::expect_equal(packbound_terra, "terra")
+})
+
+
+testthat::test_that("What package does the input object belong?",
+{
+    withr::local_package("stars")
+    withr::local_package("terra")
+    withr::local_options(list(sf_use_s2 = FALSE))
+    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
+    bcsd_stars = stars::read_stars(bcsd_path)
+
+    nc = system.file(package = "sf", "shape/nc.shp")
+    nc = sf::read_sf(nc)
+
+    datatype_stars = check_datatype(bcsd_stars)
+    datatype_sf = check_datatype(nc)
+
+    testthat::expect_equal(datatype_stars, "raster")
+    testthat::expect_equal(datatype_sf, "vector")
+})
+
+
+testthat::test_that("Format is well converted",
+{
+    withr::local_package("stars")
+    withr::local_package("terra")
+    withr::local_options(list(sf_use_s2 = FALSE))
+
+    # starts from sf/stars
+    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
+    bcsd_stars = stars::read_stars(bcsd_path)
+    nc = system.file(package = "sf", "shape/nc.shp")
+    nc = sf::read_sf(nc)
+
+    stars_bcsd_tr = switch_packbound(bcsd_stars)
+    sf_nc_tr = switch_packbound(nc)
+
+    testthat::expect_equal(check_packbound(stars_bcsd_tr), "terra")
+    testthat::expect_equal(check_packbound(sf_nc_tr), "terra")
+
+    stars_bcsd_trb = switch_packbound(stars_bcsd_tr)
+    sf_nc_trb = switch_packbound(sf_nc_tr)
+
+    testthat::expect_equal(check_packbound(stars_bcsd_trb), "sf")
+    testthat::expect_equal(check_packbound(sf_nc_trb), "sf")
+
+})
+
+
+
diff --git a/scomps/DESCRIPTION b/scomps/DESCRIPTION
index cc8b8d68..acb3b95d 100644
--- a/scomps/DESCRIPTION
+++ b/scomps/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: scomps
 Title: Scalable R geospatial computation
-Version: 0.0.2.10032023
+Version: 0.0.3.10042023
 Authors@R: 
     person("Insang", "Song", , "geoissong@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8732-3256"))
@@ -15,11 +15,13 @@ Imports:
     dplyr,
     future,
     future.apply,
+    methods,
     rlang,
     sf,
     stars,
     terra,
-    testthat
+    testthat,
+    units
 Suggests: 
     future.batchtools,
     igraph,
@@ -30,4 +32,4 @@ Suggests:
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 LitrVersionUsed: 0.9.0
-LitrId: 1af1eaeb8441cd422e37a21fe2e2deb1
+LitrId: 27d90205fd42be403e707a6a559e8eae
diff --git a/scomps/NAMESPACE b/scomps/NAMESPACE
index e7df8cf6..b8f3fc6a 100644
--- a/scomps/NAMESPACE
+++ b/scomps/NAMESPACE
@@ -12,10 +12,9 @@ export(clip_as_extent_ras)
 export(clip_as_extent_ras2)
 export(distribute_process)
 export(estimate_demands)
+export(extent_to_polygon)
 export(extract_with)
 export(extract_with_buffer)
-export(extract_with_buffer.flat)
-export(extract_with_buffer.kernel)
 export(extract_with_polygons)
 export(get_computational_regions)
 export(grid_merge)
diff --git a/scomps/R/check.R b/scomps/R/check.R
index 3e8e20c6..2e1bbcf2 100644
--- a/scomps/R/check.R
+++ b/scomps/R/check.R
@@ -8,19 +8,19 @@
 #' @export
 check_packbound <- function(input) {
   # cl_inobj = class(input)[1]
-  stopifnot("Input should be one of sf or Spat* object.\n" = any(is(input, "sf"), is(input, "stars"), is(input, "SpatVector"), is(input, "SpatRaster")))
-  if (is(input, "SpatVector") || is(input, "SpatRaster")) {
+  stopifnot("Input should be one of sf or Spat* object.\n" = any(methods::is(input, "sf"), methods::is(input, "stars"), methods::is(input, "SpatVector"), methods::is(input, "SpatRaster")))
+  if (methods::is(input, "SpatVector") || methods::is(input, "SpatRaster")) {
     return("terra")
   }
   return("sf")
 }
 
 check_datatype <- function(input) {
-  stopifnot("Input should be one of sf or Spat* object.\n" = any(is(input, "sf"), is(input, "stars"), is(input, "SpatVector"), is(input, "SpatRaster")))
-  if (any(is(input, "SpatVector"), is(input, "sf"))) {
+  stopifnot("Input should be one of sf or Spat* object.\n" = any(methods::is(input, "sf"), methods::is(input, "stars"), methods::is(input, "SpatVector"), methods::is(input, "SpatRaster")))
+  if (any(methods::is(input, "SpatVector"), methods::is(input, "sf"))) {
     return("vector")
   }
-  if (any(is(input, "SpatRaster"), is(input, "stars"))) {
+  if (any(methods::is(input, "SpatRaster"), methods::is(input, "stars"))) {
     return("raster")
   }
 }
@@ -28,11 +28,12 @@ check_datatype <- function(input) {
 #' @title check_crs2: Coordinate system checker
 #' @description The input is checked whether its coordinate system is present. If not, it is reprojected to EPSG:5179.
 #' @param input Input object one of sf or terra::Spat* object
+#' @param crs_standard character(1). A standard definition of coordinate reference system. Default is "EPSG:4326" Consult [epsg.io](https://epsg.io) for details of other CRS.
 #' @return A (reprojected) sf or SpatVector object.
 #' @export
 check_crs2 <- function(input, crs_standard = "EPSG:4326") {
   check_crs.sf <- function(input){
-    if (is.na(st_crs(input))){cat('Please check the coordinate system or its EPSG code of your input object.'); return(NULL)}
+    if (is.na(sf::st_crs(input))){cat('Please check the coordinate system or its EPSG code of your input object.'); return(NULL)}
     if (sf::st_crs(input)$epsg == crs_standard ) {
       return(input)
     } 
@@ -53,6 +54,45 @@ check_crs2 <- function(input, crs_standard = "EPSG:4326") {
           sf = check_crs.sf(input))
   }
 
+#' Generate a rectangular polygon from extent
+#' 
+#' @param extent input extent. A numeric vector with xmin/xmax/ymin/ymax, sf::st_bbox() or terra::ext() outputs.
+#' @param output_class character(1). Class of the output polygon. One of "sf" or "terra"
+#' @param crs character(1). Coordinate reference system definition.
+#' @author Insang Song
+#' @export
+extent_to_polygon <- function(extent, output_class = "terra", crs = "EPSG:4326") {
+  if (!output_class %in% c("sf", "terra")) {
+    stop("output_class should be one of 'sf' or 'terra'.\n")
+  }
+  if (methods::is(extent, "numeric")) {
+    if (is.null(attr(extent, "names"))) {
+      stop("Your extent is an unnamed numeric vector. Please define names xmin/xmax/ymin/ymax explicitly.\n")
+    }
+    extent = switch(
+      output_class,
+      sf = sf::st_bbox(extent),
+      terra = terra::ext(extent)
+    )
+  }
+
+  extent_polygon = switch(
+    output_class,
+    sf = sf::st_as_sfc(extent),
+    terra = terra::vect(extent)
+  )
+
+  extent_polygon = switch(
+    output_class,
+    sf = sf::st_set_crs(extent_polygon, sf::st_crs(crs)),
+    terra = terra::set.crs(extent_polygon, terra::crs(crs))
+  )
+
+  return(extent_polygon)
+  
+}
+
+
 #' Check if the data extent is inside the reference bounding box
 #' 
 #' @description One of the most common errors in spatial computation is rooted in the entirely or partly incomparable spatial extents of input datasets. This function returns whether your data is inside the target computational extent. It is assumed that you know and have the exact computational region. This function will return TRUE if the reference region completely contains your data's extent and FALSE otherwise.
@@ -77,10 +117,11 @@ check_bbox <- function(
   if (is.na(query_crs) || is.null(query_crs)) {
     stop("The dataset you queried has no CRS. Please make sure your dataset has the correct CRS.\n")
   }
+  query_matched = sf::st_transform(data_query, sf::st_crs(ref_crs))
+
 
-  # ...
 
-  check_result
+  check_result = sf::st_within()
   return(check_result)
 }
 
@@ -100,9 +141,9 @@ check_bbox <- function(
 #' 
 #' @export 
 check_crs <- function(x) {
-    stopifnot("Input is invalid.\n" = (is(x, "sf") || is(x, "stars") || is(x, "SpatVector") || is(x, "SpatRaster")))
+    stopifnot("Input is invalid.\n" = (methods::is(x, "sf") || methods::is(x, "stars") || methods::is(x, "SpatVector") || methods::is(x, "SpatRaster")))
     
-    if (is(x, "sf") || is(x, "stars")) {
+    if (methods::is(x, "sf") || methods::is(x, "stars")) {
         crs_wkt = sf::st_crs(x)
     } else {
         crs_wkt = terra::crs(x)
@@ -119,8 +160,8 @@ check_crs <- function(x) {
 #' @author Insang Song \email{geoissong@@gmail.com}
 #' @export 
 check_within_reference <- function(input_object, reference) {
-    stopifnot("Input is invalid.\n" = (is(x, "sf") || is(x, "stars") || is(x, "SpatVector") || is(x, "SpatRaster")))
-    stopifnot("Reference is invalid.\n" = (is(x, "sf") || is(x, "stars") || is(x, "SpatVector") || is(x, "SpatRaster")))
+    stopifnot("Input is invalid.\n" = (methods::is(x, "sf") || methods::is(x, "stars") || methods::is(x, "SpatVector") || methods::is(x, "SpatRaster")))
+    stopifnot("Reference is invalid.\n" = (methods::is(x, "sf") || methods::is(x, "stars") || methods::is(x, "SpatVector") || methods::is(x, "SpatRaster")))
 
   bbox_input <- input_object
     sf::st_bbox() |>
diff --git a/scomps/R/estimate_demands.R b/scomps/R/estimate_demands.R
index 6dff37d0..0c0bf6d7 100644
--- a/scomps/R/estimate_demands.R
+++ b/scomps/R/estimate_demands.R
@@ -6,6 +6,7 @@
 #' @param nx integer(1). 
 #' @param ny integer(1). 
 #' @param padding numeric(1). Extrusion factor 
+#' @author Insang Song
 #' @export 
 estimate_demands <- function(
   inputs,
diff --git a/scomps/R/indexing.R b/scomps/R/indexing.R
index 6fee582a..7555a3f9 100644
--- a/scomps/R/indexing.R
+++ b/scomps/R/indexing.R
@@ -10,7 +10,7 @@
 sp_indexing <- function(points_in, ncutsx, ncutsy){
   # pts <- data.table(pnts)
   points_in <- points_in |>
-    mutate(or_id = seq(1, dim(points_in)[1]))
+    dplyr::mutate(or_id = seq(1, dim(points_in)[1]))
   
   range_x  <- range(points_in$x)
   limits_x <- (range_x[1] + seq(0, ncutsx) * (range_x[2] - range_x[1]) / ncutsx)
@@ -18,7 +18,7 @@ sp_indexing <- function(points_in, ncutsx, ncutsy){
   limits_y <- (range_y[1] + seq(0, ncutsy) * (range_y[2] - range_y[1]) / ncutsy)
   
   points_in_cut <- points_in |>
-    mutate(xcut =  as.integer(cut(x, ncutsx, labels = seq(1, ncutsx))),
+    dplyr::mutate(xcut =  as.integer(cut(x, ncutsx, labels = seq(1, ncutsx))),
            ycut = as.integer(cut(y, ncutsy, labels = seq(1, ncutsy))))
   
   return(points_in_cut)
diff --git a/scomps/R/interpret_computational_domain.R b/scomps/R/interpret_computational_domain.R
index ebd48b57..90132a7f 100644
--- a/scomps/R/interpret_computational_domain.R
+++ b/scomps/R/interpret_computational_domain.R
@@ -8,7 +8,8 @@
 #' @param ny integer(1). The number of grids along y-axis.
 #' @param grid_min_features integer(1). A threshold to merging adjacent grids
 #' @param padding numeric(1). A extrusion factor to make buffer to clip actual datasets. Depending on the length unit of the CRS of input.
-#' @param unit character(1). The length unit for padding (optional). units::set_units is used for padding when sf object is used. See \link{units package vignette (web)}{https://cran.r-project.org/web/packages/units/vignettes/measurement_units_in_R.html} for the list of acceptable unit forms.
+#' @param unit character(1). The length unit for padding (optional). units::set_units is used for padding when sf object is used. See [units package vignette (web)](https://cran.r-project.org/web/packages/units/vignettes/measurement_units_in_R.html) for the list of acceptable unit forms.
+#' @param ... arguments passed to the internal function
 #' @return A set of polygons in the input class
 #' @description TODO. Using input points, the bounding box is split to the predefined numbers of columns and rows. Each grid will be buffered by the radius.   
 #' @author Insang Song 
@@ -52,7 +53,7 @@ sp_index_grid <- function(points_in, ncutsx, ncutsy){
   sp_index_grid.sf = function(points_in, ncutsx, ncutsy) {
     grid1 <- sf::st_make_grid(points_in, n = c(ncutsx, ncutsy)) |> 
       as.data.frame() |> 
-      st_as_sf()
+      sf::st_as_sf()
     grid1 <- grid1[points_in, ]
     return(grid1)
   }
@@ -82,14 +83,14 @@ sp_index_grid <- function(points_in, ncutsx, ncutsy){
 #' # library(sf)
 #' # library(igraph)
 #' # ligrary(dplyr)
-#' # dg = st_as_sfc(st_bbox(c(xmin = 0, ymin = 0, xmax = 8e5, ymax = 6e5)))
-#' # st_crs(dg) = 5070
-#' # dgs = st_as_sf(st_make_grid(dg, n = c(20, 15)))
+#' # dg = sf::st_as_sfc(st_bbox(c(xmin = 0, ymin = 0, xmax = 8e5, ymax = 6e5)))
+#' # sf::st_crs(dg) = 5070
+#' # dgs = sf::st_as_sf(st_make_grid(dg, n = c(20, 15)))
 #' # dgs$CGRIDID = seq(1, nrow(dgs))
 #' #
 #' # dg_sample = st_sample(dg, kappa = 5e-9, mu = 15, scale = 20000, type = "Thomas")
-#' # st_crs(dg_sample) = st_crs(dg)
-#' # dg_merged = grid_merge(st_as_sf(sss), dgs, 100)
+#' # sf::st_crs(dg_sample) = sf::st_crs(dg)
+#' # dg_merged = grid_merge(sf::st_as_sf(sss), dgs, 100)
 #' #### NOT RUN ####
 #' @export
 grid_merge <- function(points_in, grid_in, grid_min_features){
@@ -113,7 +114,7 @@ grid_merge <- function(points_in, grid_in, grid_min_features){
   identified = unique(identified)
   identified = identified[sapply(identified, length) > 1]
 
-  identified_graph = lapply(identified, \(x) t(combn(x, 2))) |>
+  identified_graph = lapply(identified, \(x) t(utils::combn(x, 2))) |>
     Reduce(f = rbind, x = _) |>
     unique() |>
     apply(X = _, 2, as.character) |>
@@ -137,8 +138,8 @@ grid_merge <- function(points_in, grid_in, grid_min_features){
   #   grid_out[["CGRIDID"]][target_idx] = paste("M_", paste(target_idx, collapse = "_"), sep = "")
   # }
   grid_out = grid_out |>
-    dplyr::group_by(CGRIDID) |>
-    dplyr::summarize(n_merged = n()) |>
+    dplyr::group_by(!!rlang::sym("CGRIDID")) |>
+    dplyr::summarize(n_merged = dplyr::n()) |>
     dplyr::ungroup() 
 
   ## polsby-popper test for shape compactness
@@ -175,7 +176,7 @@ grid_merge <- function(points_in, grid_in, grid_min_features){
 #' 
 #' @description Should 
 #' @param grids sf/SpatVector object. Computational grids.
-#' @param grid_id character(1) or numeric(2). Default is NULL. If NULL, all grid_ids are used. "id_from:id_to" format or c(unique(grid_id)[id_from], unique(grid_id)[id_to])
+#' @param grid_id character(1) or numeric(2). Default is NULL. If NULL, all grid_ids are used. \code{"id_from:id_to"} format or \code{c(unique(grid_id)[id_from], unique(grid_id)[id_to])}
 #' @param fun function supported in scomps. 
 #' @param ... Arguments passed to fun.
 #' @return a data.frame object with mean value
@@ -183,8 +184,7 @@ grid_merge <- function(points_in, grid_in, grid_min_features){
 #' 
 #' @export
 distribute_process <- function(grids, grid_id = NULL, fun, ...) {
-    require(future.apply)
-    
+   
     # subset using grids and grid_id
     if (!is.null(grid_id)) {
         if (is.character(grid_id)) {
@@ -202,7 +202,7 @@ distribute_process <- function(grids, grid_id = NULL, fun, ...) {
     results_distributed = future.apply::future_lapply(
         \(x, ...) {
             fun(...)
-        }, grids_target_list, points_cutslist, SIMPLIFY = FALSE,
+        }, grids_target_list, 
         future.seed = TRUE)
     results_distributed = do.call(rbind, results_distributed)
     return(results_distributed)
diff --git a/scomps/R/preprocessing.R b/scomps/R/preprocessing.R
index 8f8f6cb8..93b3ad93 100644
--- a/scomps/R/preprocessing.R
+++ b/scomps/R/preprocessing.R
@@ -27,7 +27,8 @@ set_clip_extent <- function(pnts, buffer_r) {
 #' 
 #' @param rasterpath character(1). Path to the raster file.
 #' @param win Named integer vector (4) or terra::ext() results.
-#' @param author Insang Song 
+#' @return SpatRaster object.
+#' @author Insang Song 
 #' @export 
 rast_short <- function(rasterpath, win) {
   terra::rast(rasterpath, win = win)
diff --git a/scomps/R/processing.R b/scomps/R/processing.R
index 3b08a05c..00b3e1d3 100644
--- a/scomps/R/processing.R
+++ b/scomps/R/processing.R
@@ -90,8 +90,8 @@ extract_with_polygons <- function(
     polys, surf, id, func = mean, na.rm = TRUE
     ) {
     # type check
-    stopifnot("Check class of the input points.\n" = any(is(polys, "sf"), is(polys, "SpatVector")))
-    stopifnot("Check class of the input raster.\n" = any(is(surf, "stars"), is(surf, "SpatRaster")))
+    stopifnot("Check class of the input points.\n" = any(methods::is(polys, "sf"), methods::is(polys, "SpatVector")))
+    stopifnot("Check class of the input raster.\n" = any(methods::is(surf, "stars"), methods::is(surf, "SpatRaster")))
     stopifnot(is.character(id))
 
     cls_polys = check_packbound(polys)
@@ -113,9 +113,9 @@ extract_with_polygons <- function(
     extract_with_polygons.terra = function(polys, surf, id, func) {
         extracted = terra::extract(surf, polys)
         extracted = extracted |>
-          group_by(!!sym(id)) |>
-          summarize(across(-!!sym(id), ~func)) |>
-          ungroup()
+          dplyr::group_by(!!rlang::sym(id)) |>
+          dplyr::summarize(dplyr::across(-!!rlang::sym(id), ~func)) |>
+          dplyr::ungroup()
         return(extracted)
     }
 
@@ -157,7 +157,8 @@ extract_with <- function(raster, vector, id, func = mean, mode = "polygon", ...)
 #' Calculate SEDC covariates
 #' @param point_from SpatVector object. Locations where the sum of SEDCs are calculated.
 #' @param point_to SpatVector object. Locations where each SEDC is calculated.
-#' @param sdec_bandwidth numeric(1). Distance at which the source concentration is reduced to exp(-3) (approximately 95 %)  
+#' @param id character(1). Name of the unique id field in point_to.
+#' @param sedc_bandwidth numeric(1). Distance at which the source concentration is reduced to exp(-3) (approximately 95 %)  
 #' @param threshold numeric(1). For computational efficiency, the nearest points in threshold will be selected
 #' @param target_fields character(varying). Field names in characters.
 #' @description NOTE: sf implementation is pending. Only available for terra.
@@ -185,16 +186,16 @@ calculate_sedc <- function(point_from, point_to, id, sedc_bandwidth, threshold,
 
   # summary
   near_from_to = near_from_to |>
-    as_tibble() |>
-    left_join(data.frame(point_from)) |>
-    left_join(data.frame(point_to)) |>
-    left_join(dist_near_to_df) |>
+    dplyr::as_tibble() |>
+    dplyr::left_join(data.frame(point_from)) |>
+    dplyr::left_join(data.frame(point_to)) |>
+    dplyr::left_join(dist_near_to_df) |>
     # per the definition in https://mserre.sph.unc.edu/BMElab_web/SEDCtutorial/index.html
     # exp(-3) is about 0.05
-    mutate(w_sedc = exp((-3 * dist) / sedc_bandwidth)) |>
-    group_by(!!sym(id)) |>
-    summarize(across(all_of(target_fields), list(sedc = ~sum(w_sedc * ., na.rm = TRUE)))) |>
-    ungroup()
+    dplyr::mutate(w_sedc = exp((-3 * dist) / sedc_bandwidth)) |>
+    dplyr::group_by(!!rlang::sym(id)) |>
+    dplyr::summarize(dplyr::across(dplyr::all_of(target_fields), list(sedc = ~sum(w_sedc * ., na.rm = TRUE)))) |>
+    dplyr::ungroup()
 
   invisible(near_from_to)
   
@@ -213,13 +214,13 @@ calculate_sedc <- function(point_from, point_to, id, sedc_bandwidth, threshold,
 #' library(sf)
 #' 
 #' # run
-#' nc = st_read(system.file("shape/nc.shp", package="sf"))
-#' nc = st_transform(nc, 5070)
-#' pp = st_sample(nc, size = 300)
-#' pp = st_as_sf(pp)
+#' nc = sf::st_read(system.file("shape/nc.shp", package="sf"))
+#' nc = sf::st_transform(nc, 5070)
+#' pp = sf::st_sample(nc, size = 300)
+#' pp = sf::st_as_sf(pp)
 #' pp[["id"]] = seq(1, nrow(pp))
-#' st_crs(pp) = "EPSG:5070"
-#' ppb = st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
+#' sf::st_crs(pp) = "EPSG:5070"
+#' ppb = sf::st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
 #' 
 #' system.time({ppb_nc_aw = aw_covariates(ppb, nc, 'id')})
 #' summary(ppb_nc_aw)
@@ -227,7 +228,7 @@ calculate_sedc <- function(point_from, point_to, id, sedc_bandwidth, threshold,
 #' @export
 aw_covariates <- function(poly_in, poly_weight, id_poly_in = "ID") {
     stopifnot("Inputs have invalid classes.\n" = 
-      is(poly_in, "sf") || is(poly_weight, "sf") || is(poly_in, "SpatVector") || is(poly_weight, "SpatVector"))
+      methods::is(poly_in, "sf") || methods::is(poly_weight, "sf") || methods::is(poly_in, "SpatVector") || methods::is(poly_weight, "SpatVector"))
     #check_crs()
 
     ## distinguish numeric and nonnumeric columns
@@ -239,8 +240,8 @@ aw_covariates <- function(poly_in, poly_weight, id_poly_in = "ID") {
         poly_intersected[["area_segment_"]] = terra::expanse(poly_intersected)
         poly_intersected = data.frame(poly_intersected) |>
             dplyr::group_by(!!rlang::sym(id_poly_in)) |>
-            dplyr::summarize(across(is.numeric,
-                        ~weighted.mean(., w = area_segment_))) |>
+            dplyr::summarize(dplyr::across(is.numeric,
+                        ~stats::weighted.mean(., w = area_segment_))) |>
             dplyr::ungroup()
         return(poly_intersected)
     }
@@ -270,54 +271,6 @@ aw_covariates <- function(poly_in, poly_weight, id_poly_in = "ID") {
 #ncbufagg = terra::aggregate(ncbuf, by = 'id', fun = weighted.mean, w = ncbuf_a$segarea)
 
 
-#' Subfunction: extract with buffers (flat weight; simple mean)
-#' 
-#' @export 
-extract_with_buffer.flat <- function(
-        points, surf, radius, id, qsegs, func = mean, kernel = NULL, bandwidth = NULL
-    ) {
-    # generate buffers
-    bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
-    # crop raster
-    bufs_extent = terra::ext(bufs)
-    surf_cropped = terra::crop(surf, bufs_extent)
-    name_surf_val = names(surf)
-    # extract raster values
-    surf_at_bufs = terra::extract(surf_cropped, bufs)
-    surf_at_bufs_summary = 
-        surf_at_bufs |> 
-            group_by(ID) |> 
-            summarize(across(all_of(name_surf_val), ~mean, na.rm=T)) |> 
-            ungroup()
-    return(surf_at_bufs_summary)
-}
-
-#' Subfunction: extract with buffers (kernel weight; weighted mean)
-#'
-#' @export 
-extract_with_buffer.kernel <- function(
-        points, surf, radius, id, qsegs, func = mean, kernel, bandwidth
-    ) {
-        # generate buffers
-        bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
-        # crop raster
-        bufs_extent = terra::ext(bufs)
-        surf_cropped = terra::crop(surf, bufs_extent)
-        name_surf_val = names(surf)
-
-        # TODO: kernel implementation
-
-
-        # extract raster values
-        surf_at_bufs = terra::extract(surf_cropped, bufs)
-        surf_at_bufs_summary = 
-            surf_at_bufs |> 
-                group_by(ID) |> 
-                summarize(across(all_of(name_surf_val), ~mean, na.rm=T)) |> 
-                ungroup()
-        return(surf_at_bufs_summary)
-}
-
 #' @title Extract summarized values from raster with points and a buffer radius (to be written)
 #' 
 #' @description For simplicity, it is assumed that the coordinate systems of the points and the raster are the same. Kernel function is not yet implemented. 
@@ -337,7 +290,7 @@ extract_with_buffer <- function(
     points, surf, radius, id, qsegs = 90, func = mean, kernel = NULL, bandwidth = NULL
     ) {
     # type check
-    stopifnot("Check class of the input points.\n" = is(points, "SpatVector"))
+    stopifnot("Check class of the input points.\n" = methods::is(points, "SpatVector"))
     stopifnot("Check class of the input radius.\n" = is.numeric(radius))
     stopifnot(is.character(id))
     stopifnot(is.integer(qsegs))
@@ -364,5 +317,48 @@ extract_with_buffer <- function(
 
 }
 
+# Subfunction: extract with buffers (flat weight; simple mean)
+extract_with_buffer.flat <- function(
+        points, surf, radius, id, qsegs, func = mean, kernel = NULL, bandwidth = NULL
+    ) {
+    # generate buffers
+    bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
+    # crop raster
+    bufs_extent = terra::ext(bufs)
+    surf_cropped = terra::crop(surf, bufs_extent)
+    name_surf_val = names(surf)
+    # extract raster values
+    surf_at_bufs = terra::extract(surf_cropped, bufs)
+    surf_at_bufs_summary = 
+        surf_at_bufs |> 
+            dplyr::group_by(ID) |> 
+            dplyr::summarize(dplyr::across(dplyr::all_of(name_surf_val), ~mean, na.rm=T)) |> 
+            dplyr::ungroup()
+    return(surf_at_bufs_summary)
+}
+
+
+# Subfunction: extract with buffers (kernel weight; weighted mean)
+extract_with_buffer.kernel <- function(
+        points, surf, radius, id, qsegs, func = mean, kernel, bandwidth
+    ) {
+        # generate buffers
+        bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
+        # crop raster
+        bufs_extent = terra::ext(bufs)
+        surf_cropped = terra::crop(surf, bufs_extent)
+        name_surf_val = names(surf)
 
+        # TODO: kernel implementation
+
+
+        # extract raster values
+        surf_at_bufs = terra::extract(surf_cropped, bufs)
+        surf_at_bufs_summary = 
+            surf_at_bufs |> 
+                dplyr::group_by(ID) |> 
+                dplyr::summarize(dplyr::across(dplyr::all_of(name_surf_val), ~mean, na.rm=T)) |> 
+                dplyr::ungroup()
+        return(surf_at_bufs_summary)
+}
 
diff --git a/scomps/R/switch_format.R b/scomps/R/switch_format.R
index 6616caf1..a0c38e8f 100644
--- a/scomps/R/switch_format.R
+++ b/scomps/R/switch_format.R
@@ -7,7 +7,7 @@
 #' @return Data converted to the other package class (if sf, terra; if terra, sf)
 #' @export
 switch_packbound <- function(input) {
-  stopifnot("Input should be one of sf or Spat* object.\n" = any(is(input, "sf"), is(input, "stars"), is(input, "SpatVector"), is(input, "SpatRaster")))
+  stopifnot("Input should be one of sf or Spat* object.\n" = any(methods::is(input, "sf"), methods::is(input, "stars"), methods::is(input, "SpatVector"), methods::is(input, "SpatRaster")))
   cls_input = check_packbound(input)
   type_input = check_datatype(input)
 
diff --git a/scomps/man/aw_covariates.Rd b/scomps/man/aw_covariates.Rd
index 4604c030..ca836de6 100644
--- a/scomps/man/aw_covariates.Rd
+++ b/scomps/man/aw_covariates.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
+% Please edit documentation in R/processing.R
 \name{aw_covariates}
 \alias{aw_covariates}
 \title{Computing area weighted covariates using two polygon sf or SpatVector objects}
@@ -24,13 +24,13 @@ When poly_in and poly_weight are different classes, poly_weight will be converte
 library(sf)
 
 # run
-nc = st_read(system.file("shape/nc.shp", package="sf"))
-nc = st_transform(nc, 5070)
-pp = st_sample(nc, size = 300)
-pp = st_as_sf(pp)
+nc = sf::st_read(system.file("shape/nc.shp", package="sf"))
+nc = sf::st_transform(nc, 5070)
+pp = sf::st_sample(nc, size = 300)
+pp = sf::st_as_sf(pp)
 pp[["id"]] = seq(1, nrow(pp))
-st_crs(pp) = "EPSG:5070"
-ppb = st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
+sf::st_crs(pp) = "EPSG:5070"
+ppb = sf::st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
 
 system.time({ppb_nc_aw = aw_covariates(ppb, nc, 'id')})
 summary(ppb_nc_aw)
@@ -38,4 +38,4 @@ summary(ppb_nc_aw)
 }
 \author{
 Insang Song \email{geoissong@gmail.com}
-}
\ No newline at end of file
+}
diff --git a/scomps/man/calculate_sedc.Rd b/scomps/man/calculate_sedc.Rd
index 0a164fbf..21178a77 100644
--- a/scomps/man/calculate_sedc.Rd
+++ b/scomps/man/calculate_sedc.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
+% Please edit documentation in R/processing.R
 \name{calculate_sedc}
 \alias{calculate_sedc}
 \title{Calculate SEDC covariates}
@@ -18,15 +18,17 @@ calculate_sedc(
 
 \item{point_to}{SpatVector object. Locations where each SEDC is calculated.}
 
+\item{id}{character(1). Name of the unique id field in point_to.}
+
+\item{sedc_bandwidth}{numeric(1). Distance at which the source concentration is reduced to exp(-3) (approximately 95 \%)}
+
 \item{threshold}{numeric(1). For computational efficiency, the nearest points in threshold will be selected}
 
 \item{target_fields}{character(varying). Field names in characters.}
-
-\item{sdec_bandwidth}{numeric(1). Distance at which the source concentration is reduced to exp(-3) (approximately 95 \%)}
 }
 \description{
 NOTE: sf implementation is pending. Only available for terra.
 }
 \author{
 Insang Song
-}
\ No newline at end of file
+}
diff --git a/scomps/man/check_bbox.Rd b/scomps/man/check_bbox.Rd
index f5d0fbde..444c934a 100644
--- a/scomps/man/check_bbox.Rd
+++ b/scomps/man/check_bbox.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
+% Please edit documentation in R/check.R
 \name{check_bbox}
 \alias{check_bbox}
 \title{Check if the data extent is inside the reference bounding box}
@@ -21,4 +21,4 @@ One of the most common errors in spatial computation is rooted in the entirely o
 }
 \author{
 Insang Song \email{geoissong@gmail.com}
-}
\ No newline at end of file
+}
diff --git a/scomps/man/check_crs.Rd b/scomps/man/check_crs.Rd
index ad8edfa3..6f9fa5b5 100644
--- a/scomps/man/check_crs.Rd
+++ b/scomps/man/check_crs.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
+% Please edit documentation in R/check.R
 \name{check_crs}
 \alias{check_crs}
 \title{Check Coordinate Reference System}
@@ -25,4 +25,4 @@ check_crs(nc)
 }
 \author{
 Insang Song \email{geoissong@gmail.com}
-}
\ No newline at end of file
+}
diff --git a/scomps/man/check_crs2.Rd b/scomps/man/check_crs2.Rd
index b4020d6f..c15652d6 100644
--- a/scomps/man/check_crs2.Rd
+++ b/scomps/man/check_crs2.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
+% Please edit documentation in R/check.R
 \name{check_crs2}
 \alias{check_crs2}
 \title{check_crs2: Coordinate system checker}
@@ -8,10 +8,12 @@ check_crs2(input, crs_standard = "EPSG:4326")
 }
 \arguments{
 \item{input}{Input object one of sf or terra::Spat* object}
+
+\item{crs_standard}{character(1). A standard definition of coordinate reference system. Default is "EPSG:4326" Consult \href{https://epsg.io}{epsg.io} for details of other CRS.}
 }
 \value{
 A (reprojected) sf or SpatVector object.
 }
 \description{
 The input is checked whether its coordinate system is present. If not, it is reprojected to EPSG:5179.
-}
\ No newline at end of file
+}
diff --git a/scomps/man/check_packbound.Rd b/scomps/man/check_packbound.Rd
index d2fcc528..6bda7485 100644
--- a/scomps/man/check_packbound.Rd
+++ b/scomps/man/check_packbound.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
+% Please edit documentation in R/check.R
 \name{check_packbound}
 \alias{check_packbound}
 \title{Return the package the input object is based on}
@@ -17,4 +17,4 @@ Detect whether the input object is sf or Spat* object.
 }
 \author{
 Insang Song
-}
\ No newline at end of file
+}
diff --git a/scomps/man/check_within_reference.Rd b/scomps/man/check_within_reference.Rd
index 493f1f8c..c193a975 100644
--- a/scomps/man/check_within_reference.Rd
+++ b/scomps/man/check_within_reference.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
+% Please edit documentation in R/check.R
 \name{check_within_reference}
 \alias{check_within_reference}
 \title{Check if the boundary of the vector/raster object is inside the reference}
@@ -19,4 +19,4 @@ Check if the boundary of the vector/raster object is inside the reference
 }
 \author{
 Insang Song \email{geoissong@gmail.com}
-}
\ No newline at end of file
+}
diff --git a/scomps/man/clip_as_extent.Rd b/scomps/man/clip_as_extent.Rd
index 00eaa5fa..06ec0bbf 100644
--- a/scomps/man/clip_as_extent.Rd
+++ b/scomps/man/clip_as_extent.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
+% Please edit documentation in R/processing.R
 \name{clip_as_extent}
 \alias{clip_as_extent}
 \title{Extent clipping}
@@ -23,4 +23,4 @@ Clip input vector by the expected maximum extent of computation.
 }
 \author{
 Insang Song
-}
\ No newline at end of file
+}
diff --git a/scomps/man/clip_as_extent_ras.Rd b/scomps/man/clip_as_extent_ras.Rd
index 3e756887..e6762901 100644
--- a/scomps/man/clip_as_extent_ras.Rd
+++ b/scomps/man/clip_as_extent_ras.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
+% Please edit documentation in R/processing.R
 \name{clip_as_extent_ras}
 \alias{clip_as_extent_ras}
 \title{clip_as_extent_ras: Clip input raster.}
@@ -20,4 +20,4 @@ Clip input raster by the expected maximum extent of computation.
 }
 \author{
 Insang Song
-}
\ No newline at end of file
+}
diff --git a/scomps/man/clip_as_extent_ras2.Rd b/scomps/man/clip_as_extent_ras2.Rd
index 8aa6a6d7..6d8c0e00 100644
--- a/scomps/man/clip_as_extent_ras2.Rd
+++ b/scomps/man/clip_as_extent_ras2.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
+% Please edit documentation in R/processing.R
 \name{clip_as_extent_ras2}
 \alias{clip_as_extent_ras2}
 \title{clip_as_extent_ras2: Clip input raster (version 2).}
@@ -20,4 +20,4 @@ Clip input raster by the expected maximum extent of computation.
 }
 \author{
 Insang Song
-}
\ No newline at end of file
+}
diff --git a/scomps/man/distribute_process.Rd b/scomps/man/distribute_process.Rd
index b5403e59..ebb58e82 100644
--- a/scomps/man/distribute_process.Rd
+++ b/scomps/man/distribute_process.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
+% Please edit documentation in R/interpret_computational_domain.R
 \name{distribute_process}
 \alias{distribute_process}
 \title{Process a given function in the entire or partial computational grids (under construction)}
@@ -9,7 +9,7 @@ distribute_process(grids, grid_id = NULL, fun, ...)
 \arguments{
 \item{grids}{sf/SpatVector object. Computational grids.}
 
-\item{grid_id}{character(1) or numeric(2). Default is NULL. If NULL, all grid_ids are used. "id_from:id_to" format or c(unique(grid_id)\link{id_from}, unique(grid_id)\link{id_to})}
+\item{grid_id}{character(1) or numeric(2). Default is NULL. If NULL, all grid_ids are used. \code{"id_from:id_to"} format or \code{c(unique(grid_id)[id_from], unique(grid_id)[id_to])}}
 
 \item{fun}{function supported in scomps.}
 
@@ -23,4 +23,4 @@ Should
 }
 \author{
 Insang Song \email{geoissong@gmail.com}
-}
\ No newline at end of file
+}
diff --git a/scomps/man/estimate_demands.Rd b/scomps/man/estimate_demands.Rd
index e269257e..787ad77f 100644
--- a/scomps/man/estimate_demands.Rd
+++ b/scomps/man/estimate_demands.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
+% Please edit documentation in R/estimate_demands.R
 \name{estimate_demands}
 \alias{estimate_demands}
 \title{Estimate computational demands from inputs (to be written)}
@@ -17,4 +17,7 @@ estimate_demands(inputs, nx, ny, padding)
 }
 \description{
 Estimate computational demands from inputs (to be written)
-}
\ No newline at end of file
+}
+\author{
+Insang Song
+}
diff --git a/scomps/man/extent_to_polygon.Rd b/scomps/man/extent_to_polygon.Rd
new file mode 100644
index 00000000..2874461e
--- /dev/null
+++ b/scomps/man/extent_to_polygon.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/check.R
+\name{extent_to_polygon}
+\alias{extent_to_polygon}
+\title{Generate a rectangular polygon from extent}
+\usage{
+extent_to_polygon(extent, output_class = "terra", crs = "EPSG:4326")
+}
+\arguments{
+\item{extent}{input extent. A numeric vector with xmin/xmax/ymin/ymax, sf::st_bbox() or terra::ext() outputs.}
+
+\item{output_class}{character(1). Class of the output polygon. One of "sf" or "terra"}
+
+\item{crs}{character(1). Coordinate reference system definition.}
+}
+\description{
+Generate a rectangular polygon from extent
+}
+\author{
+Insang Song
+}
diff --git a/scomps/man/extract_with.Rd b/scomps/man/extract_with.Rd
index d95b9bbb..8794f571 100644
--- a/scomps/man/extract_with.Rd
+++ b/scomps/man/extract_with.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
+% Please edit documentation in R/processing.R
 \name{extract_with}
 \alias{extract_with}
 \title{Extract raster values with point buffers or polygons}
@@ -24,4 +24,4 @@ Extract raster values with point buffers or polygons
 }
 \author{
 Insang Song \email{geoissong@gmail.com}
-}
\ No newline at end of file
+}
diff --git a/scomps/man/extract_with_buffer.Rd b/scomps/man/extract_with_buffer.Rd
index 662fc6e6..f0c3943d 100644
--- a/scomps/man/extract_with_buffer.Rd
+++ b/scomps/man/extract_with_buffer.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
+% Please edit documentation in R/processing.R
 \name{extract_with_buffer}
 \alias{extract_with_buffer}
 \title{Extract summarized values from raster with points and a buffer radius (to be written)}
@@ -40,4 +40,4 @@ For simplicity, it is assumed that the coordinate systems of the points and the
 }
 \author{
 Insang Song \email{geoissong@gmail.com}
-}
\ No newline at end of file
+}
diff --git a/scomps/man/extract_with_buffer.flat.Rd b/scomps/man/extract_with_buffer.flat.Rd
deleted file mode 100644
index 15215897..00000000
--- a/scomps/man/extract_with_buffer.flat.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
-\name{extract_with_buffer.flat}
-\alias{extract_with_buffer.flat}
-\title{Subfunction: extract with buffers (flat weight; simple mean)}
-\usage{
-extract_with_buffer.flat(
-  points,
-  surf,
-  radius,
-  id,
-  qsegs,
-  func = mean,
-  kernel = NULL,
-  bandwidth = NULL
-)
-}
-\description{
-Subfunction: extract with buffers (flat weight; simple mean)
-}
\ No newline at end of file
diff --git a/scomps/man/extract_with_buffer.kernel.Rd b/scomps/man/extract_with_buffer.kernel.Rd
deleted file mode 100644
index f00f2640..00000000
--- a/scomps/man/extract_with_buffer.kernel.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
-\name{extract_with_buffer.kernel}
-\alias{extract_with_buffer.kernel}
-\title{Subfunction: extract with buffers (kernel weight; weighted mean)}
-\usage{
-extract_with_buffer.kernel(
-  points,
-  surf,
-  radius,
-  id,
-  qsegs,
-  func = mean,
-  kernel,
-  bandwidth
-)
-}
-\description{
-Subfunction: extract with buffers (kernel weight; weighted mean)
-}
\ No newline at end of file
diff --git a/scomps/man/extract_with_polygons.Rd b/scomps/man/extract_with_polygons.Rd
index ca56635e..adaa9c6a 100644
--- a/scomps/man/extract_with_polygons.Rd
+++ b/scomps/man/extract_with_polygons.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
+% Please edit documentation in R/processing.R
 \name{extract_with_polygons}
 \alias{extract_with_polygons}
 \title{Extract summarized values from raster with generic polygons}
@@ -25,4 +25,4 @@ For simplicity, it is assumed that the coordinate systems of the points and the
 }
 \author{
 Insang Song \email{geoissong@gmail.com}
-}
\ No newline at end of file
+}
diff --git a/scomps/man/get_computational_regions.Rd b/scomps/man/get_computational_regions.Rd
index 91f578d9..6a864a55 100644
--- a/scomps/man/get_computational_regions.Rd
+++ b/scomps/man/get_computational_regions.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
+% Please edit documentation in R/interpret_computational_domain.R
 \name{get_computational_regions}
 \alias{get_computational_regions}
 \title{Get a set of computational regions}
@@ -28,7 +28,9 @@ get_computational_regions(
 
 \item{padding}{numeric(1). A extrusion factor to make buffer to clip actual datasets. Depending on the length unit of the CRS of input.}
 
-\item{unit}{character(1). The length unit for padding (optional). units::set_units is used for padding when sf object is used. See \link{units package vignette (web)}{https://cran.r-project.org/web/packages/units/vignettes/measurement_units_in_R.html} for the list of acceptable unit forms.}
+\item{unit}{character(1). The length unit for padding (optional). units::set_units is used for padding when sf object is used. See \href{https://cran.r-project.org/web/packages/units/vignettes/measurement_units_in_R.html}{units package vignette (web)} for the list of acceptable unit forms.}
+
+\item{...}{arguments passed to the internal function}
 }
 \value{
 A set of polygons in the input class
@@ -48,4 +50,4 @@ nc = st_transform(nc, "EPSG:5070")
 }
 \author{
 Insang Song
-}
\ No newline at end of file
+}
diff --git a/scomps/man/grid_merge.Rd b/scomps/man/grid_merge.Rd
index 614e7ba9..0361cece 100644
--- a/scomps/man/grid_merge.Rd
+++ b/scomps/man/grid_merge.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
+% Please edit documentation in R/interpret_computational_domain.R
 \name{grid_merge}
 \alias{grid_merge}
 \title{grid_merge: Merge grid polygons with given rules}
@@ -23,16 +23,16 @@ Merge boundary-sharing (in "Rook" contiguity) grids with fewer target features t
 # library(sf)
 # library(igraph)
 # ligrary(dplyr)
-# dg = st_as_sfc(st_bbox(c(xmin = 0, ymin = 0, xmax = 8e5, ymax = 6e5)))
-# st_crs(dg) = 5070
-# dgs = st_as_sf(st_make_grid(dg, n = c(20, 15)))
+# dg = sf::st_as_sfc(st_bbox(c(xmin = 0, ymin = 0, xmax = 8e5, ymax = 6e5)))
+# sf::st_crs(dg) = 5070
+# dgs = sf::st_as_sf(st_make_grid(dg, n = c(20, 15)))
 # dgs$CGRIDID = seq(1, nrow(dgs))
 #
 # dg_sample = st_sample(dg, kappa = 5e-9, mu = 15, scale = 20000, type = "Thomas")
-# st_crs(dg_sample) = st_crs(dg)
-# dg_merged = grid_merge(st_as_sf(sss), dgs, 100)
+# sf::st_crs(dg_sample) = sf::st_crs(dg)
+# dg_merged = grid_merge(sf::st_as_sf(sss), dgs, 100)
 #### NOT RUN ####
 }
 \author{
 Insang Song
-}
\ No newline at end of file
+}
diff --git a/scomps/man/initate_log.Rd b/scomps/man/initate_log.Rd
index a4f1fb02..6e64c090 100644
--- a/scomps/man/initate_log.Rd
+++ b/scomps/man/initate_log.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
+% Please edit documentation in R/logging.R
 \name{initate_log}
 \alias{initate_log}
 \title{Turn on logging}
@@ -21,4 +21,4 @@ Turn on logging
 }
 \author{
 Insang Song
-}
\ No newline at end of file
+}
diff --git a/scomps/man/rast_short.Rd b/scomps/man/rast_short.Rd
index 02a91ccb..de4acd9f 100644
--- a/scomps/man/rast_short.Rd
+++ b/scomps/man/rast_short.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
+% Please edit documentation in R/preprocessing.R
 \name{rast_short}
 \alias{rast_short}
 \title{Quick call for SpatRaster with a window}
@@ -10,9 +10,13 @@ rast_short(rasterpath, win)
 \item{rasterpath}{character(1). Path to the raster file.}
 
 \item{win}{Named integer vector (4) or terra::ext() results.}
-
-\item{author}{Insang Song}
+}
+\value{
+SpatRaster object.
 }
 \description{
 Quick call for SpatRaster with a window
-}
\ No newline at end of file
+}
+\author{
+Insang Song
+}
diff --git a/scomps/man/set_clip_extent.Rd b/scomps/man/set_clip_extent.Rd
index 5d9267d4..4fb91191 100644
--- a/scomps/man/set_clip_extent.Rd
+++ b/scomps/man/set_clip_extent.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
+% Please edit documentation in R/preprocessing.R
 \name{set_clip_extent}
 \alias{set_clip_extent}
 \title{Setting the clipping extent}
@@ -19,4 +19,4 @@ Return clipping extent with buffer radius. It assumes the input CRS is projected
 }
 \author{
 Insang Song
-}
\ No newline at end of file
+}
diff --git a/scomps/man/sp_index_grid.Rd b/scomps/man/sp_index_grid.Rd
index 9a492214..bf0d4ac5 100644
--- a/scomps/man/sp_index_grid.Rd
+++ b/scomps/man/sp_index_grid.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
+% Please edit documentation in R/interpret_computational_domain.R
 \name{sp_index_grid}
 \alias{sp_index_grid}
 \title{sp_index_grid: Generate grid polygons}
@@ -21,4 +21,4 @@ Returns a sf object that includes x- and y- index by using two inputs ncutsx and
 }
 \author{
 Insang Song
-}
\ No newline at end of file
+}
diff --git a/scomps/man/sp_indexing.Rd b/scomps/man/sp_indexing.Rd
index 56dccd96..f4da1434 100644
--- a/scomps/man/sp_indexing.Rd
+++ b/scomps/man/sp_indexing.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
+% Please edit documentation in R/indexing.R
 \name{sp_indexing}
 \alias{sp_indexing}
 \title{Create integer indices for grid}
@@ -18,4 +18,4 @@ Returns a tibble object that includes x- and y- index by using two inputs ncutsx
 }
 \author{
 Insang Song
-}
\ No newline at end of file
+}
diff --git a/scomps/man/switch_packbound.Rd b/scomps/man/switch_packbound.Rd
index 084fb468..18eafb22 100644
--- a/scomps/man/switch_packbound.Rd
+++ b/scomps/man/switch_packbound.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
+% Please edit documentation in R/switch_format.R
 \name{switch_packbound}
 \alias{switch_packbound}
 \title{Switch spatial data class}
@@ -17,4 +17,4 @@ Convert stars into SpatRaster and vice versa; sf into SpatVector and vice versa.
 }
 \author{
 Insang Song
-}
\ No newline at end of file
+}
diff --git a/scomps/man/validate_and_repair_vectors.Rd b/scomps/man/validate_and_repair_vectors.Rd
index 539ef863..e8447ca9 100644
--- a/scomps/man/validate_and_repair_vectors.Rd
+++ b/scomps/man/validate_and_repair_vectors.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in scomps_rmarkdown_litr.rmd.
+% Please edit documentation in R/validate.R
 \name{validate_and_repair_vectors}
 \alias{validate_and_repair_vectors}
 \title{Validate and repair input vector data}
@@ -17,4 +17,4 @@ It tries repairing input vector data. Vector validity violation usually appears
 }
 \author{
 Insang Song
-}
\ No newline at end of file
+}
diff --git a/scomps/vignettes/v00_good_practice_parallelization.Rmd b/scomps/vignettes/v00_good_practice_parallelization.Rmd
new file mode 100644
index 00000000..8966a59d
--- /dev/null
+++ b/scomps/vignettes/v00_good_practice_parallelization.Rmd
@@ -0,0 +1,39 @@
+---
+title: "Good practice of scomps with HPC"
+date: "`r Sys.Date()`"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{good_practice_hpc}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+
+```{r}
+knitr::opts_chunk$set(warning = FALSE, message = FALSE)
+
+```
+
+## Assumptions
+- Users have an accessible HPC at your work
+- Data are stored in distributed file systems (usually incorporated into the HPC system)
+
+
+## Basic workflow
+
+### Practice for minimizing errors
+- Consider using `try()` or `tryCatch()` not to a tiny error will halt all the work without any results 
+    - Especially with the higher-level functions
+- "IPDE -- Inspect, Predict, Decide, Execute" all the time
+
+### Raster-Vector overlay
+- Make `sp_index_grid()` to get padded grid objects
+- Convert sf/SpatVector objects into `terra::ext()` compatible named numeric vector
+    - For example: `c(xmin=0, ymin=0, xmax=10, ymax=10)`
+- Make list objects with: 
+    - An extent vector in each element
+    - Preprocessed vector objects with respect to each extent vector in the first list
+    - Preferably all lists are named 
+- Write a `future.apply` script running through the extent list object
+- Run a small amount of data to estimate the total computational demand
+- Submit a job with a proper amount of computational assets
diff --git a/scomps/vignettes/v01_generate_computational_grid.Rmd b/scomps/vignettes/v01_generate_computational_grid.Rmd
new file mode 100644
index 00000000..4bc1aaf2
--- /dev/null
+++ b/scomps/vignettes/v01_generate_computational_grid.Rmd
@@ -0,0 +1,46 @@
+---
+title: "Generate computational grids"
+date: "`r Sys.Date()`"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{computational_grids}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+
+```{r}
+knitr::opts_chunk$set(warning = FALSE, message = FALSE)
+
+```
+
+
+## Prepare input data
+```{r}
+library(scomps)
+library(sf)
+library(terra)
+library(stars)
+library(dplyr)
+
+```
+
+## Computational grids
+```{r}
+# your_grid = scomps::sp_index_grid()
+
+```
+
+
+## Visualize computational grids
+```{r}
+# library(mapsf)
+# mf_map(your_grid$geometry)
+
+
+```
+
+
+
+## Notes
+- Computational grids are the exhaustive split of the entire study region. You should take a square buffer of each grid to clip the target raster or vector.
diff --git a/scomps_rmarkdown_litr.html b/scomps_rmarkdown_litr.html
index 55aba55e..44adce73 100644
--- a/scomps_rmarkdown_litr.html
+++ b/scomps_rmarkdown_litr.html
@@ -11,7 +11,7 @@
 
 
 
-
+
 
 Creating the scomps R package
 
@@ -353,7 +353,7 @@
 
Creating the scomps R
 package

 
Insang Song

-
2023-09-03

+
2023-10-04

 
 
 
@@ -368,7 +368,7 @@ 
Package setup

   path = ".",
   fields = list(
     Package = params$package_name,
-    Version = "0.0.2.10032023",
+    Version = "0.0.3.10042023",
     Title = "Scalable R geospatial computation",
     Description = "A package for scalable geospatial computation for environmental health research",
     `Authors@R` = person(
@@ -388,6 +388,8 @@ 
Package setup

 usethis::use_package("stars")
 usethis::use_package("rlang") # Default is "Imports"
 usethis::use_package("testthat")
+usethis::use_package("units")
+usethis::use_package("methods")
 usethis::use_package("logr", "Suggests") # Default is "Imports"
 usethis::use_package("future") # Default is "Imports"
 usethis::use_package("future.apply") # Default is "Imports"
@@ -407,11 +409,11 @@ 
Package setup

Vignettes 1

-
litr::add_vignettes("../tools/vignettes-sources/00_good_practice_parallelization.Rmd")
+
litr::add_vignettes("../tools/vignettes-sources/v00_good_practice_parallelization.Rmd")

Vignettes 2

-
litr::add_vignettes("../tools/vignettes-sources/01_generate_computational_grid.Rmd")
+
litr::add_vignettes("../tools/vignettes-sources/v01_generate_computational_grid.Rmd")
@@ -426,19 +428,19 @@

Create functions

#' @export check_packbound <- function(input) { # cl_inobj = class(input)[1] - stopifnot("Input should be one of sf or Spat* object.\n" = any(is(input, "sf"), is(input, "stars"), is(input, "SpatVector"), is(input, "SpatRaster"))) - if (is(input, "SpatVector") || is(input, "SpatRaster")) { + stopifnot("Input should be one of sf or Spat* object.\n" = any(methods::is(input, "sf"), methods::is(input, "stars"), methods::is(input, "SpatVector"), methods::is(input, "SpatRaster"))) + if (methods::is(input, "SpatVector") || methods::is(input, "SpatRaster")) { return("terra") } return("sf") } check_datatype <- function(input) { - stopifnot("Input should be one of sf or Spat* object.\n" = any(is(input, "sf"), is(input, "stars"), is(input, "SpatVector"), is(input, "SpatRaster"))) - if (any(is(input, "SpatVector"), is(input, "sf"))) { + stopifnot("Input should be one of sf or Spat* object.\n" = any(methods::is(input, "sf"), methods::is(input, "stars"), methods::is(input, "SpatVector"), methods::is(input, "SpatRaster"))) + if (any(methods::is(input, "SpatVector"), methods::is(input, "sf"))) { return("vector") } - if (any(is(input, "SpatRaster"), is(input, "stars"))) { + if (any(methods::is(input, "SpatRaster"), methods::is(input, "stars"))) { return("raster") } } @@ -487,7 +489,7 @@

Create functions

#' @return Data converted to the other package class (if sf, terra; if terra, sf) #' @export switch_packbound <- function(input) { - stopifnot("Input should be one of sf or Spat* object.\n" = any(is(input, "sf"), is(input, "stars"), is(input, "SpatVector"), is(input, "SpatRaster"))) + stopifnot("Input should be one of sf or Spat* object.\n" = any(methods::is(input, "sf"), methods::is(input, "stars"), methods::is(input, "SpatVector"), methods::is(input, "SpatRaster"))) cls_input = check_packbound(input) type_input = check_datatype(input) @@ -536,11 +538,12 @@

Create functions

#' @title check_crs2: Coordinate system checker
 #' @description The input is checked whether its coordinate system is present. If not, it is reprojected to EPSG:5179.
 #' @param input Input object one of sf or terra::Spat* object
+#' @param crs_standard character(1). A standard definition of coordinate reference system. Default is "EPSG:4326" Consult [epsg.io](https://epsg.io) for details of other CRS.
 #' @return A (reprojected) sf or SpatVector object.
 #' @export
 check_crs2 <- function(input, crs_standard = "EPSG:4326") {
   check_crs.sf <- function(input){
-    if (is.na(st_crs(input))){cat('Please check the coordinate system or its EPSG code of your input object.'); return(NULL)}
+    if (is.na(sf::st_crs(input))){cat('Please check the coordinate system or its EPSG code of your input object.'); return(NULL)}
     if (sf::st_crs(input)$epsg == crs_standard ) {
       return(input)
     } 
@@ -697,7 +700,7 @@ 
Create functions

 sp_indexing <- function(points_in, ncutsx, ncutsy){
   # pts <- data.table(pnts)
   points_in <- points_in |>
-    mutate(or_id = seq(1, dim(points_in)[1]))
+    dplyr::mutate(or_id = seq(1, dim(points_in)[1]))
   
   range_x  <- range(points_in$x)
   limits_x <- (range_x[1] + seq(0, ncutsx) * (range_x[2] - range_x[1]) / ncutsx)
@@ -705,7 +708,7 @@ 
Create functions

   limits_y <- (range_y[1] + seq(0, ncutsy) * (range_y[2] - range_y[1]) / ncutsy)
   
   points_in_cut <- points_in |>
-    mutate(xcut =  as.integer(cut(x, ncutsx, labels = seq(1, ncutsx))),
+    dplyr::mutate(xcut =  as.integer(cut(x, ncutsx, labels = seq(1, ncutsx))),
            ycut = as.integer(cut(y, ncutsy, labels = seq(1, ncutsy))))
   
   return(points_in_cut)
@@ -714,7 +717,8 @@ 
Create functions

 #' 
 #' @param rasterpath character(1). Path to the raster file.
 #' @param win Named integer vector (4) or terra::ext() results.
-#' @param author Insang Song 
+#' @return SpatRaster object.
+#' @author Insang Song 
 #' @export 
 rast_short <- function(rasterpath, win) {
   terra::rast(rasterpath, win = win)
@@ -726,6 +730,7 @@ 
Create functions

 #' @param nx integer(1). 
 #' @param ny integer(1). 
 #' @param padding numeric(1). Extrusion factor 
+#' @author Insang Song
 #' @export 
 estimate_demands <- function(
   inputs,
@@ -749,7 +754,8 @@ 
Create functions

 #' @param ny integer(1). The number of grids along y-axis.
 #' @param grid_min_features integer(1). A threshold to merging adjacent grids
 #' @param padding numeric(1). A extrusion factor to make buffer to clip actual datasets. Depending on the length unit of the CRS of input.
-#' @param unit character(1). The length unit for padding (optional). units::set_units is used for padding when sf object is used. See \link{units package vignette (web)}{https://cran.r-project.org/web/packages/units/vignettes/measurement_units_in_R.html} for the list of acceptable unit forms.
+#' @param unit character(1). The length unit for padding (optional). units::set_units is used for padding when sf object is used. See [units package vignette (web)](https://cran.r-project.org/web/packages/units/vignettes/measurement_units_in_R.html) for the list of acceptable unit forms.
+#' @param ... arguments passed to the internal function
 #' @return A set of polygons in the input class
 #' @description TODO. Using input points, the bounding box is split to the predefined numbers of columns and rows. Each grid will be buffered by the radius.   
 #' @author Insang Song 
@@ -793,7 +799,7 @@ 
Create functions

   sp_index_grid.sf = function(points_in, ncutsx, ncutsy) {
     grid1 <- sf::st_make_grid(points_in, n = c(ncutsx, ncutsy)) |> 
       as.data.frame() |> 
-      st_as_sf()
+      sf::st_as_sf()
     grid1 <- grid1[points_in, ]
     return(grid1)
   }
@@ -823,14 +829,14 @@ 
Create functions

 #' # library(sf)
 #' # library(igraph)
 #' # ligrary(dplyr)
-#' # dg = st_as_sfc(st_bbox(c(xmin = 0, ymin = 0, xmax = 8e5, ymax = 6e5)))
-#' # st_crs(dg) = 5070
-#' # dgs = st_as_sf(st_make_grid(dg, n = c(20, 15)))
+#' # dg = sf::st_as_sfc(st_bbox(c(xmin = 0, ymin = 0, xmax = 8e5, ymax = 6e5)))
+#' # sf::st_crs(dg) = 5070
+#' # dgs = sf::st_as_sf(st_make_grid(dg, n = c(20, 15)))
 #' # dgs$CGRIDID = seq(1, nrow(dgs))
 #' #
 #' # dg_sample = st_sample(dg, kappa = 5e-9, mu = 15, scale = 20000, type = "Thomas")
-#' # st_crs(dg_sample) = st_crs(dg)
-#' # dg_merged = grid_merge(st_as_sf(sss), dgs, 100)
+#' # sf::st_crs(dg_sample) = sf::st_crs(dg)
+#' # dg_merged = grid_merge(sf::st_as_sf(sss), dgs, 100)
 #' #### NOT RUN ####
 #' @export
 grid_merge <- function(points_in, grid_in, grid_min_features){
@@ -854,7 +860,7 @@ 
Create functions

   identified = unique(identified)
   identified = identified[sapply(identified, length) > 1]
 
-  identified_graph = lapply(identified, \(x) t(combn(x, 2))) |>
+  identified_graph = lapply(identified, \(x) t(utils::combn(x, 2))) |>
     Reduce(f = rbind, x = _) |>
     unique() |>
     apply(X = _, 2, as.character) |>
@@ -878,8 +884,8 @@ 
Create functions

   #   grid_out[["CGRIDID"]][target_idx] = paste("M_", paste(target_idx, collapse = "_"), sep = "")
   # }
   grid_out = grid_out |>
-    dplyr::group_by(CGRIDID) |>
-    dplyr::summarize(n_merged = n()) |>
+    dplyr::group_by(!!rlang::sym("CGRIDID")) |>
+    dplyr::summarize(n_merged = dplyr::n()) |>
     dplyr::ungroup() 
 
   ## polsby-popper test for shape compactness
@@ -910,6 +916,44 @@ 
Create functions

 }
 
 
+
+
#' Generate a rectangular polygon from extent
+#' 
+#' @param extent input extent. A numeric vector with xmin/xmax/ymin/ymax, sf::st_bbox() or terra::ext() outputs.
+#' @param output_class character(1). Class of the output polygon. One of "sf" or "terra"
+#' @param crs character(1). Coordinate reference system definition.
+#' @author Insang Song
+#' @export
+extent_to_polygon <- function(extent, output_class = "terra", crs = "EPSG:4326") {
+  if (!output_class %in% c("sf", "terra")) {
+    stop("output_class should be one of 'sf' or 'terra'.\n")
+  }
+  if (methods::is(extent, "numeric")) {
+    if (is.null(attr(extent, "names"))) {
+      stop("Your extent is an unnamed numeric vector. Please define names xmin/xmax/ymin/ymax explicitly.\n")
+    }
+    extent = switch(
+      output_class,
+      sf = sf::st_bbox(extent),
+      terra = terra::ext(extent)
+    )
+  }
+
+  extent_polygon = switch(
+    output_class,
+    sf = sf::st_as_sfc(extent),
+    terra = terra::vect(extent)
+  )
+
+  extent_polygon = switch(
+    output_class,
+    sf = sf::st_set_crs(extent_polygon, sf::st_crs(crs)),
+    terra = terra::set.crs(extent_polygon, terra::crs(crs))
+  )
+
+  return(extent_polygon)
+  
+}
 
#' Check if the data extent is inside the reference bounding box
 #' 
@@ -935,25 +979,14 @@ 
Create functions

   if (is.na(query_crs) || is.null(query_crs)) {
     stop("The dataset you queried has no CRS. Please make sure your dataset has the correct CRS.\n")
   }
+  query_matched = sf::st_transform(data_query, sf::st_crs(ref_crs))
+
 
-  # ...
 
-  check_result
+  check_result = sf::st_within()
   return(check_result)
 }
 
-
-
#' Check if the data extent is inside the reference bounding box
-#' 
-#' @description One of the most common errors in spatial computation is rooted in the entirely or partly incomparable spatial extents of input datasets. This function returns whether your data is inside the target computational extent. It is assumed that you know and have the exact computational region. This function will return TRUE if the reference region completely contains your data's extent and FALSE otherwise.
-#' @param data_query sf*/stars/SpatVector/SpatRaster object.
-#' @param reference sf*/stars/SpatVector/SpatRaster object or a named numeric vector with four names (xmin, ymin, xmax, and ymax).
-#' @param reference_crs Well-known-text-formatted or EPSG code of the reference's coordinate system. Only required when a named numeric vector is passed to reference. 
-#' @return TRUE (the queried data extent is completely within the reference bounding box) or FALSE 
-#' @author Insang Song \email{geoissong@@gmail.com}
-#' 
-#' @export
-
 
#' @title Extract summarized values from raster with generic polygons
 #' 
@@ -971,8 +1004,8 @@ 
Create functions

     polys, surf, id, func = mean, na.rm = TRUE
     ) {
     # type check
-    stopifnot("Check class of the input points.\n" = any(is(polys, "sf"), is(polys, "SpatVector")))
-    stopifnot("Check class of the input raster.\n" = any(is(surf, "stars"), is(surf, "SpatRaster")))
+    stopifnot("Check class of the input points.\n" = any(methods::is(polys, "sf"), methods::is(polys, "SpatVector")))
+    stopifnot("Check class of the input raster.\n" = any(methods::is(surf, "stars"), methods::is(surf, "SpatRaster")))
     stopifnot(is.character(id))
 
     cls_polys = check_packbound(polys)
@@ -994,9 +1027,9 @@ 
Create functions

     extract_with_polygons.terra = function(polys, surf, id, func) {
         extracted = terra::extract(surf, polys)
         extracted = extracted |>
-          group_by(!!sym(id)) |>
-          summarize(across(-!!sym(id), ~func)) |>
-          ungroup()
+          dplyr::group_by(!!rlang::sym(id)) |>
+          dplyr::summarize(dplyr::across(-!!rlang::sym(id), ~func)) |>
+          dplyr::ungroup()
         return(extracted)
     }
 
@@ -1047,9 +1080,9 @@ 
Create functions

 #' 
 #' @export 
 check_crs <- function(x) {
-    stopifnot("Input is invalid.\n" = (is(x, "sf") || is(x, "stars") || is(x, "SpatVector") || is(x, "SpatRaster")))
+    stopifnot("Input is invalid.\n" = (methods::is(x, "sf") || methods::is(x, "stars") || methods::is(x, "SpatVector") || methods::is(x, "SpatRaster")))
     
-    if (is(x, "sf") || is(x, "stars")) {
+    if (methods::is(x, "sf") || methods::is(x, "stars")) {
         crs_wkt = sf::st_crs(x)
     } else {
         crs_wkt = terra::crs(x)
@@ -1065,8 +1098,8 @@ 
Create functions

 #' @author Insang Song \email{geoissong@@gmail.com}
 #' @export 
 check_within_reference <- function(input_object, reference) {
-    stopifnot("Input is invalid.\n" = (is(x, "sf") || is(x, "stars") || is(x, "SpatVector") || is(x, "SpatRaster")))
-    stopifnot("Reference is invalid.\n" = (is(x, "sf") || is(x, "stars") || is(x, "SpatVector") || is(x, "SpatRaster")))
+    stopifnot("Input is invalid.\n" = (methods::is(x, "sf") || methods::is(x, "stars") || methods::is(x, "SpatVector") || methods::is(x, "SpatRaster")))
+    stopifnot("Reference is invalid.\n" = (methods::is(x, "sf") || methods::is(x, "stars") || methods::is(x, "SpatVector") || methods::is(x, "SpatRaster")))
 
   bbox_input <- input_object
     sf::st_bbox() |>
@@ -1086,7 +1119,8 @@ 
Create functions

 
#' Calculate SEDC covariates
 #' @param point_from SpatVector object. Locations where the sum of SEDCs are calculated.
 #' @param point_to SpatVector object. Locations where each SEDC is calculated.
-#' @param sdec_bandwidth numeric(1). Distance at which the source concentration is reduced to exp(-3) (approximately 95 %)  
+#' @param id character(1). Name of the unique id field in point_to.
+#' @param sedc_bandwidth numeric(1). Distance at which the source concentration is reduced to exp(-3) (approximately 95 %)  
 #' @param threshold numeric(1). For computational efficiency, the nearest points in threshold will be selected
 #' @param target_fields character(varying). Field names in characters.
 #' @description NOTE: sf implementation is pending. Only available for terra.
@@ -1114,16 +1148,16 @@ 
Create functions

 
   # summary
   near_from_to = near_from_to |>
-    as_tibble() |>
-    left_join(data.frame(point_from)) |>
-    left_join(data.frame(point_to)) |>
-    left_join(dist_near_to_df) |>
+    dplyr::as_tibble() |>
+    dplyr::left_join(data.frame(point_from)) |>
+    dplyr::left_join(data.frame(point_to)) |>
+    dplyr::left_join(dist_near_to_df) |>
     # per the definition in https://mserre.sph.unc.edu/BMElab_web/SEDCtutorial/index.html
     # exp(-3) is about 0.05
-    mutate(w_sedc = exp((-3 * dist) / sedc_bandwidth)) |>
-    group_by(!!sym(id)) |>
-    summarize(across(all_of(target_fields), list(sedc = ~sum(w_sedc * ., na.rm = TRUE)))) |>
-    ungroup()
+    dplyr::mutate(w_sedc = exp((-3 * dist) / sedc_bandwidth)) |>
+    dplyr::group_by(!!rlang::sym(id)) |>
+    dplyr::summarize(dplyr::across(dplyr::all_of(target_fields), list(sedc = ~sum(w_sedc * ., na.rm = TRUE)))) |>
+    dplyr::ungroup()
 
   invisible(near_from_to)
   
@@ -1141,13 +1175,13 @@ 
Create functions

 #' library(sf)
 #' 
 #' # run
-#' nc = st_read(system.file("shape/nc.shp", package="sf"))
-#' nc = st_transform(nc, 5070)
-#' pp = st_sample(nc, size = 300)
-#' pp = st_as_sf(pp)
+#' nc = sf::st_read(system.file("shape/nc.shp", package="sf"))
+#' nc = sf::st_transform(nc, 5070)
+#' pp = sf::st_sample(nc, size = 300)
+#' pp = sf::st_as_sf(pp)
 #' pp[["id"]] = seq(1, nrow(pp))
-#' st_crs(pp) = "EPSG:5070"
-#' ppb = st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
+#' sf::st_crs(pp) = "EPSG:5070"
+#' ppb = sf::st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
 #' 
 #' system.time({ppb_nc_aw = aw_covariates(ppb, nc, 'id')})
 #' summary(ppb_nc_aw)
@@ -1155,7 +1189,7 @@ 
Create functions

 #' @export
 aw_covariates <- function(poly_in, poly_weight, id_poly_in = "ID") {
     stopifnot("Inputs have invalid classes.\n" = 
-      is(poly_in, "sf") || is(poly_weight, "sf") || is(poly_in, "SpatVector") || is(poly_weight, "SpatVector"))
+      methods::is(poly_in, "sf") || methods::is(poly_weight, "sf") || methods::is(poly_in, "SpatVector") || methods::is(poly_weight, "SpatVector"))
     #check_crs()
 
     ## distinguish numeric and nonnumeric columns
@@ -1167,8 +1201,8 @@ 
Create functions

         poly_intersected[["area_segment_"]] = terra::expanse(poly_intersected)
         poly_intersected = data.frame(poly_intersected) |>
             dplyr::group_by(!!rlang::sym(id_poly_in)) |>
-            dplyr::summarize(across(is.numeric,
-                        ~weighted.mean(., w = area_segment_))) |>
+            dplyr::summarize(dplyr::across(is.numeric,
+                        ~stats::weighted.mean(., w = area_segment_))) |>
             dplyr::ungroup()
         return(poly_intersected)
     }
@@ -1197,52 +1231,6 @@ 
Create functions

 
 #ncbufagg = terra::aggregate(ncbuf, by = 'id', fun = weighted.mean, w = ncbuf_a$segarea)
 

-
#' Subfunction: extract with buffers (flat weight; simple mean)
-#' 
-#' @export 
-extract_with_buffer.flat <- function(
-        points, surf, radius, id, qsegs, func = mean, kernel = NULL, bandwidth = NULL
-    ) {
-    # generate buffers
-    bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
-    # crop raster
-    bufs_extent = terra::ext(bufs)
-    surf_cropped = terra::crop(surf, bufs_extent)
-    name_surf_val = names(surf)
-    # extract raster values
-    surf_at_bufs = terra::extract(surf_cropped, bufs)
-    surf_at_bufs_summary = 
-        surf_at_bufs |> 
-            group_by(ID) |> 
-            summarize(across(all_of(name_surf_val), ~mean, na.rm=T)) |> 
-            ungroup()
-    return(surf_at_bufs_summary)
-}

-
#' Subfunction: extract with buffers (kernel weight; weighted mean)
-#'
-#' @export 
-extract_with_buffer.kernel <- function(
-        points, surf, radius, id, qsegs, func = mean, kernel, bandwidth
-    ) {
-        # generate buffers
-        bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
-        # crop raster
-        bufs_extent = terra::ext(bufs)
-        surf_cropped = terra::crop(surf, bufs_extent)
-        name_surf_val = names(surf)
-
-        # TODO: kernel implementation
-
-
-        # extract raster values
-        surf_at_bufs = terra::extract(surf_cropped, bufs)
-        surf_at_bufs_summary = 
-            surf_at_bufs |> 
-                group_by(ID) |> 
-                summarize(across(all_of(name_surf_val), ~mean, na.rm=T)) |> 
-                ungroup()
-        return(surf_at_bufs_summary)
-}

 
#' @title Extract summarized values from raster with points and a buffer radius (to be written)
 #' 
 #' @description For simplicity, it is assumed that the coordinate systems of the points and the raster are the same. Kernel function is not yet implemented. 
@@ -1262,7 +1250,7 @@ 
Create functions

     points, surf, radius, id, qsegs = 90, func = mean, kernel = NULL, bandwidth = NULL
     ) {
     # type check
-    stopifnot("Check class of the input points.\n" = is(points, "SpatVector"))
+    stopifnot("Check class of the input points.\n" = methods::is(points, "SpatVector"))
     stopifnot("Check class of the input radius.\n" = is.numeric(radius))
     stopifnot(is.character(id))
     stopifnot(is.integer(qsegs))
@@ -1289,13 +1277,56 @@ 
Create functions

 
 }
 
+# Subfunction: extract with buffers (flat weight; simple mean)
+extract_with_buffer.flat <- function(
+        points, surf, radius, id, qsegs, func = mean, kernel = NULL, bandwidth = NULL
+    ) {
+    # generate buffers
+    bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
+    # crop raster
+    bufs_extent = terra::ext(bufs)
+    surf_cropped = terra::crop(surf, bufs_extent)
+    name_surf_val = names(surf)
+    # extract raster values
+    surf_at_bufs = terra::extract(surf_cropped, bufs)
+    surf_at_bufs_summary = 
+        surf_at_bufs |> 
+            dplyr::group_by(ID) |> 
+            dplyr::summarize(dplyr::across(dplyr::all_of(name_surf_val), ~mean, na.rm=T)) |> 
+            dplyr::ungroup()
+    return(surf_at_bufs_summary)
+}
+
+
+# Subfunction: extract with buffers (kernel weight; weighted mean)
+extract_with_buffer.kernel <- function(
+        points, surf, radius, id, qsegs, func = mean, kernel, bandwidth
+    ) {
+        # generate buffers
+        bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
+        # crop raster
+        bufs_extent = terra::ext(bufs)
+        surf_cropped = terra::crop(surf, bufs_extent)
+        name_surf_val = names(surf)
 
+        # TODO: kernel implementation
+
+
+        # extract raster values
+        surf_at_bufs = terra::extract(surf_cropped, bufs)
+        surf_at_bufs_summary = 
+            surf_at_bufs |> 
+                dplyr::group_by(ID) |> 
+                dplyr::summarize(dplyr::across(dplyr::all_of(name_surf_val), ~mean, na.rm=T)) |> 
+                dplyr::ungroup()
+        return(surf_at_bufs_summary)
+}
 

 
#' @title Process a given function in the entire or partial computational grids (under construction)
 #' 
 #' @description Should 
 #' @param grids sf/SpatVector object. Computational grids.
-#' @param grid_id character(1) or numeric(2). Default is NULL. If NULL, all grid_ids are used. "id_from:id_to" format or c(unique(grid_id)[id_from], unique(grid_id)[id_to])
+#' @param grid_id character(1) or numeric(2). Default is NULL. If NULL, all grid_ids are used. \code{"id_from:id_to"} format or \code{c(unique(grid_id)[id_from], unique(grid_id)[id_to])}
 #' @param fun function supported in scomps. 
 #' @param ... Arguments passed to fun.
 #' @return a data.frame object with mean value
@@ -1303,8 +1334,7 @@ 
Create functions

 #' 
 #' @export
 distribute_process <- function(grids, grid_id = NULL, fun, ...) {
-    require(future.apply)
-    
+   
     # subset using grids and grid_id
     if (!is.null(grid_id)) {
         if (is.character(grid_id)) {
@@ -1322,7 +1352,7 @@ 
Create functions

     results_distributed = future.apply::future_lapply(
         \(x, ...) {
             fun(...)
-        }, grids_target_list, points_cutslist, SIMPLIFY = FALSE,
+        }, grids_target_list, 
         future.seed = TRUE)
     results_distributed = do.call(rbind, results_distributed)
     return(results_distributed)
@@ -1334,19 +1364,21 @@ 
Documenting the package and building

 
We finish by running commands that will document, build, and install
 the package. It may also be a good idea to check the package from within
 this file.

-
litr::document() # <-- use instead of devtools::document()
+
# litr::document() # <-- use instead of devtools::document()
+devtools::document(".")
 devtools::test()
 devtools::build()
-devtools::install(build_vignettes = TRUE, dependencies = F)
+devtools::install(dependencies = F, build_vignettes = TRUE)
 # devtools::check(document = FALSE)
 

 
## ℹ Updating scomps documentation
 ## ℹ Loading scomps

-
## Warning: [check.R:92] @description requires a value

+
## Warning: [check.R:133] @description requires a value

 
## Warning: [processing.R:139] @return requires a value

 
## Writing 'NAMESPACE'
 ## Writing 'check_packbound.Rd'
 ## Writing 'check_crs2.Rd'
+## Writing 'extent_to_polygon.Rd'
 ## Writing 'check_bbox.Rd'
 ## Writing 'check_crs.Rd'
 ## Writing 'check_within_reference.Rd'
@@ -1366,8 +1398,6 @@ 
Documenting the package and building

 ## Writing 'extract_with.Rd'
 ## Writing 'calculate_sedc.Rd'
 ## Writing 'aw_covariates.Rd'
-## Writing 'extract_with_buffer.flat.Rd'
-## Writing 'extract_with_buffer.kernel.Rd'
 ## Writing 'extract_with_buffer.Rd'
 ## Writing 'switch_packbound.Rd'
 ## Writing 'validate_and_repair_vectors.Rd'

@@ -1376,9 +1406,9 @@ 
Documenting the package and building

 ## 
 ## ⠏ |         0 | tests                                                           pr, tas, 
 ## pr, tas, 
+## pr, tas, 
 ## 
-## ⠹ |         3 | tests                                                           pr, tas, 
-## 
+## ⠼ |         5 | tests                                                           
 ## ✔ |         8 | tests
 ## 
 ## ══ Results ═════════════════════════════════════════════════════════════════════
@@ -1389,19 +1419,13 @@ 
Documenting the package and building

 ## * checking DESCRIPTION meta-information ... OK
 ## * installing the package to build vignettes
 ## * creating vignettes ... OK
-## * excluding invalid files
-## Subdirectory 'inst/doc' contains invalid file names:
-##   ‘00_good_practice_parallelization.Rmd’
-##   ‘01_generate_computational_grid.Rmd’
-##   ‘00_good_practice_parallelization.html’
-##   ‘01_generate_computational_grid.html’
 ## * checking for LF line-endings in source and make files and shell scripts
 ## * checking for empty or unneeded directories
 ## Removed empty directory ‘scomps/build’
-## * building ‘scomps_0.0.2.10032023.tar.gz’
+## * building ‘scomps_0.0.3.10042023.tar.gz’
 ## Warning: invalid uid value replaced by that for user 'nobody'
 ## Warning: invalid gid value replaced by that for user 'nobody'

-
## [1] "/Users/songi2/Documents/GitHub/Scalable_GIS/scomps_0.0.2.10032023.tar.gz"

+
## [1] "/Users/songi2/Documents/GitHub/Scalable_GIS/scomps_0.0.3.10042023.tar.gz"

 
## Skipping 1 packages ahead of CRAN: data.table

 
## ── R CMD build ─────────────────────────────────────────────────────────────────
 ## * checking for file ‘/Users/songi2/Documents/GitHub/Scalable_GIS/scomps/DESCRIPTION’ ... OK
@@ -1409,21 +1433,15 @@ 
Documenting the package and building

 ## * checking DESCRIPTION meta-information ... OK
 ## * installing the package to build vignettes
 ## * creating vignettes ... OK
-## * excluding invalid files
-## Subdirectory 'inst/doc' contains invalid file names:
-##   ‘00_good_practice_parallelization.Rmd’
-##   ‘01_generate_computational_grid.Rmd’
-##   ‘00_good_practice_parallelization.html’
-##   ‘01_generate_computational_grid.html’
 ## * checking for LF line-endings in source and make files and shell scripts
 ## * checking for empty or unneeded directories
 ## Removed empty directory ‘scomps/build’
-## * building ‘scomps_0.0.2.10032023.tar.gz’
+## * building ‘scomps_0.0.3.10042023.tar.gz’
 ## Warning: invalid uid value replaced by that for user 'nobody'
 ## Warning: invalid gid value replaced by that for user 'nobody'
 ## 
 ## Running /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL \
-##   /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmptULHMx/scomps_0.0.2.10032023.tar.gz \
+##   /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmpdIhnyr/scomps_0.0.3.10042023.tar.gz \
 ##   --install-tests 
 ## * installing to library ‘/Users/songi2/Library/R/arm64/4.3/library’
 ## * installing *source* package ‘scomps’ ...
diff --git a/scomps_rmarkdown_litr.rmd b/scomps_rmarkdown_litr.rmd
index f0f3b5ed..854d21e4 100644
--- a/scomps_rmarkdown_litr.rmd
+++ b/scomps_rmarkdown_litr.rmd
@@ -1,7 +1,7 @@
 ---
 title: "Creating the ``r params$package_name`` R package"
 author: "Insang Song"
-date: "2023-09-03"
+date: "2023-10-04"
 knit: litr::render
 output: litr::litr_html_document
 params:
@@ -21,7 +21,7 @@ usethis::create_package(
   path = ".",
   fields = list(
     Package = params$package_name,
-    Version = "0.0.2.10032023",
+    Version = "0.0.3.10042023",
     Title = "Scalable R geospatial computation",
     Description = "A package for scalable geospatial computation for environmental health research",
     `Authors@R` = person(
@@ -41,6 +41,8 @@ usethis::use_package("terra") # Default is "Imports"
 usethis::use_package("stars")
 usethis::use_package("rlang") # Default is "Imports"
 usethis::use_package("testthat")
+usethis::use_package("units")
+usethis::use_package("methods")
 usethis::use_package("logr", "Suggests") # Default is "Imports"
 usethis::use_package("future") # Default is "Imports"
 usethis::use_package("future.apply") # Default is "Imports"
@@ -67,13 +69,13 @@ usethis::use_mit_license(copyright_holder = "I. Song")
 ### Vignettes 1
 
 ```{r}
-litr::add_vignettes("../tools/vignettes-sources/00_good_practice_parallelization.Rmd")
+litr::add_vignettes("../tools/vignettes-sources/v00_good_practice_parallelization.Rmd")
 ```
 
 ### Vignettes 2
 
 ```{r}
-litr::add_vignettes("../tools/vignettes-sources/01_generate_computational_grid.Rmd")
+litr::add_vignettes("../tools/vignettes-sources/v01_generate_computational_grid.Rmd")
 ```
 
 
@@ -89,19 +91,19 @@ litr::add_vignettes("../tools/vignettes-sources/01_generate_computational_grid.R
 #' @export
 check_packbound <- function(input) {
   # cl_inobj = class(input)[1]
-  stopifnot("Input should be one of sf or Spat* object.\n" = any(is(input, "sf"), is(input, "stars"), is(input, "SpatVector"), is(input, "SpatRaster")))
-  if (is(input, "SpatVector") || is(input, "SpatRaster")) {
+  stopifnot("Input should be one of sf or Spat* object.\n" = any(methods::is(input, "sf"), methods::is(input, "stars"), methods::is(input, "SpatVector"), methods::is(input, "SpatRaster")))
+  if (methods::is(input, "SpatVector") || methods::is(input, "SpatRaster")) {
     return("terra")
   }
   return("sf")
 }
 
 check_datatype <- function(input) {
-  stopifnot("Input should be one of sf or Spat* object.\n" = any(is(input, "sf"), is(input, "stars"), is(input, "SpatVector"), is(input, "SpatRaster")))
-  if (any(is(input, "SpatVector"), is(input, "sf"))) {
+  stopifnot("Input should be one of sf or Spat* object.\n" = any(methods::is(input, "sf"), methods::is(input, "stars"), methods::is(input, "SpatVector"), methods::is(input, "SpatRaster")))
+  if (any(methods::is(input, "SpatVector"), methods::is(input, "sf"))) {
     return("vector")
   }
-  if (any(is(input, "SpatRaster"), is(input, "stars"))) {
+  if (any(methods::is(input, "SpatRaster"), methods::is(input, "stars"))) {
     return("raster")
   }
 }
@@ -152,7 +154,7 @@ testthat::test_that("What package does the input object belong?",
 #' @return Data converted to the other package class (if sf, terra; if terra, sf)
 #' @export
 switch_packbound <- function(input) {
-  stopifnot("Input should be one of sf or Spat* object.\n" = any(is(input, "sf"), is(input, "stars"), is(input, "SpatVector"), is(input, "SpatRaster")))
+  stopifnot("Input should be one of sf or Spat* object.\n" = any(methods::is(input, "sf"), methods::is(input, "stars"), methods::is(input, "SpatVector"), methods::is(input, "SpatRaster")))
   cls_input = check_packbound(input)
   type_input = check_datatype(input)
 
@@ -206,11 +208,12 @@ testthat::test_that("Format is well converted",
 #' @title check_crs2: Coordinate system checker
 #' @description The input is checked whether its coordinate system is present. If not, it is reprojected to EPSG:5179.
 #' @param input Input object one of sf or terra::Spat* object
+#' @param crs_standard character(1). A standard definition of coordinate reference system. Default is "EPSG:4326" Consult [epsg.io](https://epsg.io) for details of other CRS.
 #' @return A (reprojected) sf or SpatVector object.
 #' @export
 check_crs2 <- function(input, crs_standard = "EPSG:4326") {
   check_crs.sf <- function(input){
-    if (is.na(st_crs(input))){cat('Please check the coordinate system or its EPSG code of your input object.'); return(NULL)}
+    if (is.na(sf::st_crs(input))){cat('Please check the coordinate system or its EPSG code of your input object.'); return(NULL)}
     if (sf::st_crs(input)$epsg == crs_standard ) {
       return(input)
     } 
@@ -393,7 +396,7 @@ clip_as_extent_ras2 <- function(points_in, buffer_r, nqsegs=180, ras){
 sp_indexing <- function(points_in, ncutsx, ncutsy){
   # pts <- data.table(pnts)
   points_in <- points_in |>
-    mutate(or_id = seq(1, dim(points_in)[1]))
+    dplyr::mutate(or_id = seq(1, dim(points_in)[1]))
   
   range_x  <- range(points_in$x)
   limits_x <- (range_x[1] + seq(0, ncutsx) * (range_x[2] - range_x[1]) / ncutsx)
@@ -401,7 +404,7 @@ sp_indexing <- function(points_in, ncutsx, ncutsy){
   limits_y <- (range_y[1] + seq(0, ncutsy) * (range_y[2] - range_y[1]) / ncutsy)
   
   points_in_cut <- points_in |>
-    mutate(xcut =  as.integer(cut(x, ncutsx, labels = seq(1, ncutsx))),
+    dplyr::mutate(xcut =  as.integer(cut(x, ncutsx, labels = seq(1, ncutsx))),
            ycut = as.integer(cut(y, ncutsy, labels = seq(1, ncutsy))))
   
   return(points_in_cut)
@@ -413,7 +416,8 @@ sp_indexing <- function(points_in, ncutsx, ncutsy){
 #' 
 #' @param rasterpath character(1). Path to the raster file.
 #' @param win Named integer vector (4) or terra::ext() results.
-#' @param author Insang Song 
+#' @return SpatRaster object.
+#' @author Insang Song 
 #' @export 
 rast_short <- function(rasterpath, win) {
   terra::rast(rasterpath, win = win)
@@ -430,6 +434,7 @@ rast_short <- function(rasterpath, win) {
 #' @param nx integer(1). 
 #' @param ny integer(1). 
 #' @param padding numeric(1). Extrusion factor 
+#' @author Insang Song
 #' @export 
 estimate_demands <- function(
   inputs,
@@ -457,7 +462,8 @@ estimate_demands <- function(
 #' @param ny integer(1). The number of grids along y-axis.
 #' @param grid_min_features integer(1). A threshold to merging adjacent grids
 #' @param padding numeric(1). A extrusion factor to make buffer to clip actual datasets. Depending on the length unit of the CRS of input.
-#' @param unit character(1). The length unit for padding (optional). units::set_units is used for padding when sf object is used. See \link{units package vignette (web)}{https://cran.r-project.org/web/packages/units/vignettes/measurement_units_in_R.html} for the list of acceptable unit forms.
+#' @param unit character(1). The length unit for padding (optional). units::set_units is used for padding when sf object is used. See [units package vignette (web)](https://cran.r-project.org/web/packages/units/vignettes/measurement_units_in_R.html) for the list of acceptable unit forms.
+#' @param ... arguments passed to the internal function
 #' @return A set of polygons in the input class
 #' @description TODO. Using input points, the bounding box is split to the predefined numbers of columns and rows. Each grid will be buffered by the radius.   
 #' @author Insang Song 
@@ -501,7 +507,7 @@ sp_index_grid <- function(points_in, ncutsx, ncutsy){
   sp_index_grid.sf = function(points_in, ncutsx, ncutsy) {
     grid1 <- sf::st_make_grid(points_in, n = c(ncutsx, ncutsy)) |> 
       as.data.frame() |> 
-      st_as_sf()
+      sf::st_as_sf()
     grid1 <- grid1[points_in, ]
     return(grid1)
   }
@@ -531,14 +537,14 @@ sp_index_grid <- function(points_in, ncutsx, ncutsy){
 #' # library(sf)
 #' # library(igraph)
 #' # ligrary(dplyr)
-#' # dg = st_as_sfc(st_bbox(c(xmin = 0, ymin = 0, xmax = 8e5, ymax = 6e5)))
-#' # st_crs(dg) = 5070
-#' # dgs = st_as_sf(st_make_grid(dg, n = c(20, 15)))
+#' # dg = sf::st_as_sfc(st_bbox(c(xmin = 0, ymin = 0, xmax = 8e5, ymax = 6e5)))
+#' # sf::st_crs(dg) = 5070
+#' # dgs = sf::st_as_sf(st_make_grid(dg, n = c(20, 15)))
 #' # dgs$CGRIDID = seq(1, nrow(dgs))
 #' #
 #' # dg_sample = st_sample(dg, kappa = 5e-9, mu = 15, scale = 20000, type = "Thomas")
-#' # st_crs(dg_sample) = st_crs(dg)
-#' # dg_merged = grid_merge(st_as_sf(sss), dgs, 100)
+#' # sf::st_crs(dg_sample) = sf::st_crs(dg)
+#' # dg_merged = grid_merge(sf::st_as_sf(sss), dgs, 100)
 #' #### NOT RUN ####
 #' @export
 grid_merge <- function(points_in, grid_in, grid_min_features){
@@ -562,7 +568,7 @@ grid_merge <- function(points_in, grid_in, grid_min_features){
   identified = unique(identified)
   identified = identified[sapply(identified, length) > 1]
 
-  identified_graph = lapply(identified, \(x) t(combn(x, 2))) |>
+  identified_graph = lapply(identified, \(x) t(utils::combn(x, 2))) |>
     Reduce(f = rbind, x = _) |>
     unique() |>
     apply(X = _, 2, as.character) |>
@@ -586,8 +592,8 @@ grid_merge <- function(points_in, grid_in, grid_min_features){
   #   grid_out[["CGRIDID"]][target_idx] = paste("M_", paste(target_idx, collapse = "_"), sep = "")
   # }
   grid_out = grid_out |>
-    dplyr::group_by(CGRIDID) |>
-    dplyr::summarize(n_merged = n()) |>
+    dplyr::group_by(!!rlang::sym("CGRIDID")) |>
+    dplyr::summarize(n_merged = dplyr::n()) |>
     dplyr::ungroup() 
 
   ## polsby-popper test for shape compactness
@@ -621,7 +627,46 @@ grid_merge <- function(points_in, grid_in, grid_min_features){
 
 ```
 
+```{r, send_to = "R/check.R"}
+#' Generate a rectangular polygon from extent
+#' 
+#' @param extent input extent. A numeric vector with xmin/xmax/ymin/ymax, sf::st_bbox() or terra::ext() outputs.
+#' @param output_class character(1). Class of the output polygon. One of "sf" or "terra"
+#' @param crs character(1). Coordinate reference system definition.
+#' @author Insang Song
+#' @export
+extent_to_polygon <- function(extent, output_class = "terra", crs = "EPSG:4326") {
+  if (!output_class %in% c("sf", "terra")) {
+    stop("output_class should be one of 'sf' or 'terra'.\n")
+  }
+  if (methods::is(extent, "numeric")) {
+    if (is.null(attr(extent, "names"))) {
+      stop("Your extent is an unnamed numeric vector. Please define names xmin/xmax/ymin/ymax explicitly.\n")
+    }
+    extent = switch(
+      output_class,
+      sf = sf::st_bbox(extent),
+      terra = terra::ext(extent)
+    )
+  }
+
+  extent_polygon = switch(
+    output_class,
+    sf = sf::st_as_sfc(extent),
+    terra = terra::vect(extent)
+  )
+
+  extent_polygon = switch(
+    output_class,
+    sf = sf::st_set_crs(extent_polygon, sf::st_crs(crs)),
+    terra = terra::set.crs(extent_polygon, terra::crs(crs))
+  )
 
+  return(extent_polygon)
+  
+}
+
+```
 
 ```{r, send_to = "R/check.R"}
 #' Check if the data extent is inside the reference bounding box
@@ -648,10 +693,11 @@ check_bbox <- function(
   if (is.na(query_crs) || is.null(query_crs)) {
     stop("The dataset you queried has no CRS. Please make sure your dataset has the correct CRS.\n")
   }
+  query_matched = sf::st_transform(data_query, sf::st_crs(ref_crs))
+
 
-  # ...
 
-  check_result
+  check_result = sf::st_within()
   return(check_result)
 }
 
@@ -659,7 +705,9 @@ check_bbox <- function(
 ```
 
 
-```{r}
+```{r, include=FALSE}
+#
+#
 #' Check if the data extent is inside the reference bounding box
 #' 
 #' @description One of the most common errors in spatial computation is rooted in the entirely or partly incomparable spatial extents of input datasets. This function returns whether your data is inside the target computational extent. It is assumed that you know and have the exact computational region. This function will return TRUE if the reference region completely contains your data's extent and FALSE otherwise.
@@ -691,8 +739,8 @@ extract_with_polygons <- function(
     polys, surf, id, func = mean, na.rm = TRUE
     ) {
     # type check
-    stopifnot("Check class of the input points.\n" = any(is(polys, "sf"), is(polys, "SpatVector")))
-    stopifnot("Check class of the input raster.\n" = any(is(surf, "stars"), is(surf, "SpatRaster")))
+    stopifnot("Check class of the input points.\n" = any(methods::is(polys, "sf"), methods::is(polys, "SpatVector")))
+    stopifnot("Check class of the input raster.\n" = any(methods::is(surf, "stars"), methods::is(surf, "SpatRaster")))
     stopifnot(is.character(id))
 
     cls_polys = check_packbound(polys)
@@ -714,9 +762,9 @@ extract_with_polygons <- function(
     extract_with_polygons.terra = function(polys, surf, id, func) {
         extracted = terra::extract(surf, polys)
         extracted = extracted |>
-          group_by(!!sym(id)) |>
-          summarize(across(-!!sym(id), ~func)) |>
-          ungroup()
+          dplyr::group_by(!!rlang::sym(id)) |>
+          dplyr::summarize(dplyr::across(-!!rlang::sym(id), ~func)) |>
+          dplyr::ungroup()
         return(extracted)
     }
 
@@ -773,9 +821,9 @@ extract_with <- function(raster, vector, id, func = mean, mode = "polygon", ...)
 #' 
 #' @export 
 check_crs <- function(x) {
-    stopifnot("Input is invalid.\n" = (is(x, "sf") || is(x, "stars") || is(x, "SpatVector") || is(x, "SpatRaster")))
+    stopifnot("Input is invalid.\n" = (methods::is(x, "sf") || methods::is(x, "stars") || methods::is(x, "SpatVector") || methods::is(x, "SpatRaster")))
     
-    if (is(x, "sf") || is(x, "stars")) {
+    if (methods::is(x, "sf") || methods::is(x, "stars")) {
         crs_wkt = sf::st_crs(x)
     } else {
         crs_wkt = terra::crs(x)
@@ -795,8 +843,8 @@ check_crs <- function(x) {
 #' @author Insang Song \email{geoissong@@gmail.com}
 #' @export 
 check_within_reference <- function(input_object, reference) {
-    stopifnot("Input is invalid.\n" = (is(x, "sf") || is(x, "stars") || is(x, "SpatVector") || is(x, "SpatRaster")))
-    stopifnot("Reference is invalid.\n" = (is(x, "sf") || is(x, "stars") || is(x, "SpatVector") || is(x, "SpatRaster")))
+    stopifnot("Input is invalid.\n" = (methods::is(x, "sf") || methods::is(x, "stars") || methods::is(x, "SpatVector") || methods::is(x, "SpatRaster")))
+    stopifnot("Reference is invalid.\n" = (methods::is(x, "sf") || methods::is(x, "stars") || methods::is(x, "SpatVector") || methods::is(x, "SpatRaster")))
 
   bbox_input <- input_object
     sf::st_bbox() |>
@@ -820,7 +868,8 @@ check_within_reference <- function(input_object, reference) {
 #' Calculate SEDC covariates
 #' @param point_from SpatVector object. Locations where the sum of SEDCs are calculated.
 #' @param point_to SpatVector object. Locations where each SEDC is calculated.
-#' @param sdec_bandwidth numeric(1). Distance at which the source concentration is reduced to exp(-3) (approximately 95 %)  
+#' @param id character(1). Name of the unique id field in point_to.
+#' @param sedc_bandwidth numeric(1). Distance at which the source concentration is reduced to exp(-3) (approximately 95 %)  
 #' @param threshold numeric(1). For computational efficiency, the nearest points in threshold will be selected
 #' @param target_fields character(varying). Field names in characters.
 #' @description NOTE: sf implementation is pending. Only available for terra.
@@ -848,16 +897,16 @@ calculate_sedc <- function(point_from, point_to, id, sedc_bandwidth, threshold,
 
   # summary
   near_from_to = near_from_to |>
-    as_tibble() |>
-    left_join(data.frame(point_from)) |>
-    left_join(data.frame(point_to)) |>
-    left_join(dist_near_to_df) |>
+    dplyr::as_tibble() |>
+    dplyr::left_join(data.frame(point_from)) |>
+    dplyr::left_join(data.frame(point_to)) |>
+    dplyr::left_join(dist_near_to_df) |>
     # per the definition in https://mserre.sph.unc.edu/BMElab_web/SEDCtutorial/index.html
     # exp(-3) is about 0.05
-    mutate(w_sedc = exp((-3 * dist) / sedc_bandwidth)) |>
-    group_by(!!sym(id)) |>
-    summarize(across(all_of(target_fields), list(sedc = ~sum(w_sedc * ., na.rm = TRUE)))) |>
-    ungroup()
+    dplyr::mutate(w_sedc = exp((-3 * dist) / sedc_bandwidth)) |>
+    dplyr::group_by(!!rlang::sym(id)) |>
+    dplyr::summarize(dplyr::across(dplyr::all_of(target_fields), list(sedc = ~sum(w_sedc * ., na.rm = TRUE)))) |>
+    dplyr::ungroup()
 
   invisible(near_from_to)
   
@@ -878,13 +927,13 @@ calculate_sedc <- function(point_from, point_to, id, sedc_bandwidth, threshold,
 #' library(sf)
 #' 
 #' # run
-#' nc = st_read(system.file("shape/nc.shp", package="sf"))
-#' nc = st_transform(nc, 5070)
-#' pp = st_sample(nc, size = 300)
-#' pp = st_as_sf(pp)
+#' nc = sf::st_read(system.file("shape/nc.shp", package="sf"))
+#' nc = sf::st_transform(nc, 5070)
+#' pp = sf::st_sample(nc, size = 300)
+#' pp = sf::st_as_sf(pp)
 #' pp[["id"]] = seq(1, nrow(pp))
-#' st_crs(pp) = "EPSG:5070"
-#' ppb = st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
+#' sf::st_crs(pp) = "EPSG:5070"
+#' ppb = sf::st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
 #' 
 #' system.time({ppb_nc_aw = aw_covariates(ppb, nc, 'id')})
 #' summary(ppb_nc_aw)
@@ -892,7 +941,7 @@ calculate_sedc <- function(point_from, point_to, id, sedc_bandwidth, threshold,
 #' @export
 aw_covariates <- function(poly_in, poly_weight, id_poly_in = "ID") {
     stopifnot("Inputs have invalid classes.\n" = 
-      is(poly_in, "sf") || is(poly_weight, "sf") || is(poly_in, "SpatVector") || is(poly_weight, "SpatVector"))
+      methods::is(poly_in, "sf") || methods::is(poly_weight, "sf") || methods::is(poly_in, "SpatVector") || methods::is(poly_weight, "SpatVector"))
     #check_crs()
 
     ## distinguish numeric and nonnumeric columns
@@ -904,8 +953,8 @@ aw_covariates <- function(poly_in, poly_weight, id_poly_in = "ID") {
         poly_intersected[["area_segment_"]] = terra::expanse(poly_intersected)
         poly_intersected = data.frame(poly_intersected) |>
             dplyr::group_by(!!rlang::sym(id_poly_in)) |>
-            dplyr::summarize(across(is.numeric,
-                        ~weighted.mean(., w = area_segment_))) |>
+            dplyr::summarize(dplyr::across(is.numeric,
+                        ~stats::weighted.mean(., w = area_segment_))) |>
             dplyr::ungroup()
         return(poly_intersected)
     }
@@ -936,58 +985,6 @@ aw_covariates <- function(poly_in, poly_weight, id_poly_in = "ID") {
 
 ```
 
-```{r, send_to = "R/processing.R"}
-#' Subfunction: extract with buffers (flat weight; simple mean)
-#' 
-#' @export 
-extract_with_buffer.flat <- function(
-        points, surf, radius, id, qsegs, func = mean, kernel = NULL, bandwidth = NULL
-    ) {
-    # generate buffers
-    bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
-    # crop raster
-    bufs_extent = terra::ext(bufs)
-    surf_cropped = terra::crop(surf, bufs_extent)
-    name_surf_val = names(surf)
-    # extract raster values
-    surf_at_bufs = terra::extract(surf_cropped, bufs)
-    surf_at_bufs_summary = 
-        surf_at_bufs |> 
-            group_by(ID) |> 
-            summarize(across(all_of(name_surf_val), ~mean, na.rm=T)) |> 
-            ungroup()
-    return(surf_at_bufs_summary)
-}
-```
-
-```{r, send_to = "R/processing.R"}
-#' Subfunction: extract with buffers (kernel weight; weighted mean)
-#'
-#' @export 
-extract_with_buffer.kernel <- function(
-        points, surf, radius, id, qsegs, func = mean, kernel, bandwidth
-    ) {
-        # generate buffers
-        bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
-        # crop raster
-        bufs_extent = terra::ext(bufs)
-        surf_cropped = terra::crop(surf, bufs_extent)
-        name_surf_val = names(surf)
-
-        # TODO: kernel implementation
-
-
-        # extract raster values
-        surf_at_bufs = terra::extract(surf_cropped, bufs)
-        surf_at_bufs_summary = 
-            surf_at_bufs |> 
-                group_by(ID) |> 
-                summarize(across(all_of(name_surf_val), ~mean, na.rm=T)) |> 
-                ungroup()
-        return(surf_at_bufs_summary)
-}
-```
-
 
 ```{r, send_to = "R/processing.R"}
 #' @title Extract summarized values from raster with points and a buffer radius (to be written)
@@ -1009,7 +1006,7 @@ extract_with_buffer <- function(
     points, surf, radius, id, qsegs = 90, func = mean, kernel = NULL, bandwidth = NULL
     ) {
     # type check
-    stopifnot("Check class of the input points.\n" = is(points, "SpatVector"))
+    stopifnot("Check class of the input points.\n" = methods::is(points, "SpatVector"))
     stopifnot("Check class of the input radius.\n" = is.numeric(radius))
     stopifnot(is.character(id))
     stopifnot(is.integer(qsegs))
@@ -1036,7 +1033,50 @@ extract_with_buffer <- function(
 
 }
 
+# Subfunction: extract with buffers (flat weight; simple mean)
+extract_with_buffer.flat <- function(
+        points, surf, radius, id, qsegs, func = mean, kernel = NULL, bandwidth = NULL
+    ) {
+    # generate buffers
+    bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
+    # crop raster
+    bufs_extent = terra::ext(bufs)
+    surf_cropped = terra::crop(surf, bufs_extent)
+    name_surf_val = names(surf)
+    # extract raster values
+    surf_at_bufs = terra::extract(surf_cropped, bufs)
+    surf_at_bufs_summary = 
+        surf_at_bufs |> 
+            dplyr::group_by(ID) |> 
+            dplyr::summarize(dplyr::across(dplyr::all_of(name_surf_val), ~mean, na.rm=T)) |> 
+            dplyr::ungroup()
+    return(surf_at_bufs_summary)
+}
+
 
+# Subfunction: extract with buffers (kernel weight; weighted mean)
+extract_with_buffer.kernel <- function(
+        points, surf, radius, id, qsegs, func = mean, kernel, bandwidth
+    ) {
+        # generate buffers
+        bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
+        # crop raster
+        bufs_extent = terra::ext(bufs)
+        surf_cropped = terra::crop(surf, bufs_extent)
+        name_surf_val = names(surf)
+
+        # TODO: kernel implementation
+
+
+        # extract raster values
+        surf_at_bufs = terra::extract(surf_cropped, bufs)
+        surf_at_bufs_summary = 
+            surf_at_bufs |> 
+                dplyr::group_by(ID) |> 
+                dplyr::summarize(dplyr::across(dplyr::all_of(name_surf_val), ~mean, na.rm=T)) |> 
+                dplyr::ungroup()
+        return(surf_at_bufs_summary)
+}
 
 ```
 
@@ -1046,7 +1086,7 @@ extract_with_buffer <- function(
 #' 
 #' @description Should 
 #' @param grids sf/SpatVector object. Computational grids.
-#' @param grid_id character(1) or numeric(2). Default is NULL. If NULL, all grid_ids are used. "id_from:id_to" format or c(unique(grid_id)[id_from], unique(grid_id)[id_to])
+#' @param grid_id character(1) or numeric(2). Default is NULL. If NULL, all grid_ids are used. \code{"id_from:id_to"} format or \code{c(unique(grid_id)[id_from], unique(grid_id)[id_to])}
 #' @param fun function supported in scomps. 
 #' @param ... Arguments passed to fun.
 #' @return a data.frame object with mean value
@@ -1054,8 +1094,7 @@ extract_with_buffer <- function(
 #' 
 #' @export
 distribute_process <- function(grids, grid_id = NULL, fun, ...) {
-    require(future.apply)
-    
+   
     # subset using grids and grid_id
     if (!is.null(grid_id)) {
         if (is.character(grid_id)) {
@@ -1073,7 +1112,7 @@ distribute_process <- function(grids, grid_id = NULL, fun, ...) {
     results_distributed = future.apply::future_lapply(
         \(x, ...) {
             fun(...)
-        }, grids_target_list, points_cutslist, SIMPLIFY = FALSE,
+        }, grids_target_list, 
         future.seed = TRUE)
     results_distributed = do.call(rbind, results_distributed)
     return(results_distributed)
@@ -1086,10 +1125,11 @@ distribute_process <- function(grids, grid_id = NULL, fun, ...) {
 We finish by running commands that will document, build, and install the package.  It may also be a good idea to check the package from within this file.
 
 ```{r}
-litr::document() # <-- use instead of devtools::document()
+# litr::document() # <-- use instead of devtools::document()
+devtools::document(".")
 devtools::test()
 devtools::build()
-devtools::install(build_vignettes = TRUE, dependencies = F)
+devtools::install(dependencies = F, build_vignettes = TRUE)
 # devtools::check(document = FALSE)
 
 ```
\ No newline at end of file
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new file mode 100644
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HcmV?d00001

diff --git a/tools/vignettes-sources/v00_good_practice_parallelization.Rmd b/tools/vignettes-sources/v00_good_practice_parallelization.Rmd
new file mode 100644
index 00000000..8966a59d
--- /dev/null
+++ b/tools/vignettes-sources/v00_good_practice_parallelization.Rmd
@@ -0,0 +1,39 @@
+---
+title: "Good practice of scomps with HPC"
+date: "`r Sys.Date()`"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{good_practice_hpc}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+
+```{r}
+knitr::opts_chunk$set(warning = FALSE, message = FALSE)
+
+```
+
+## Assumptions
+- Users have an accessible HPC at your work
+- Data are stored in distributed file systems (usually incorporated into the HPC system)
+
+
+## Basic workflow
+
+### Practice for minimizing errors
+- Consider using `try()` or `tryCatch()` not to a tiny error will halt all the work without any results 
+    - Especially with the higher-level functions
+- "IPDE -- Inspect, Predict, Decide, Execute" all the time
+
+### Raster-Vector overlay
+- Make `sp_index_grid()` to get padded grid objects
+- Convert sf/SpatVector objects into `terra::ext()` compatible named numeric vector
+    - For example: `c(xmin=0, ymin=0, xmax=10, ymax=10)`
+- Make list objects with: 
+    - An extent vector in each element
+    - Preprocessed vector objects with respect to each extent vector in the first list
+    - Preferably all lists are named 
+- Write a `future.apply` script running through the extent list object
+- Run a small amount of data to estimate the total computational demand
+- Submit a job with a proper amount of computational assets
diff --git a/tools/vignettes-sources/v01_generate_computational_grid.Rmd b/tools/vignettes-sources/v01_generate_computational_grid.Rmd
new file mode 100644
index 00000000..4bc1aaf2
--- /dev/null
+++ b/tools/vignettes-sources/v01_generate_computational_grid.Rmd
@@ -0,0 +1,46 @@
+---
+title: "Generate computational grids"
+date: "`r Sys.Date()`"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{computational_grids}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+
+```{r}
+knitr::opts_chunk$set(warning = FALSE, message = FALSE)
+
+```
+
+
+## Prepare input data
+```{r}
+library(scomps)
+library(sf)
+library(terra)
+library(stars)
+library(dplyr)
+
+```
+
+## Computational grids
+```{r}
+# your_grid = scomps::sp_index_grid()
+
+```
+
+
+## Visualize computational grids
+```{r}
+# library(mapsf)
+# mf_map(your_grid$geometry)
+
+
+```
+
+
+
+## Notes
+- Computational grids are the exhaustive split of the entire study region. You should take a square buffer of each grid to clip the target raster or vector.

From 1264a32fa0912f2433236d1a49a287841cfa94ef Mon Sep 17 00:00:00 2001
From: Insang Song 
Date: Wed, 4 Oct 2023 14:33:12 -0400
Subject: [PATCH 21/21] Linting - all = are replaced with <- - Other linting
 errors were fixed   - function argument list and beginning bracket are
 separated   - Exception      - Two-space indentation      - 80 character
 lines

---
 scomps.Rcheck/00_pkg_src/scomps/DESCRIPTION   |  21 -
 scomps.Rcheck/00_pkg_src/scomps/LICENSE       |   2 -
 scomps.Rcheck/00_pkg_src/scomps/NAMESPACE     |  27 -
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diff --git a/scomps.Rcheck/00_pkg_src/scomps/DESCRIPTION b/scomps.Rcheck/00_pkg_src/scomps/DESCRIPTION
deleted file mode 100644
index eae7ecd6..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/DESCRIPTION
+++ /dev/null
@@ -1,21 +0,0 @@
-Package: scomps
-Title: Scalable R geospatial computation
-Version: 0.0.3.10042023
-Authors@R: 
-    person("Insang", "Song", , "geoissong@gmail.com", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0001-8732-3256"))
-Description: A package for scalable geospatial computation for
-    environmental health research
-License: MIT + file LICENSE
-Encoding: UTF-8
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
-Imports: covr, dplyr, future, future.apply, methods, rlang, sf, stars,
-        terra, testthat, units
-Suggests: future.batchtools, igraph, knitr, logr, rmarkdown, withr
-VignetteBuilder: knitr
-Config/testthat/edition: 3
-NeedsCompilation: no
-Packaged: 2023-10-04 15:41:03 UTC; songi2
-Author: Insang Song [aut, cre] ()
-Maintainer: Insang Song 
diff --git a/scomps.Rcheck/00_pkg_src/scomps/LICENSE b/scomps.Rcheck/00_pkg_src/scomps/LICENSE
deleted file mode 100644
index 74e6421f..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/LICENSE
+++ /dev/null
@@ -1,2 +0,0 @@
-YEAR: 2023
-COPYRIGHT HOLDER: I. Song
diff --git a/scomps.Rcheck/00_pkg_src/scomps/NAMESPACE b/scomps.Rcheck/00_pkg_src/scomps/NAMESPACE
deleted file mode 100644
index b8f3fc6a..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/NAMESPACE
+++ /dev/null
@@ -1,27 +0,0 @@
-# Generated by roxygen2: do not edit by hand
-
-export(aw_covariates)
-export(calculate_sedc)
-export(check_bbox)
-export(check_crs)
-export(check_crs2)
-export(check_packbound)
-export(check_within_reference)
-export(clip_as_extent)
-export(clip_as_extent_ras)
-export(clip_as_extent_ras2)
-export(distribute_process)
-export(estimate_demands)
-export(extent_to_polygon)
-export(extract_with)
-export(extract_with_buffer)
-export(extract_with_polygons)
-export(get_computational_regions)
-export(grid_merge)
-export(initate_log)
-export(rast_short)
-export(set_clip_extent)
-export(sp_index_grid)
-export(sp_indexing)
-export(switch_packbound)
-export(validate_and_repair_vectors)
diff --git a/scomps.Rcheck/00_pkg_src/scomps/R/check.R b/scomps.Rcheck/00_pkg_src/scomps/R/check.R
deleted file mode 100644
index 2e1bbcf2..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/R/check.R
+++ /dev/null
@@ -1,180 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' @title Return the package the input object is based on
-#' @description Detect whether the input object is sf or Spat* object.
-#' @author Insang Song
-#' @param input Spat* in terra or sf object.
-#' @return A character object; one of 'terra' and 'sf'
-#' @export
-check_packbound <- function(input) {
-  # cl_inobj = class(input)[1]
-  stopifnot("Input should be one of sf or Spat* object.\n" = any(methods::is(input, "sf"), methods::is(input, "stars"), methods::is(input, "SpatVector"), methods::is(input, "SpatRaster")))
-  if (methods::is(input, "SpatVector") || methods::is(input, "SpatRaster")) {
-    return("terra")
-  }
-  return("sf")
-}
-
-check_datatype <- function(input) {
-  stopifnot("Input should be one of sf or Spat* object.\n" = any(methods::is(input, "sf"), methods::is(input, "stars"), methods::is(input, "SpatVector"), methods::is(input, "SpatRaster")))
-  if (any(methods::is(input, "SpatVector"), methods::is(input, "sf"))) {
-    return("vector")
-  }
-  if (any(methods::is(input, "SpatRaster"), methods::is(input, "stars"))) {
-    return("raster")
-  }
-}
-
-#' @title check_crs2: Coordinate system checker
-#' @description The input is checked whether its coordinate system is present. If not, it is reprojected to EPSG:5179.
-#' @param input Input object one of sf or terra::Spat* object
-#' @param crs_standard character(1). A standard definition of coordinate reference system. Default is "EPSG:4326" Consult [epsg.io](https://epsg.io) for details of other CRS.
-#' @return A (reprojected) sf or SpatVector object.
-#' @export
-check_crs2 <- function(input, crs_standard = "EPSG:4326") {
-  check_crs.sf <- function(input){
-    if (is.na(sf::st_crs(input))){cat('Please check the coordinate system or its EPSG code of your input object.'); return(NULL)}
-    if (sf::st_crs(input)$epsg == crs_standard ) {
-      return(input)
-    } 
-    input_transformed <- sf::st_transform(input, sf::st_crs(crs_standard))
-    return(input_transformed)
-  }
-
-  check_crs.terra <- function(input) {
-    if (terra::crs(input, describe = TRUE)$code == crs_standard) {
-      return(input)
-    }
-    input_transformed = terra::project(input, terra::crs(crs_standard))
-    return(input_transformed)
-  }
-    detected = check_packbound(input)
-    switch(detected,
-          terra = check_crs.terra(input),
-          sf = check_crs.sf(input))
-  }
-
-#' Generate a rectangular polygon from extent
-#' 
-#' @param extent input extent. A numeric vector with xmin/xmax/ymin/ymax, sf::st_bbox() or terra::ext() outputs.
-#' @param output_class character(1). Class of the output polygon. One of "sf" or "terra"
-#' @param crs character(1). Coordinate reference system definition.
-#' @author Insang Song
-#' @export
-extent_to_polygon <- function(extent, output_class = "terra", crs = "EPSG:4326") {
-  if (!output_class %in% c("sf", "terra")) {
-    stop("output_class should be one of 'sf' or 'terra'.\n")
-  }
-  if (methods::is(extent, "numeric")) {
-    if (is.null(attr(extent, "names"))) {
-      stop("Your extent is an unnamed numeric vector. Please define names xmin/xmax/ymin/ymax explicitly.\n")
-    }
-    extent = switch(
-      output_class,
-      sf = sf::st_bbox(extent),
-      terra = terra::ext(extent)
-    )
-  }
-
-  extent_polygon = switch(
-    output_class,
-    sf = sf::st_as_sfc(extent),
-    terra = terra::vect(extent)
-  )
-
-  extent_polygon = switch(
-    output_class,
-    sf = sf::st_set_crs(extent_polygon, sf::st_crs(crs)),
-    terra = terra::set.crs(extent_polygon, terra::crs(crs))
-  )
-
-  return(extent_polygon)
-  
-}
-
-
-#' Check if the data extent is inside the reference bounding box
-#' 
-#' @description One of the most common errors in spatial computation is rooted in the entirely or partly incomparable spatial extents of input datasets. This function returns whether your data is inside the target computational extent. It is assumed that you know and have the exact computational region. This function will return TRUE if the reference region completely contains your data's extent and FALSE otherwise.
-#' @param data_query sf*/stars/SpatVector/SpatRaster object.
-#' @param reference sf*/stars/SpatVector/SpatRaster object or a named numeric vector with four names (xmin, ymin, xmax, and ymax).
-#' @param reference_crs Well-known-text-formatted or EPSG code of the reference's coordinate system. Only required when a named numeric vector is passed to reference. 
-#' @return TRUE (the queried data extent is completely within the reference bounding box) or FALSE 
-#' @author Insang Song \email{geoissong@@gmail.com}
-#' 
-#' @export
-check_bbox <- function(
-  data_query, reference, reference_crs = NULL
-) {
-  if (is.numeric(reference) && is.null(reference_crs)) {
-    stop("CRS should be entered when the reference extent is a vector.\n")
-  }
-  if (is.numeric(reference) && !is.null(reference_crs)) {
-    reference = sf::st_as_sfc(sf::st_bbox(reference), crs = reference_crs)
-  }
-  query_crs = check_crs(data_query)
-  ref_crs = check_crs(reference)
-  if (is.na(query_crs) || is.null(query_crs)) {
-    stop("The dataset you queried has no CRS. Please make sure your dataset has the correct CRS.\n")
-  }
-  query_matched = sf::st_transform(data_query, sf::st_crs(ref_crs))
-
-
-
-  check_result = sf::st_within()
-  return(check_result)
-}
-
-
-
-#' Check Coordinate Reference System
-#' @param x sf/stars/SpatVector/SpatRaster object.
-#' @return A st_crs or crs object.
-#' @description 
-#' @author Insang Song \email{geoissong@@gmail.com}
-#' @examples 
-#' # data
-#' library(sf)
-#' ncpath = system.file("shape/nc.shp", package = "sf")
-#' nc = read_sf(ncpath)
-#' check_crs(nc)
-#' 
-#' @export 
-check_crs <- function(x) {
-    stopifnot("Input is invalid.\n" = (methods::is(x, "sf") || methods::is(x, "stars") || methods::is(x, "SpatVector") || methods::is(x, "SpatRaster")))
-    
-    if (methods::is(x, "sf") || methods::is(x, "stars")) {
-        crs_wkt = sf::st_crs(x)
-    } else {
-        crs_wkt = terra::crs(x)
-    }
-
-    stopifnot("No CRS is defined in the input. Please consult the metadata or the data source.\n" = !is.na(crs_wkt) || crs_wkt != "")
-    return(crs_wkt)
-}
-
-#' Check if the boundary of the vector/raster object is inside the reference
-#' @param input_object sf/stars/SpatVector/SpatRaster object.
-#' @param reference sf/stars/SpatVector/SpatRaster object.
-#' @return logical
-#' @author Insang Song \email{geoissong@@gmail.com}
-#' @export 
-check_within_reference <- function(input_object, reference) {
-    stopifnot("Input is invalid.\n" = (methods::is(x, "sf") || methods::is(x, "stars") || methods::is(x, "SpatVector") || methods::is(x, "SpatRaster")))
-    stopifnot("Reference is invalid.\n" = (methods::is(x, "sf") || methods::is(x, "stars") || methods::is(x, "SpatVector") || methods::is(x, "SpatRaster")))
-
-  bbox_input <- input_object
-    sf::st_bbox() |>
-    sf::st_as_sfc()
-  
-  bbox_reference = reference |>
-    sf::st_bbox() |>
-    sf::st_as_sfc()
-
-  iswithin = sf::st_covered_by(bbox_input, bbox_reference)
-  iswithin = length(iswithin[[1]])
-  iswithin = (iswithin == 1)
-  invisible(iswithin)
-}
-
-
diff --git a/scomps.Rcheck/00_pkg_src/scomps/R/estimate_demands.R b/scomps.Rcheck/00_pkg_src/scomps/R/estimate_demands.R
deleted file mode 100644
index 0c0bf6d7..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/R/estimate_demands.R
+++ /dev/null
@@ -1,24 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' Estimate computational demands from inputs (to be written)
-#' 
-#' @param inputs a list of sf/Spat* objects or file paths
-#' @param nx integer(1). 
-#' @param ny integer(1). 
-#' @param padding numeric(1). Extrusion factor 
-#' @author Insang Song
-#' @export 
-estimate_demands <- function(
-  inputs,
-  nx, ny,
-  padding
-) {
-  ## cpu 
-  ## memory
-  ## estimate maximum coverage
-  ## clipped data size
-  ## total distributed memory
-  ## return a list of total demands 
-  ## print summary of results
-}
-
diff --git a/scomps.Rcheck/00_pkg_src/scomps/R/indexing.R b/scomps.Rcheck/00_pkg_src/scomps/R/indexing.R
deleted file mode 100644
index 7555a3f9..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/R/indexing.R
+++ /dev/null
@@ -1,25 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' @title Create integer indices for grid
-#' @description Returns a tibble object that includes x- and y- index by using two inputs ncutsx and ncutsy, which are x- and y-directional splits, respectively.
-#' @author Insang Song
-#' @param points_in sf object. 
-#' @param ncutsx integer(1). The number of splits along x-axis.
-#' @param ncutsy integer(1). The number of splits along y-axis.
-#' @export
-sp_indexing <- function(points_in, ncutsx, ncutsy){
-  # pts <- data.table(pnts)
-  points_in <- points_in |>
-    dplyr::mutate(or_id = seq(1, dim(points_in)[1]))
-  
-  range_x  <- range(points_in$x)
-  limits_x <- (range_x[1] + seq(0, ncutsx) * (range_x[2] - range_x[1]) / ncutsx)
-  range_y  <- range(points_in$y)
-  limits_y <- (range_y[1] + seq(0, ncutsy) * (range_y[2] - range_y[1]) / ncutsy)
-  
-  points_in_cut <- points_in |>
-    dplyr::mutate(xcut =  as.integer(cut(x, ncutsx, labels = seq(1, ncutsx))),
-           ycut = as.integer(cut(y, ncutsy, labels = seq(1, ncutsy))))
-  
-  return(points_in_cut)
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/R/interpret_computational_domain.R b/scomps.Rcheck/00_pkg_src/scomps/R/interpret_computational_domain.R
deleted file mode 100644
index 90132a7f..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/R/interpret_computational_domain.R
+++ /dev/null
@@ -1,210 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' Get a set of computational regions
-#' 
-#' @param input sf or Spat* object.
-#' @param mode character(1). Mode of region construction. One of "grid" (simple grid regardless of the number of features in each grid), "density" (clustering-based varying grids), "grid_advanced" (merging adjacent grids with smaller number of features than grid_min_features). 
-#' @param nx integer(1). The number of grids along x-axis.
-#' @param ny integer(1). The number of grids along y-axis.
-#' @param grid_min_features integer(1). A threshold to merging adjacent grids
-#' @param padding numeric(1). A extrusion factor to make buffer to clip actual datasets. Depending on the length unit of the CRS of input.
-#' @param unit character(1). The length unit for padding (optional). units::set_units is used for padding when sf object is used. See [units package vignette (web)](https://cran.r-project.org/web/packages/units/vignettes/measurement_units_in_R.html) for the list of acceptable unit forms.
-#' @param ... arguments passed to the internal function
-#' @return A set of polygons in the input class
-#' @description TODO. Using input points, the bounding box is split to the predefined numbers of columns and rows. Each grid will be buffered by the radius.   
-#' @author Insang Song 
-#' @examples 
-#' # data
-#' library(sf)
-#' ncpath = system.file("shape/nc.shp", package = "sf")
-#' nc = read_sf(ncpath)
-#' nc = st_transform(nc, "EPSG:5070")
-#' # run
-#' # nc_comp_region = get_computational_regions(nc, nx = 12, ny = 8)
-#' 
-#' @export 
-get_computational_regions <- function(input, mode = "grid", nx = 10, ny = 10, grid_min_features = 30, padding = NULL, unit = NULL, ...) {
-  # type check
-  package_detected = check_packbound(input)
-  # stopifnot("Invalid input.\n" = !any(grepl("^(sf|Spat)", class(input))))
-  stopifnot("Argument mode should be one of 'grid', 'grid_advanced', or 'density'.\n" = !mode %in% c("grid", "grid_advanced", "density"))
-  stopifnot("Ensure that nx, ny, and grid_min_features are all integer.\n" = all(is.integer(nx), is.integer(y), is.integer(grid_min_features)))
-  stopifnot("padding should be numeric. We convert padding to numeric...\n" = !is.numeric(padding))
-  # valid unit compatible with units::set_units?
-
-    # if (detected_pnts == "sf") {
-    # }
-    # if (detected_pnts == "terra") {
-    #   grid1$ID = seq(1, nrow(grid1))
-    # }
-  }
-
-#' @title sp_index_grid: Generate grid polygons
-#' @description Returns a sf object that includes x- and y- index by using two inputs ncutsx and ncutsy, which are x- and y-directional splits, respectively.
-#' @author Insang Song
-#' @param points_in sf or SpatVector object. Target points of computation.
-#' @param ncutsx integer(1). The number of splits along x-axis.
-#' @param ncutsy integer(1). The number of splits along y-axis.
-#' @return A sf or SpatVector object of computation grids with unique grid id (CGRIDID).
-#' @export
-sp_index_grid <- function(points_in, ncutsx, ncutsy){
-  package_detected = check_packbound(points_in)
-
-  sp_index_grid.sf = function(points_in, ncutsx, ncutsy) {
-    grid1 <- sf::st_make_grid(points_in, n = c(ncutsx, ncutsy)) |> 
-      as.data.frame() |> 
-      sf::st_as_sf()
-    grid1 <- grid1[points_in, ]
-    return(grid1)
-  }
-  sp_index_grid.terra = function(points_in, ncutsx, ncutsy) {
-    grid1 <- terra::rast(points_in, nrows = ncutsy, ncols = ncutsx)
-    grid1 <- terra::as.polygons(grid1)
-    return(grid1)
-  }
-  grid_out = switch(package_detected,
-        sf = sp_index_grid.sf(points_in, ncutsx, ncutsy),
-        terra = sp_index_grid.terra(points_in, ncutsx, ncutsy))
-    
-  grid_out$CGRIDID = seq(1, nrow(x = grid_out)) 
-  return(grid_out)
-
-}
-
-
-#' @title grid_merge: Merge grid polygons with given rules
-#' @description Merge boundary-sharing (in "Rook" contiguity) grids with fewer target features than the threshold. This function strongly assumes that the input is returned from the sp_index_grid, which has 'CGRIDID' as the unique id field.
-#' @author Insang Song
-#' @param points_in sf or SpatVector object. Target points of computation.
-#' @param grid_in sf or SpatVector object. The grid generated by sp_index_grid
-#' @param grid_min_features integer(1). Threshold to merge adjacent grids.
-#' @return A sf or SpatVector object of computation grids.
-#' @examples
-#' # library(sf)
-#' # library(igraph)
-#' # ligrary(dplyr)
-#' # dg = sf::st_as_sfc(st_bbox(c(xmin = 0, ymin = 0, xmax = 8e5, ymax = 6e5)))
-#' # sf::st_crs(dg) = 5070
-#' # dgs = sf::st_as_sf(st_make_grid(dg, n = c(20, 15)))
-#' # dgs$CGRIDID = seq(1, nrow(dgs))
-#' #
-#' # dg_sample = st_sample(dg, kappa = 5e-9, mu = 15, scale = 20000, type = "Thomas")
-#' # sf::st_crs(dg_sample) = sf::st_crs(dg)
-#' # dg_merged = grid_merge(sf::st_as_sf(sss), dgs, 100)
-#' #### NOT RUN ####
-#' @export
-grid_merge <- function(points_in, grid_in, grid_min_features){
-  package_detected = check_packbound(points_in)
-  if (package_detected == "terra") {
-    points_in = sf::st_as_sf(points_in)
-    grid_in = sf::st_as_sf(grid_in)
-  }
-
-  n_points_in_grid = lengths(sf::st_intersects(grid_in, points_in))
-  grid_self = sf::st_relate(grid_in, grid_in, pattern = "2********")
-  grid_rook = sf::st_relate(grid_in, grid_in, pattern = "F***1****")
-  grid_rooks = mapply(c, grid_self, grid_rook, SIMPLIFY = FALSE)
-  grid_lt_threshold = (n_points_in_grid < grid_min_features)
-  stopifnot("Threshold is too low. Please try higher threshold.\n" = sum(grid_lt_threshold) != 0)
-  grid_lt_threshold = seq(1, nrow(grid_in))[grid_lt_threshold]
-
-  # This part does not work as expected. Should investigate edge list and actual row index of the grid object; 
-  identified = lapply(grid_rooks, \(x) sort(x[which(x %in% grid_lt_threshold)]))
-  identified = identified[grid_lt_threshold]
-  identified = unique(identified)
-  identified = identified[sapply(identified, length) > 1]
-
-  identified_graph = lapply(identified, \(x) t(utils::combn(x, 2))) |>
-    Reduce(f = rbind, x = _) |>
-    unique() |>
-    apply(X = _, 2, as.character) |>
-    igraph::graph_from_edgelist(el = _, directed = 0) |>
-    igraph::mst() |>
-    igraph::components()
-  # return(identified_graph)
-
-  identified_graph_member = identified_graph$membership
-
-  merge_idx = as.integer(names(identified_graph_member))
-  merge_member = split(merge_idx, identified_graph_member)
-  merge_member_label = unlist(lapply(merge_member, \(x) paste(x, collapse = "_")))
-  merge_member_label = merge_member_label[identified_graph_member]
-
-  # sf object manipulation
-  grid_out = grid_in
-  grid_out[["CGRIDID"]][merge_idx] = merge_member_label
-  # for (k in seq_along(merge_member_label)) {
-  #   target_idx = merge_member_label[[k]]
-  #   grid_out[["CGRIDID"]][target_idx] = paste("M_", paste(target_idx, collapse = "_"), sep = "")
-  # }
-  grid_out = grid_out |>
-    dplyr::group_by(!!rlang::sym("CGRIDID")) |>
-    dplyr::summarize(n_merged = dplyr::n()) |>
-    dplyr::ungroup() 
-
-  ## polsby-popper test for shape compactness
-  grid_merged = grid_out[which(grid_out$n_merged > 1),]
-  grid_merged_area = as.numeric(sf::st_area(grid_merged))
-  grid_merged_perimeter = as.numeric(sf::st_length(sf::st_cast(grid_merged, "LINESTRING")))
-  grid_merged_pptest = (4 * pi * grid_merged_area) / (grid_merged_perimeter ^ 2)
-
-  # pptest value is bounded [0,1]; 0.3 threshold is groundless at this moment, possibly will make it defined by users.
-  if (max(unique(identified_graph_member)) > floor(0.1 * nrow(grid_in)) || any(grid_merged_pptest < 0.3)) {
-    warning("The reduced computational regions have too complex shapes. Consider increasing thresholds or using the original grids.\n")
-  }
-
-  return(grid_out)
-
-  # union unique sets into one
-  # identified_relation = matrix(NA, length(identified), length(identified))
-  # diag(identified_relation) = lengths(identified)
-
-  # for (i in seq_len(length(identified))) {
-  #   for (j in seq(i, length(identified))) {
-  #     identified_relation[i, j] = length(intersect(identified[[i]], identified[[j]]))
-  #     identified_relation[j, i] = identified_relation[i, j]
-  #   }
-  # }
-  # # identified_relation = max(identified_relation) - identified_relation
-  # return(as.dist(identified_relation))
-}
-
-
-
-
-#' @title Process a given function in the entire or partial computational grids (under construction)
-#' 
-#' @description Should 
-#' @param grids sf/SpatVector object. Computational grids.
-#' @param grid_id character(1) or numeric(2). Default is NULL. If NULL, all grid_ids are used. \code{"id_from:id_to"} format or \code{c(unique(grid_id)[id_from], unique(grid_id)[id_to])}
-#' @param fun function supported in scomps. 
-#' @param ... Arguments passed to fun.
-#' @return a data.frame object with mean value
-#' @author Insang Song \email{geoissong@@gmail.com}
-#' 
-#' @export
-distribute_process <- function(grids, grid_id = NULL, fun, ...) {
-   
-    # subset using grids and grid_id
-    if (!is.null(grid_id)) {
-        if (is.character(grid_id)) {
-            grid_id_parsed = strsplit(grid_id, ":", fixed = TRUE)[[1]]
-            grid_ids = c(which(unique(grids[["CGRIDID"]]) == grid_id_parsed[1]),
-                         which(unique(grids[["CGRIDID"]]) == grid_id_parsed[2]))
-        }
-        if (is.numeric(grid_id)) {
-            grid_ids = unique(grids[["CGRIDID"]])[grid_id]
-        }
-    }
-    grids_target = grids[grid_ids,]
-    grids_target_list = split(grids_target, grids_target[["CGRIDID"]])
-
-    results_distributed = future.apply::future_lapply(
-        \(x, ...) {
-            fun(...)
-        }, grids_target_list, 
-        future.seed = TRUE)
-    results_distributed = do.call(rbind, results_distributed)
-    return(results_distributed)
-}
-
diff --git a/scomps.Rcheck/00_pkg_src/scomps/R/logging.R b/scomps.Rcheck/00_pkg_src/scomps/R/logging.R
deleted file mode 100644
index 87a7dab2..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/R/logging.R
+++ /dev/null
@@ -1,20 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' Turn on logging
-#' @author Insang Song
-#' @param expr expression. Any function call to be logged.
-#' @param dolog logical(1). Will the messages be logged.
-#' @param logpath character(1). Log file path with the full log file name.
-#' @return Nothing. It will export a log file in the specified path as logpath.
-#' @export
-initate_log <- function(expr, dolog = FALSE, logpath) {
-  if (!dolog) {
-    return(NULL)
-  }
-  logr::log_path(logpath)
-  try(expr)
-  logr::log_close()
-  return(NULL)
-}
-
-
diff --git a/scomps.Rcheck/00_pkg_src/scomps/R/preprocessing.R b/scomps.Rcheck/00_pkg_src/scomps/R/preprocessing.R
deleted file mode 100644
index 93b3ad93..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/R/preprocessing.R
+++ /dev/null
@@ -1,36 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' Setting the clipping extent
-#' @description Return clipping extent with buffer radius. It assumes the input CRS is projected and linear unit is meters.
-#' @author Insang Song
-#' @param pnts One of sf or vect class. Target points of computation.
-#' @param buffer_r numeric(1). Buffer radius. It is assumed in metres 
-#' @return A terra::ext or sfc_POLYGON object of the computation extent.
-#' @export
-set_clip_extent <- function(pnts, buffer_r) {
-  detected = check_packbound(pnts)
-  if (detected == "terra") {
-    ext_input = terra::ext(pnts)
-    # Note that `+` operation on terra::ext output accounts for the operand as it is.
-    ext_input = ext_input + (1.1 * buffer_r + 30)
-  }
-  if (detected == "sf") {
-    ext_input <- pnts |> sf::st_bbox()
-    # Note that `+` operation on st_bbox output simply adds the number; we add a vector here.
-    ext_input <- ext_input + ((1.1 * c(-1, -1, 1, 1) * buffer_r) + 30)
-    ext_input <- sf::st_as_sfc(ext_input)
-  }
-  return(ext_input)
-}
-
-#' Quick call for SpatRaster with a window
-#' 
-#' @param rasterpath character(1). Path to the raster file.
-#' @param win Named integer vector (4) or terra::ext() results.
-#' @return SpatRaster object.
-#' @author Insang Song 
-#' @export 
-rast_short <- function(rasterpath, win) {
-  terra::rast(rasterpath, win = win)
-}
-
diff --git a/scomps.Rcheck/00_pkg_src/scomps/R/processing.R b/scomps.Rcheck/00_pkg_src/scomps/R/processing.R
deleted file mode 100644
index 00b3e1d3..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/R/processing.R
+++ /dev/null
@@ -1,364 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' Extent clipping
-#' @description Clip input vector by the expected maximum extent of computation. 
-#' @author Insang Song
-#' @param pnts sf or SpatVector object
-#' @param buffer_r numeric(1). buffer radius. this value will be automatically multiplied by 1.25
-#' @param nqsegs integer(1). the number of points per a quarter circle; SOON TO BE DEPRECATED
-#' @param target_input sf or SpatVector object to be clipped
-#' @return A clipped sf or SpatVector object.
-#' @export
-clip_as_extent <- function(pnts, buffer_r, nqsegs=NULL, target_input){
-  if (any(sapply(list(pnts, buffer_r, target_input), is.null))) {
-    stop("One or more required arguments are NULL. Please check.\n")
-  }
-  detected_pnts = check_packbound(pnts)
-  detected_target = check_packbound(target_input)
-
-  if (detected_pnts != detected_target) {
-    warning("Inputs are not the same class.\n")
-    target_input = switch(detected_target,
-        sf = terra::vect(target_input),
-        terra = sf::st_as_sf(target_input))
-  }
-  
-  ext_input = set_clip_extent(pnts, buffer_r)
-  cat("Clip target features with the input feature extent...\n")
-  if (detected_pnts == "sf") {
-    cae = ext_input |>
-      sf::st_intersection(x = target_input)
-  }
-  if (detected_pnts == "terra") {
-    cae = terra::intersect(target_input, ext_input)
-  }
-   
-  return(cae)
-}
-
-#' @title clip_as_extent_ras: Clip input raster.
-#' @description Clip input raster by the expected maximum extent of computation. 
-#' @author Insang Song
-#' @param pnts sf or SpatVector object
-#' @param buffer_r numeric(1). buffer radius. this value will be automatically multiplied by 1.25
-#' @param nqsegs integer(1). the number of points per a quarter circle
-#' @param ras SpatRaster object to be clipped
-#' @export
-clip_as_extent_ras <- function(pnts, buffer_r, nqsegs = 180, ras){
-  if (any(sapply(list(pnts, buffer_r, ras), is.null))) {
-    stop("Any of required arguments are NULL. Please check.\n")
-  }
-  ext_input = set_clip_extent(pnts, buffer_r) |>
-    terra::ext()
-
-  cae <- terra::crop(ras, ext_input, snap = 'out')
-  return(cae)
-}
-
-#' @title clip_as_extent_ras2: Clip input raster (version 2).
-#' @description Clip input raster by the expected maximum extent of computation. 
-#' @author Insang Song
-#' @param points_in sf or SpatVector object
-#' @param buffer_r numeric(1). buffer radius. this value will be automatically multiplied by 1.25
-#' @param nqsegs integer(1). the number of points per a quarter circle
-#' @param ras SpatRaster object to be clipped
-#' @export
-clip_as_extent_ras2 <- function(points_in, buffer_r, nqsegs=180, ras){
-  if (any(sapply(list(points_in, buffer_r, ras), is.null))) {
-    stop("Any of required arguments are NULL. Please check.\n")
-  }
-  ext_input = set_clip_extent(points_in, buffer_r) |>
-    terra::ext()
-
-  cae <- terra::crop(ras, ext_input, snap = 'out')
-  return(cae)
-}
-
-#' @title Extract summarized values from raster with generic polygons
-#' 
-#' @description For simplicity, it is assumed that the coordinate systems of the points and the raster are the same. Kernel function is not yet implemented. 
-#' @param polys sf/SpatVector object. Polygons.
-#' @param surf stars/SpatRaster object. A raster of whatnot a summary will be calculated
-#' @param id character(1). Unique identifier of each point.
-#' @param func a function taking one argument. For example, function(x) mean(x, na.rm = TRUE) or \(x) mode(x, na.rm = TRUE)
-#' @param na.rm logical(1). NA values are omitted when summary is calculated.
-#' @return a data.frame object with function value
-#' @author Insang Song \email{geoissong@@gmail.com}
-#' 
-#' @export
-extract_with_polygons <- function(
-    polys, surf, id, func = mean, na.rm = TRUE
-    ) {
-    # type check
-    stopifnot("Check class of the input points.\n" = any(methods::is(polys, "sf"), methods::is(polys, "SpatVector")))
-    stopifnot("Check class of the input raster.\n" = any(methods::is(surf, "stars"), methods::is(surf, "SpatRaster")))
-    stopifnot(is.character(id))
-
-    cls_polys = check_packbound(polys)
-    cls_surf = check_packbound(surf)
-
-    if (cls_polys != cls_surf) {
-      polys = switch_packbound(polys)
-    }
-
-    extract_with_polygons.sf = function(polys, surf, id, func) {
-        extracted = stars::st_extract(x = surf, at = polys, FUN = func)
-        # extracted = extracted |>
-        #   group_by(!!sym(id)) |>
-        #   summarize(across(-!!sym(id), ~func)) |>
-        #   ungroup()
-        return(extracted)
-    }
-
-    extract_with_polygons.terra = function(polys, surf, id, func) {
-        extracted = terra::extract(surf, polys)
-        extracted = extracted |>
-          dplyr::group_by(!!rlang::sym(id)) |>
-          dplyr::summarize(dplyr::across(-!!rlang::sym(id), ~func)) |>
-          dplyr::ungroup()
-        return(extracted)
-    }
-
-    extracted_poly = switch(
-        cls_surf,
-        sf = extract_with_polygons.sf(polys = polys, surf = surf, id = id, func = func),
-        terra = extract_with_polygons.terra(polys = polys, surf = surf, id = id, func = func)
-    )
-    return(extracted_poly)
-}
-
-
-#' Extract raster values with point buffers or polygons
-#' 
-#' @param raster SpatRaster object. 
-#' @param vector SpatVector object.
-#' @param id character(1). Unique identifier of each point.
-#' @param func function taking one numeric vector argument.
-#' @param mode one of "polygon" (generic polygons to extract raster values with) or "buffer" (point with buffer radius)
-#' @param ... various. Passed to extract_with_buffer. See \code{?extract_with_buffer} for details.
-#' @return 
-#' @author Insang Song \email{geoissong@@gmail.com}
-#' @export
-extract_with <- function(raster, vector, id, func = mean, mode = "polygon", ...) {
-    if (!mode %in% c("polygon", "buffer")) {
-      stop("Argument 'mode' should be one of 'polygon' or 'buffer'.\n")
-    }
-    stopifnot(is.character(id))
-    stopifnot(id %in% names(vector))
-
-    extracted = 
-      switch(mode,
-        polygon = extract_with_polygons(vector, raster, id, func),
-        buffer = extract_with_buffer(vector, raster, id = id, func = func, ...))
-    return(extracted)
-}
-
-
-#' Calculate SEDC covariates
-#' @param point_from SpatVector object. Locations where the sum of SEDCs are calculated.
-#' @param point_to SpatVector object. Locations where each SEDC is calculated.
-#' @param id character(1). Name of the unique id field in point_to.
-#' @param sedc_bandwidth numeric(1). Distance at which the source concentration is reduced to exp(-3) (approximately 95 %)  
-#' @param threshold numeric(1). For computational efficiency, the nearest points in threshold will be selected
-#' @param target_fields character(varying). Field names in characters.
-#' @description NOTE: sf implementation is pending. Only available for terra.
-#' @author Insang Song
-#' @export
-calculate_sedc <- function(point_from, point_to, id, sedc_bandwidth, threshold, target_fields) {
-  # define sources, set SEDC exponential decay range
-  len_point_from = seq_len(nrow(point_from))
-  len_point_to = seq_len(nrow(point_to))
-
-  point_from$from_id = len_point_from
-  # select egrid_v only if closer than 3e5 meters from each aqs
-  point_from_buf = terra::buffer(point_from_buf, threshold = threshold, quadsegs = 90)
-  point_to = point_to[point_from_buf,]
-  point_to$to_id = len_point_to
-
-  # near features with distance argument: only returns integer indices
-  near_from_to = terra::nearby(point_from, point_to, distance = threshold)
-  # attaching actual distance
-  dist_near_to = terra::distance(point_from, point_to)
-  dist_near_to_df = as.vector(dist_near_to)
-  # adding integer indices
-  dist_near_to_tdf = expand.grid(from_id = len_point_from, to_id = len_point_to)
-  dist_near_to_df = cbind(dist_near_to_tdf, dist = dist_near_to_df)
-
-  # summary
-  near_from_to = near_from_to |>
-    dplyr::as_tibble() |>
-    dplyr::left_join(data.frame(point_from)) |>
-    dplyr::left_join(data.frame(point_to)) |>
-    dplyr::left_join(dist_near_to_df) |>
-    # per the definition in https://mserre.sph.unc.edu/BMElab_web/SEDCtutorial/index.html
-    # exp(-3) is about 0.05
-    dplyr::mutate(w_sedc = exp((-3 * dist) / sedc_bandwidth)) |>
-    dplyr::group_by(!!rlang::sym(id)) |>
-    dplyr::summarize(dplyr::across(dplyr::all_of(target_fields), list(sedc = ~sum(w_sedc * ., na.rm = TRUE)))) |>
-    dplyr::ungroup()
-
-  invisible(near_from_to)
-  
-}
-
-
-#' Computing area weighted covariates using two polygon sf or SpatVector objects
-#' @param poly_in A sf/SpatVector object at weighted means will be calculated.
-#' @param poly_weight A sf/SpatVector object from which weighted means will be calculated.
-#' @param id_poly_in character(1). The unique identifier of each polygon in poly_in
-#' @return A data.frame with all numeric fields of area-weighted means.
-#' @description When poly_in and poly_weight are different classes, poly_weight will be converted to the class of poly_in. 
-#' @author Insang Song \email{geoissong@@gmail.com}
-#' @examples 
-#' # package
-#' library(sf)
-#' 
-#' # run
-#' nc = sf::st_read(system.file("shape/nc.shp", package="sf"))
-#' nc = sf::st_transform(nc, 5070)
-#' pp = sf::st_sample(nc, size = 300)
-#' pp = sf::st_as_sf(pp)
-#' pp[["id"]] = seq(1, nrow(pp))
-#' sf::st_crs(pp) = "EPSG:5070"
-#' ppb = sf::st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
-#' 
-#' system.time({ppb_nc_aw = aw_covariates(ppb, nc, 'id')})
-#' summary(ppb_nc_aw)
-#' #### Example of aw_covariates ends ####
-#' @export
-aw_covariates <- function(poly_in, poly_weight, id_poly_in = "ID") {
-    stopifnot("Inputs have invalid classes.\n" = 
-      methods::is(poly_in, "sf") || methods::is(poly_weight, "sf") || methods::is(poly_in, "SpatVector") || methods::is(poly_weight, "SpatVector"))
-    #check_crs()
-
-    ## distinguish numeric and nonnumeric columns
-    index_numeric = grep("(integer|numeric)", unlist(sapply(poly_weight, class)))
-    
-    aw_covariates.terra = function(poly_in, poly_weight, id_poly_in = id_poly_in) {
-        
-        poly_intersected = terra::intersect(poly_in, poly_weight)
-        poly_intersected[["area_segment_"]] = terra::expanse(poly_intersected)
-        poly_intersected = data.frame(poly_intersected) |>
-            dplyr::group_by(!!rlang::sym(id_poly_in)) |>
-            dplyr::summarize(dplyr::across(is.numeric,
-                        ~stats::weighted.mean(., w = area_segment_))) |>
-            dplyr::ungroup()
-        return(poly_intersected)
-    }
-
-    class_poly_in = check_packbound(poly_in)
-    class_poly_weight = check_packbound(poly_weight)
-
-    if (class_poly_in != class_poly_weight) {
-      class_poly_weight = switch_packbound(class_poly_weight)
-    }
-    
-    switch(class_poly_in,
-        sf = sf::st_interpolate_aw(poly_weight[,index_numeric], poly_in, extensive = FALSE),
-        terra = aw_covariates.terra(poly_in, poly_weight[,index_numeric], id_poly_in = id_poly_in))
-    
-}
-
-# ncbuf = terra::intersect(vect(ppb), vect(nc))
-# ncbuf_a = ncbuf
-# ncbuf_a$segarea = expanse(ncbuf_a)
-# ncbuf_k = data.frame(ncbuf_a) |>
-#   dplyr::group_by(id) |>
-#   dplyr::summarize(across(is.numeric,
-#                ~weighted.mean(., w = segarea))) |>
-#   dplyr::ungroup()
-
-#ncbufagg = terra::aggregate(ncbuf, by = 'id', fun = weighted.mean, w = ncbuf_a$segarea)
-
-
-#' @title Extract summarized values from raster with points and a buffer radius (to be written)
-#' 
-#' @description For simplicity, it is assumed that the coordinate systems of the points and the raster are the same. Kernel function is not yet implemented. 
-#' @param points SpatVector object. Coordinates where buffers will be generated
-#' @param surf SpatRaster object. A raster of whatnot a summary will be calculated
-#' @param radius numeric(1). Buffer radius. here we assume circular buffers only
-#' @param id character(1). Unique identifier of each point.
-#' @param qsegs integer(1). Number of vertices at a quarter of a circle. Default is 90.
-#' @param func a function taking a numeric vector argument.
-#' @param kernel character(1). Name of a kernel function (yet to be implemented)
-#' @param bandwidth numeric(1). Kernel bandwidth.
-#' @return a data.frame object with mean value
-#' @author Insang Song \email{geoissong@@gmail.com}
-#' 
-#' @export
-extract_with_buffer <- function(
-    points, surf, radius, id, qsegs = 90, func = mean, kernel = NULL, bandwidth = NULL
-    ) {
-    # type check
-    stopifnot("Check class of the input points.\n" = methods::is(points, "SpatVector"))
-    stopifnot("Check class of the input radius.\n" = is.numeric(radius))
-    stopifnot(is.character(id))
-    stopifnot(is.integer(qsegs))
-
-    if (!is.null(kernel)) {
-        extracted = extract_with_buffer.flat(points = points,
-                                      surf = surf,
-                                      radius = radius,
-                                      id = id,
-                                      func = func,
-                                      qsegs = qsegs)
-        return(extracted)
-    }
-
-    extracted = extract_with_buffer.kernel(points = points,
-                                           surf = surf,
-                                           radius = radius,
-                                           id = id,
-                                           func = func,
-                                           qsegs = qsegs,
-                                           kernel = kernel,
-                                           bandwidth = bandwidth)
-    return(extracted)
-
-}
-
-# Subfunction: extract with buffers (flat weight; simple mean)
-extract_with_buffer.flat <- function(
-        points, surf, radius, id, qsegs, func = mean, kernel = NULL, bandwidth = NULL
-    ) {
-    # generate buffers
-    bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
-    # crop raster
-    bufs_extent = terra::ext(bufs)
-    surf_cropped = terra::crop(surf, bufs_extent)
-    name_surf_val = names(surf)
-    # extract raster values
-    surf_at_bufs = terra::extract(surf_cropped, bufs)
-    surf_at_bufs_summary = 
-        surf_at_bufs |> 
-            dplyr::group_by(ID) |> 
-            dplyr::summarize(dplyr::across(dplyr::all_of(name_surf_val), ~mean, na.rm=T)) |> 
-            dplyr::ungroup()
-    return(surf_at_bufs_summary)
-}
-
-
-# Subfunction: extract with buffers (kernel weight; weighted mean)
-extract_with_buffer.kernel <- function(
-        points, surf, radius, id, qsegs, func = mean, kernel, bandwidth
-    ) {
-        # generate buffers
-        bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
-        # crop raster
-        bufs_extent = terra::ext(bufs)
-        surf_cropped = terra::crop(surf, bufs_extent)
-        name_surf_val = names(surf)
-
-        # TODO: kernel implementation
-
-
-        # extract raster values
-        surf_at_bufs = terra::extract(surf_cropped, bufs)
-        surf_at_bufs_summary = 
-            surf_at_bufs |> 
-                dplyr::group_by(ID) |> 
-                dplyr::summarize(dplyr::across(dplyr::all_of(name_surf_val), ~mean, na.rm=T)) |> 
-                dplyr::ungroup()
-        return(surf_at_bufs_summary)
-}
-
diff --git a/scomps.Rcheck/00_pkg_src/scomps/R/switch_format.R b/scomps.Rcheck/00_pkg_src/scomps/R/switch_format.R
deleted file mode 100644
index a0c38e8f..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/R/switch_format.R
+++ /dev/null
@@ -1,25 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' @title Switch spatial data class
-#' @description Convert stars into SpatRaster and vice versa; sf into SpatVector and vice versa.
-#' @author Insang Song
-#' @param input Spat* in terra or sf object.
-#' @return Data converted to the other package class (if sf, terra; if terra, sf)
-#' @export
-switch_packbound <- function(input) {
-  stopifnot("Input should be one of sf or Spat* object.\n" = any(methods::is(input, "sf"), methods::is(input, "stars"), methods::is(input, "SpatVector"), methods::is(input, "SpatRaster")))
-  cls_input = check_packbound(input)
-  type_input = check_datatype(input)
-
-  switched = 
-  switch(cls_input,
-    sf = switch(type_input,
-      vector = terra::vect(input),
-      raster = terra::rast(input)
-    ),
-    terra = switch(type_input,
-      vector = sf::st_as_sf(input),
-      raster = stars::st_as_stars(input)))
-
-  invisible(switched)
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/R/validate.R b/scomps.Rcheck/00_pkg_src/scomps/R/validate.R
deleted file mode 100644
index 545869c2..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/R/validate.R
+++ /dev/null
@@ -1,18 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand
-
-#' Validate and repair input vector data
-#' @description It tries repairing input vector data. Vector validity violation usually appears in polygon data with self-crossing or hole orders. This function will pass the input_vector object to sf::st_make_valid() (if input_vector is sf) or terra::makeValid() (if input_vector is SpatVector). May take some time depending on the geometry complexity.
-#' @author Insang Song
-#' @param input_vector One of sf or vect class. Target points of computation.
-#' @return A repaired sf or SpatVector object depending on the class of input_vector.
-#' @export
-validate_and_repair_vectors <- function(input_vector) {
-  detected = check_packbound(input_vector)
-
-  validated = switch(detected,
-    terra = terra::makeValid(input_vector),
-    sf = sf::st_make_valid(input_vector))
-
-  return(validated)
-}
-
diff --git a/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v00_good_practice_parallelization.R b/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v00_good_practice_parallelization.R
deleted file mode 100644
index c639e81d..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v00_good_practice_parallelization.R
+++ /dev/null
@@ -1,4 +0,0 @@
-## -----------------------------------------------------------------------------
-knitr::opts_chunk$set(warning = FALSE, message = FALSE)
-
-
diff --git a/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v00_good_practice_parallelization.Rmd b/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v00_good_practice_parallelization.Rmd
deleted file mode 100644
index 8966a59d..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v00_good_practice_parallelization.Rmd
+++ /dev/null
@@ -1,39 +0,0 @@
----
-title: "Good practice of scomps with HPC"
-date: "`r Sys.Date()`"
-output: rmarkdown::html_vignette
-vignette: >
-  %\VignetteIndexEntry{good_practice_hpc}
-  %\VignetteEngine{knitr::rmarkdown}
-  %\VignetteEncoding{UTF-8}
----
-
-
-```{r}
-knitr::opts_chunk$set(warning = FALSE, message = FALSE)
-
-```
-
-## Assumptions
-- Users have an accessible HPC at your work
-- Data are stored in distributed file systems (usually incorporated into the HPC system)
-
-
-## Basic workflow
-
-### Practice for minimizing errors
-- Consider using `try()` or `tryCatch()` not to a tiny error will halt all the work without any results 
-    - Especially with the higher-level functions
-- "IPDE -- Inspect, Predict, Decide, Execute" all the time
-
-### Raster-Vector overlay
-- Make `sp_index_grid()` to get padded grid objects
-- Convert sf/SpatVector objects into `terra::ext()` compatible named numeric vector
-    - For example: `c(xmin=0, ymin=0, xmax=10, ymax=10)`
-- Make list objects with: 
-    - An extent vector in each element
-    - Preprocessed vector objects with respect to each extent vector in the first list
-    - Preferably all lists are named 
-- Write a `future.apply` script running through the extent list object
-- Run a small amount of data to estimate the total computational demand
-- Submit a job with a proper amount of computational assets
diff --git a/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v00_good_practice_parallelization.html b/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v00_good_practice_parallelization.html
deleted file mode 100644
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+++ /dev/null
@@ -1,408 +0,0 @@
-
-
-
-
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-
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-
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-
Good practice of scomps with HPC

-
2023-10-04

-
-
-
-
knitr::opts_chunk$set(warning = FALSE, message = FALSE)

-

-
Assumptions

-
    
-
  • Users have an accessible HPC at your work
    • 
-
  • Data are stored in distributed file systems (usually incorporated
-into the HPC system)
    • 
-

-

-

-
Basic workflow

-

-
Practice for minimizing errors

-
    
-
  • Consider using try() or tryCatch() not to
-a tiny error will halt all the work without any results
-
      
-
    • Especially with the higher-level functions
      • 
-
    • 
-
  • “IPDE – Inspect, Predict, Decide, Execute” all the time
    • 
-

-

-

-
Raster-Vector overlay

-
    
-
  • Make sp_index_grid() to get padded grid objects
    • 
-
  • Convert sf/SpatVector objects into terra::ext()
-compatible named numeric vector
-
      
-
    • For example: c(xmin=0, ymin=0, xmax=10, ymax=10)
      • 
-
    • 
-
  • Make list objects with:
-
      
-
    • An extent vector in each element
      • 
-
    • Preprocessed vector objects with respect to each extent vector in
-the first list
      • 
-
    • Preferably all lists are named
      • 
-
    • 
-
  • Write a future.apply script running through the extent
-list object
    • 
-
  • Run a small amount of data to estimate the total computational
-demand
    • 
-
  • Submit a job with a proper amount of computational assets
    • 
-

-

-

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diff --git a/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v01_generate_computational_grid.R b/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v01_generate_computational_grid.R
deleted file mode 100644
index aa3d29fc..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v01_generate_computational_grid.R
+++ /dev/null
@@ -1,22 +0,0 @@
-## -----------------------------------------------------------------------------
-knitr::opts_chunk$set(warning = FALSE, message = FALSE)
-
-
-## -----------------------------------------------------------------------------
-library(scomps)
-library(sf)
-library(terra)
-library(stars)
-library(dplyr)
-
-
-## -----------------------------------------------------------------------------
-# your_grid = scomps::sp_index_grid()
-
-
-## -----------------------------------------------------------------------------
-# library(mapsf)
-# mf_map(your_grid$geometry)
-
-
-
diff --git a/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v01_generate_computational_grid.Rmd b/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v01_generate_computational_grid.Rmd
deleted file mode 100644
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--- a/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v01_generate_computational_grid.Rmd
+++ /dev/null
@@ -1,46 +0,0 @@
----
-title: "Generate computational grids"
-date: "`r Sys.Date()`"
-output: rmarkdown::html_vignette
-vignette: >
-  %\VignetteIndexEntry{computational_grids}
-  %\VignetteEngine{knitr::rmarkdown}
-  %\VignetteEncoding{UTF-8}
----
-
-
-```{r}
-knitr::opts_chunk$set(warning = FALSE, message = FALSE)
-
-```
-
-
-## Prepare input data
-```{r}
-library(scomps)
-library(sf)
-library(terra)
-library(stars)
-library(dplyr)
-
-```
-
-## Computational grids
-```{r}
-# your_grid = scomps::sp_index_grid()
-
-```
-
-
-## Visualize computational grids
-```{r}
-# library(mapsf)
-# mf_map(your_grid$geometry)
-
-
-```
-
-
-
-## Notes
-- Computational grids are the exhaustive split of the entire study region. You should take a square buffer of each grid to clip the target raster or vector.
diff --git a/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v01_generate_computational_grid.html b/scomps.Rcheck/00_pkg_src/scomps/inst/doc/v01_generate_computational_grid.html
deleted file mode 100644
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+++ /dev/null
@@ -1,388 +0,0 @@
-
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Generate computational grids

-
2023-10-04

-
-
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-
knitr::opts_chunk$set(warning = FALSE, message = FALSE)

-

-
Prepare input data

-
library(scomps)
-library(sf)
-library(terra)
-library(stars)
-library(dplyr)

-

-

-
Computational grids

-
# your_grid = scomps::sp_index_grid()

-

-

-
Visualize computational grids

-
# library(mapsf)
-# mf_map(your_grid$geometry)

-

-

-
Notes

-
    
-
  • Computational grids are the exhaustive split of the entire study
-region. You should take a square buffer of each grid to clip the target
-raster or vector.
    • 
-

-

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diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/aw_covariates.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/aw_covariates.Rd
deleted file mode 100644
index ca836de6..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/man/aw_covariates.Rd
+++ /dev/null
@@ -1,41 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/processing.R
-\name{aw_covariates}
-\alias{aw_covariates}
-\title{Computing area weighted covariates using two polygon sf or SpatVector objects}
-\usage{
-aw_covariates(poly_in, poly_weight, id_poly_in = "ID")
-}
-\arguments{
-\item{poly_in}{A sf/SpatVector object at weighted means will be calculated.}
-
-\item{poly_weight}{A sf/SpatVector object from which weighted means will be calculated.}
-
-\item{id_poly_in}{character(1). The unique identifier of each polygon in poly_in}
-}
-\value{
-A data.frame with all numeric fields of area-weighted means.
-}
-\description{
-When poly_in and poly_weight are different classes, poly_weight will be converted to the class of poly_in.
-}
-\examples{
-# package
-library(sf)
-
-# run
-nc = sf::st_read(system.file("shape/nc.shp", package="sf"))
-nc = sf::st_transform(nc, 5070)
-pp = sf::st_sample(nc, size = 300)
-pp = sf::st_as_sf(pp)
-pp[["id"]] = seq(1, nrow(pp))
-sf::st_crs(pp) = "EPSG:5070"
-ppb = sf::st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
-
-system.time({ppb_nc_aw = aw_covariates(ppb, nc, 'id')})
-summary(ppb_nc_aw)
-#### Example of aw_covariates ends ####
-}
-\author{
-Insang Song \email{geoissong@gmail.com}
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/calculate_sedc.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/calculate_sedc.Rd
deleted file mode 100644
index 21178a77..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/man/calculate_sedc.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/processing.R
-\name{calculate_sedc}
-\alias{calculate_sedc}
-\title{Calculate SEDC covariates}
-\usage{
-calculate_sedc(
-  point_from,
-  point_to,
-  id,
-  sedc_bandwidth,
-  threshold,
-  target_fields
-)
-}
-\arguments{
-\item{point_from}{SpatVector object. Locations where the sum of SEDCs are calculated.}
-
-\item{point_to}{SpatVector object. Locations where each SEDC is calculated.}
-
-\item{id}{character(1). Name of the unique id field in point_to.}
-
-\item{sedc_bandwidth}{numeric(1). Distance at which the source concentration is reduced to exp(-3) (approximately 95 \%)}
-
-\item{threshold}{numeric(1). For computational efficiency, the nearest points in threshold will be selected}
-
-\item{target_fields}{character(varying). Field names in characters.}
-}
-\description{
-NOTE: sf implementation is pending. Only available for terra.
-}
-\author{
-Insang Song
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/check_bbox.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/check_bbox.Rd
deleted file mode 100644
index 444c934a..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/man/check_bbox.Rd
+++ /dev/null
@@ -1,24 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/check.R
-\name{check_bbox}
-\alias{check_bbox}
-\title{Check if the data extent is inside the reference bounding box}
-\usage{
-check_bbox(data_query, reference, reference_crs = NULL)
-}
-\arguments{
-\item{data_query}{sf*/stars/SpatVector/SpatRaster object.}
-
-\item{reference}{sf*/stars/SpatVector/SpatRaster object or a named numeric vector with four names (xmin, ymin, xmax, and ymax).}
-
-\item{reference_crs}{Well-known-text-formatted or EPSG code of the reference's coordinate system. Only required when a named numeric vector is passed to reference.}
-}
-\value{
-TRUE (the queried data extent is completely within the reference bounding box) or FALSE
-}
-\description{
-One of the most common errors in spatial computation is rooted in the entirely or partly incomparable spatial extents of input datasets. This function returns whether your data is inside the target computational extent. It is assumed that you know and have the exact computational region. This function will return TRUE if the reference region completely contains your data's extent and FALSE otherwise.
-}
-\author{
-Insang Song \email{geoissong@gmail.com}
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/check_crs.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/check_crs.Rd
deleted file mode 100644
index 6f9fa5b5..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/man/check_crs.Rd
+++ /dev/null
@@ -1,28 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/check.R
-\name{check_crs}
-\alias{check_crs}
-\title{Check Coordinate Reference System}
-\usage{
-check_crs(x)
-}
-\arguments{
-\item{x}{sf/stars/SpatVector/SpatRaster object.}
-}
-\value{
-A st_crs or crs object.
-}
-\description{
-Check Coordinate Reference System
-}
-\examples{
-# data
-library(sf)
-ncpath = system.file("shape/nc.shp", package = "sf")
-nc = read_sf(ncpath)
-check_crs(nc)
-
-}
-\author{
-Insang Song \email{geoissong@gmail.com}
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/check_crs2.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/check_crs2.Rd
deleted file mode 100644
index c15652d6..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/man/check_crs2.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/check.R
-\name{check_crs2}
-\alias{check_crs2}
-\title{check_crs2: Coordinate system checker}
-\usage{
-check_crs2(input, crs_standard = "EPSG:4326")
-}
-\arguments{
-\item{input}{Input object one of sf or terra::Spat* object}
-
-\item{crs_standard}{character(1). A standard definition of coordinate reference system. Default is "EPSG:4326" Consult \href{https://epsg.io}{epsg.io} for details of other CRS.}
-}
-\value{
-A (reprojected) sf or SpatVector object.
-}
-\description{
-The input is checked whether its coordinate system is present. If not, it is reprojected to EPSG:5179.
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/check_packbound.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/check_packbound.Rd
deleted file mode 100644
index 6bda7485..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/man/check_packbound.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/check.R
-\name{check_packbound}
-\alias{check_packbound}
-\title{Return the package the input object is based on}
-\usage{
-check_packbound(input)
-}
-\arguments{
-\item{input}{Spat* in terra or sf object.}
-}
-\value{
-A character object; one of 'terra' and 'sf'
-}
-\description{
-Detect whether the input object is sf or Spat* object.
-}
-\author{
-Insang Song
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/check_within_reference.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/check_within_reference.Rd
deleted file mode 100644
index c193a975..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/man/check_within_reference.Rd
+++ /dev/null
@@ -1,22 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/check.R
-\name{check_within_reference}
-\alias{check_within_reference}
-\title{Check if the boundary of the vector/raster object is inside the reference}
-\usage{
-check_within_reference(input_object, reference)
-}
-\arguments{
-\item{input_object}{sf/stars/SpatVector/SpatRaster object.}
-
-\item{reference}{sf/stars/SpatVector/SpatRaster object.}
-}
-\value{
-logical
-}
-\description{
-Check if the boundary of the vector/raster object is inside the reference
-}
-\author{
-Insang Song \email{geoissong@gmail.com}
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/clip_as_extent.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/clip_as_extent.Rd
deleted file mode 100644
index 06ec0bbf..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/man/clip_as_extent.Rd
+++ /dev/null
@@ -1,26 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/processing.R
-\name{clip_as_extent}
-\alias{clip_as_extent}
-\title{Extent clipping}
-\usage{
-clip_as_extent(pnts, buffer_r, nqsegs = NULL, target_input)
-}
-\arguments{
-\item{pnts}{sf or SpatVector object}
-
-\item{buffer_r}{numeric(1). buffer radius. this value will be automatically multiplied by 1.25}
-
-\item{nqsegs}{integer(1). the number of points per a quarter circle; SOON TO BE DEPRECATED}
-
-\item{target_input}{sf or SpatVector object to be clipped}
-}
-\value{
-A clipped sf or SpatVector object.
-}
-\description{
-Clip input vector by the expected maximum extent of computation.
-}
-\author{
-Insang Song
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/clip_as_extent_ras.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/clip_as_extent_ras.Rd
deleted file mode 100644
index e6762901..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/man/clip_as_extent_ras.Rd
+++ /dev/null
@@ -1,23 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/processing.R
-\name{clip_as_extent_ras}
-\alias{clip_as_extent_ras}
-\title{clip_as_extent_ras: Clip input raster.}
-\usage{
-clip_as_extent_ras(pnts, buffer_r, nqsegs = 180, ras)
-}
-\arguments{
-\item{pnts}{sf or SpatVector object}
-
-\item{buffer_r}{numeric(1). buffer radius. this value will be automatically multiplied by 1.25}
-
-\item{nqsegs}{integer(1). the number of points per a quarter circle}
-
-\item{ras}{SpatRaster object to be clipped}
-}
-\description{
-Clip input raster by the expected maximum extent of computation.
-}
-\author{
-Insang Song
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/clip_as_extent_ras2.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/clip_as_extent_ras2.Rd
deleted file mode 100644
index 6d8c0e00..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/man/clip_as_extent_ras2.Rd
+++ /dev/null
@@ -1,23 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/processing.R
-\name{clip_as_extent_ras2}
-\alias{clip_as_extent_ras2}
-\title{clip_as_extent_ras2: Clip input raster (version 2).}
-\usage{
-clip_as_extent_ras2(points_in, buffer_r, nqsegs = 180, ras)
-}
-\arguments{
-\item{points_in}{sf or SpatVector object}
-
-\item{buffer_r}{numeric(1). buffer radius. this value will be automatically multiplied by 1.25}
-
-\item{nqsegs}{integer(1). the number of points per a quarter circle}
-
-\item{ras}{SpatRaster object to be clipped}
-}
-\description{
-Clip input raster by the expected maximum extent of computation.
-}
-\author{
-Insang Song
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/distribute_process.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/distribute_process.Rd
deleted file mode 100644
index ebb58e82..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/man/distribute_process.Rd
+++ /dev/null
@@ -1,26 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/interpret_computational_domain.R
-\name{distribute_process}
-\alias{distribute_process}
-\title{Process a given function in the entire or partial computational grids (under construction)}
-\usage{
-distribute_process(grids, grid_id = NULL, fun, ...)
-}
-\arguments{
-\item{grids}{sf/SpatVector object. Computational grids.}
-
-\item{grid_id}{character(1) or numeric(2). Default is NULL. If NULL, all grid_ids are used. \code{"id_from:id_to"} format or \code{c(unique(grid_id)[id_from], unique(grid_id)[id_to])}}
-
-\item{fun}{function supported in scomps.}
-
-\item{...}{Arguments passed to fun.}
-}
-\value{
-a data.frame object with mean value
-}
-\description{
-Should
-}
-\author{
-Insang Song \email{geoissong@gmail.com}
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/estimate_demands.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/estimate_demands.Rd
deleted file mode 100644
index 787ad77f..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/man/estimate_demands.Rd
+++ /dev/null
@@ -1,23 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/estimate_demands.R
-\name{estimate_demands}
-\alias{estimate_demands}
-\title{Estimate computational demands from inputs (to be written)}
-\usage{
-estimate_demands(inputs, nx, ny, padding)
-}
-\arguments{
-\item{inputs}{a list of sf/Spat* objects or file paths}
-
-\item{nx}{integer(1).}
-
-\item{ny}{integer(1).}
-
-\item{padding}{numeric(1). Extrusion factor}
-}
-\description{
-Estimate computational demands from inputs (to be written)
-}
-\author{
-Insang Song
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/extent_to_polygon.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/extent_to_polygon.Rd
deleted file mode 100644
index 2874461e..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/man/extent_to_polygon.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/check.R
-\name{extent_to_polygon}
-\alias{extent_to_polygon}
-\title{Generate a rectangular polygon from extent}
-\usage{
-extent_to_polygon(extent, output_class = "terra", crs = "EPSG:4326")
-}
-\arguments{
-\item{extent}{input extent. A numeric vector with xmin/xmax/ymin/ymax, sf::st_bbox() or terra::ext() outputs.}
-
-\item{output_class}{character(1). Class of the output polygon. One of "sf" or "terra"}
-
-\item{crs}{character(1). Coordinate reference system definition.}
-}
-\description{
-Generate a rectangular polygon from extent
-}
-\author{
-Insang Song
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/extract_with.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/extract_with.Rd
deleted file mode 100644
index 8794f571..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/man/extract_with.Rd
+++ /dev/null
@@ -1,27 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/processing.R
-\name{extract_with}
-\alias{extract_with}
-\title{Extract raster values with point buffers or polygons}
-\usage{
-extract_with(raster, vector, id, func = mean, mode = "polygon", ...)
-}
-\arguments{
-\item{raster}{SpatRaster object.}
-
-\item{vector}{SpatVector object.}
-
-\item{id}{character(1). Unique identifier of each point.}
-
-\item{func}{function taking one numeric vector argument.}
-
-\item{mode}{one of "polygon" (generic polygons to extract raster values with) or "buffer" (point with buffer radius)}
-
-\item{...}{various. Passed to extract_with_buffer. See \code{?extract_with_buffer} for details.}
-}
-\description{
-Extract raster values with point buffers or polygons
-}
-\author{
-Insang Song \email{geoissong@gmail.com}
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/extract_with_buffer.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/extract_with_buffer.Rd
deleted file mode 100644
index f0c3943d..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/man/extract_with_buffer.Rd
+++ /dev/null
@@ -1,43 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/processing.R
-\name{extract_with_buffer}
-\alias{extract_with_buffer}
-\title{Extract summarized values from raster with points and a buffer radius (to be written)}
-\usage{
-extract_with_buffer(
-  points,
-  surf,
-  radius,
-  id,
-  qsegs = 90,
-  func = mean,
-  kernel = NULL,
-  bandwidth = NULL
-)
-}
-\arguments{
-\item{points}{SpatVector object. Coordinates where buffers will be generated}
-
-\item{surf}{SpatRaster object. A raster of whatnot a summary will be calculated}
-
-\item{radius}{numeric(1). Buffer radius. here we assume circular buffers only}
-
-\item{id}{character(1). Unique identifier of each point.}
-
-\item{qsegs}{integer(1). Number of vertices at a quarter of a circle. Default is 90.}
-
-\item{func}{a function taking a numeric vector argument.}
-
-\item{kernel}{character(1). Name of a kernel function (yet to be implemented)}
-
-\item{bandwidth}{numeric(1). Kernel bandwidth.}
-}
-\value{
-a data.frame object with mean value
-}
-\description{
-For simplicity, it is assumed that the coordinate systems of the points and the raster are the same. Kernel function is not yet implemented.
-}
-\author{
-Insang Song \email{geoissong@gmail.com}
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/extract_with_polygons.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/extract_with_polygons.Rd
deleted file mode 100644
index adaa9c6a..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/man/extract_with_polygons.Rd
+++ /dev/null
@@ -1,28 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/processing.R
-\name{extract_with_polygons}
-\alias{extract_with_polygons}
-\title{Extract summarized values from raster with generic polygons}
-\usage{
-extract_with_polygons(polys, surf, id, func = mean, na.rm = TRUE)
-}
-\arguments{
-\item{polys}{sf/SpatVector object. Polygons.}
-
-\item{surf}{stars/SpatRaster object. A raster of whatnot a summary will be calculated}
-
-\item{id}{character(1). Unique identifier of each point.}
-
-\item{func}{a function taking one argument. For example, function(x) mean(x, na.rm = TRUE) or \(x) mode(x, na.rm = TRUE)}
-
-\item{na.rm}{logical(1). NA values are omitted when summary is calculated.}
-}
-\value{
-a data.frame object with function value
-}
-\description{
-For simplicity, it is assumed that the coordinate systems of the points and the raster are the same. Kernel function is not yet implemented.
-}
-\author{
-Insang Song \email{geoissong@gmail.com}
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/get_computational_regions.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/get_computational_regions.Rd
deleted file mode 100644
index 6a864a55..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/man/get_computational_regions.Rd
+++ /dev/null
@@ -1,53 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/interpret_computational_domain.R
-\name{get_computational_regions}
-\alias{get_computational_regions}
-\title{Get a set of computational regions}
-\usage{
-get_computational_regions(
-  input,
-  mode = "grid",
-  nx = 10,
-  ny = 10,
-  grid_min_features = 30,
-  padding = NULL,
-  unit = NULL,
-  ...
-)
-}
-\arguments{
-\item{input}{sf or Spat* object.}
-
-\item{mode}{character(1). Mode of region construction. One of "grid" (simple grid regardless of the number of features in each grid), "density" (clustering-based varying grids), "grid_advanced" (merging adjacent grids with smaller number of features than grid_min_features).}
-
-\item{nx}{integer(1). The number of grids along x-axis.}
-
-\item{ny}{integer(1). The number of grids along y-axis.}
-
-\item{grid_min_features}{integer(1). A threshold to merging adjacent grids}
-
-\item{padding}{numeric(1). A extrusion factor to make buffer to clip actual datasets. Depending on the length unit of the CRS of input.}
-
-\item{unit}{character(1). The length unit for padding (optional). units::set_units is used for padding when sf object is used. See \href{https://cran.r-project.org/web/packages/units/vignettes/measurement_units_in_R.html}{units package vignette (web)} for the list of acceptable unit forms.}
-
-\item{...}{arguments passed to the internal function}
-}
-\value{
-A set of polygons in the input class
-}
-\description{
-TODO. Using input points, the bounding box is split to the predefined numbers of columns and rows. Each grid will be buffered by the radius.
-}
-\examples{
-# data
-library(sf)
-ncpath = system.file("shape/nc.shp", package = "sf")
-nc = read_sf(ncpath)
-nc = st_transform(nc, "EPSG:5070")
-# run
-# nc_comp_region = get_computational_regions(nc, nx = 12, ny = 8)
-
-}
-\author{
-Insang Song
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/grid_merge.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/grid_merge.Rd
deleted file mode 100644
index 0361cece..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/man/grid_merge.Rd
+++ /dev/null
@@ -1,38 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/interpret_computational_domain.R
-\name{grid_merge}
-\alias{grid_merge}
-\title{grid_merge: Merge grid polygons with given rules}
-\usage{
-grid_merge(points_in, grid_in, grid_min_features)
-}
-\arguments{
-\item{points_in}{sf or SpatVector object. Target points of computation.}
-
-\item{grid_in}{sf or SpatVector object. The grid generated by sp_index_grid}
-
-\item{grid_min_features}{integer(1). Threshold to merge adjacent grids.}
-}
-\value{
-A sf or SpatVector object of computation grids.
-}
-\description{
-Merge boundary-sharing (in "Rook" contiguity) grids with fewer target features than the threshold. This function strongly assumes that the input is returned from the sp_index_grid, which has 'CGRIDID' as the unique id field.
-}
-\examples{
-# library(sf)
-# library(igraph)
-# ligrary(dplyr)
-# dg = sf::st_as_sfc(st_bbox(c(xmin = 0, ymin = 0, xmax = 8e5, ymax = 6e5)))
-# sf::st_crs(dg) = 5070
-# dgs = sf::st_as_sf(st_make_grid(dg, n = c(20, 15)))
-# dgs$CGRIDID = seq(1, nrow(dgs))
-#
-# dg_sample = st_sample(dg, kappa = 5e-9, mu = 15, scale = 20000, type = "Thomas")
-# sf::st_crs(dg_sample) = sf::st_crs(dg)
-# dg_merged = grid_merge(sf::st_as_sf(sss), dgs, 100)
-#### NOT RUN ####
-}
-\author{
-Insang Song
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/initate_log.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/initate_log.Rd
deleted file mode 100644
index 6e64c090..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/man/initate_log.Rd
+++ /dev/null
@@ -1,24 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/logging.R
-\name{initate_log}
-\alias{initate_log}
-\title{Turn on logging}
-\usage{
-initate_log(expr, dolog = FALSE, logpath)
-}
-\arguments{
-\item{expr}{expression. Any function call to be logged.}
-
-\item{dolog}{logical(1). Will the messages be logged.}
-
-\item{logpath}{character(1). Log file path with the full log file name.}
-}
-\value{
-Nothing. It will export a log file in the specified path as logpath.
-}
-\description{
-Turn on logging
-}
-\author{
-Insang Song
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/rast_short.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/rast_short.Rd
deleted file mode 100644
index de4acd9f..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/man/rast_short.Rd
+++ /dev/null
@@ -1,22 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/preprocessing.R
-\name{rast_short}
-\alias{rast_short}
-\title{Quick call for SpatRaster with a window}
-\usage{
-rast_short(rasterpath, win)
-}
-\arguments{
-\item{rasterpath}{character(1). Path to the raster file.}
-
-\item{win}{Named integer vector (4) or terra::ext() results.}
-}
-\value{
-SpatRaster object.
-}
-\description{
-Quick call for SpatRaster with a window
-}
-\author{
-Insang Song
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/set_clip_extent.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/set_clip_extent.Rd
deleted file mode 100644
index 4fb91191..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/man/set_clip_extent.Rd
+++ /dev/null
@@ -1,22 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/preprocessing.R
-\name{set_clip_extent}
-\alias{set_clip_extent}
-\title{Setting the clipping extent}
-\usage{
-set_clip_extent(pnts, buffer_r)
-}
-\arguments{
-\item{pnts}{One of sf or vect class. Target points of computation.}
-
-\item{buffer_r}{numeric(1). Buffer radius. It is assumed in metres}
-}
-\value{
-A terra::ext or sfc_POLYGON object of the computation extent.
-}
-\description{
-Return clipping extent with buffer radius. It assumes the input CRS is projected and linear unit is meters.
-}
-\author{
-Insang Song
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/sp_index_grid.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/sp_index_grid.Rd
deleted file mode 100644
index bf0d4ac5..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/man/sp_index_grid.Rd
+++ /dev/null
@@ -1,24 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/interpret_computational_domain.R
-\name{sp_index_grid}
-\alias{sp_index_grid}
-\title{sp_index_grid: Generate grid polygons}
-\usage{
-sp_index_grid(points_in, ncutsx, ncutsy)
-}
-\arguments{
-\item{points_in}{sf or SpatVector object. Target points of computation.}
-
-\item{ncutsx}{integer(1). The number of splits along x-axis.}
-
-\item{ncutsy}{integer(1). The number of splits along y-axis.}
-}
-\value{
-A sf or SpatVector object of computation grids with unique grid id (CGRIDID).
-}
-\description{
-Returns a sf object that includes x- and y- index by using two inputs ncutsx and ncutsy, which are x- and y-directional splits, respectively.
-}
-\author{
-Insang Song
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/sp_indexing.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/sp_indexing.Rd
deleted file mode 100644
index f4da1434..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/man/sp_indexing.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/indexing.R
-\name{sp_indexing}
-\alias{sp_indexing}
-\title{Create integer indices for grid}
-\usage{
-sp_indexing(points_in, ncutsx, ncutsy)
-}
-\arguments{
-\item{points_in}{sf object.}
-
-\item{ncutsx}{integer(1). The number of splits along x-axis.}
-
-\item{ncutsy}{integer(1). The number of splits along y-axis.}
-}
-\description{
-Returns a tibble object that includes x- and y- index by using two inputs ncutsx and ncutsy, which are x- and y-directional splits, respectively.
-}
-\author{
-Insang Song
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/switch_packbound.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/switch_packbound.Rd
deleted file mode 100644
index 18eafb22..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/man/switch_packbound.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/switch_format.R
-\name{switch_packbound}
-\alias{switch_packbound}
-\title{Switch spatial data class}
-\usage{
-switch_packbound(input)
-}
-\arguments{
-\item{input}{Spat* in terra or sf object.}
-}
-\value{
-Data converted to the other package class (if sf, terra; if terra, sf)
-}
-\description{
-Convert stars into SpatRaster and vice versa; sf into SpatVector and vice versa.
-}
-\author{
-Insang Song
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/man/validate_and_repair_vectors.Rd b/scomps.Rcheck/00_pkg_src/scomps/man/validate_and_repair_vectors.Rd
deleted file mode 100644
index e8447ca9..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/man/validate_and_repair_vectors.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/validate.R
-\name{validate_and_repair_vectors}
-\alias{validate_and_repair_vectors}
-\title{Validate and repair input vector data}
-\usage{
-validate_and_repair_vectors(input_vector)
-}
-\arguments{
-\item{input_vector}{One of sf or vect class. Target points of computation.}
-}
-\value{
-A repaired sf or SpatVector object depending on the class of input_vector.
-}
-\description{
-It tries repairing input vector data. Vector validity violation usually appears in polygon data with self-crossing or hole orders. This function will pass the input_vector object to sf::st_make_valid() (if input_vector is sf) or terra::makeValid() (if input_vector is SpatVector). May take some time depending on the geometry complexity.
-}
-\author{
-Insang Song
-}
diff --git a/scomps.Rcheck/00_pkg_src/scomps/tests/testthat.R b/scomps.Rcheck/00_pkg_src/scomps/tests/testthat.R
deleted file mode 100644
index b465b524..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/tests/testthat.R
+++ /dev/null
@@ -1,12 +0,0 @@
-# This file is part of the standard setup for testthat.
-# It is recommended that you do not modify it.
-#
-# Where should you do additional test configuration?
-# Learn more about the roles of various files in:
-# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
-# * https://testthat.r-lib.org/articles/special-files.html
-
-library(testthat)
-library(scomps)
-
-test_check("scomps")
diff --git a/scomps.Rcheck/00_pkg_src/scomps/tests/testthat/tests.R b/scomps.Rcheck/00_pkg_src/scomps/tests/testthat/tests.R
deleted file mode 100644
index 6efa4142..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/tests/testthat/tests.R
+++ /dev/null
@@ -1,65 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand  
-testthat::test_that("What package does the input object belong?",
-{
-    withr::local_package("stars")
-    withr::local_package("terra")
-    withr::local_options(list(sf_use_s2 = FALSE))
-    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
-    bcsd_stars = stars::read_stars(bcsd_path)
-
-    packbound_stars = check_packbound(bcsd_stars)
-    sprast_bcsd = terra::rast(bcsd_path)
-    packbound_terra = check_packbound(sprast_bcsd)
-
-    testthat::expect_equal(packbound_stars, "sf")
-    testthat::expect_equal(packbound_terra, "terra")
-})
-
-
-testthat::test_that("What package does the input object belong?",
-{
-    withr::local_package("stars")
-    withr::local_package("terra")
-    withr::local_options(list(sf_use_s2 = FALSE))
-    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
-    bcsd_stars = stars::read_stars(bcsd_path)
-
-    nc = system.file(package = "sf", "shape/nc.shp")
-    nc = sf::read_sf(nc)
-
-    datatype_stars = check_datatype(bcsd_stars)
-    datatype_sf = check_datatype(nc)
-
-    testthat::expect_equal(datatype_stars, "raster")
-    testthat::expect_equal(datatype_sf, "vector")
-})
-
-
-testthat::test_that("Format is well converted",
-{
-    withr::local_package("stars")
-    withr::local_package("terra")
-    withr::local_options(list(sf_use_s2 = FALSE))
-
-    # starts from sf/stars
-    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
-    bcsd_stars = stars::read_stars(bcsd_path)
-    nc = system.file(package = "sf", "shape/nc.shp")
-    nc = sf::read_sf(nc)
-
-    stars_bcsd_tr = switch_packbound(bcsd_stars)
-    sf_nc_tr = switch_packbound(nc)
-
-    testthat::expect_equal(check_packbound(stars_bcsd_tr), "terra")
-    testthat::expect_equal(check_packbound(sf_nc_tr), "terra")
-
-    stars_bcsd_trb = switch_packbound(stars_bcsd_tr)
-    sf_nc_trb = switch_packbound(sf_nc_tr)
-
-    testthat::expect_equal(check_packbound(stars_bcsd_trb), "sf")
-    testthat::expect_equal(check_packbound(sf_nc_trb), "sf")
-
-})
-
-
-
diff --git a/scomps.Rcheck/00_pkg_src/scomps/vignettes/v00_good_practice_parallelization.Rmd b/scomps.Rcheck/00_pkg_src/scomps/vignettes/v00_good_practice_parallelization.Rmd
deleted file mode 100644
index 8966a59d..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/vignettes/v00_good_practice_parallelization.Rmd
+++ /dev/null
@@ -1,39 +0,0 @@
----
-title: "Good practice of scomps with HPC"
-date: "`r Sys.Date()`"
-output: rmarkdown::html_vignette
-vignette: >
-  %\VignetteIndexEntry{good_practice_hpc}
-  %\VignetteEngine{knitr::rmarkdown}
-  %\VignetteEncoding{UTF-8}
----
-
-
-```{r}
-knitr::opts_chunk$set(warning = FALSE, message = FALSE)
-
-```
-
-## Assumptions
-- Users have an accessible HPC at your work
-- Data are stored in distributed file systems (usually incorporated into the HPC system)
-
-
-## Basic workflow
-
-### Practice for minimizing errors
-- Consider using `try()` or `tryCatch()` not to a tiny error will halt all the work without any results 
-    - Especially with the higher-level functions
-- "IPDE -- Inspect, Predict, Decide, Execute" all the time
-
-### Raster-Vector overlay
-- Make `sp_index_grid()` to get padded grid objects
-- Convert sf/SpatVector objects into `terra::ext()` compatible named numeric vector
-    - For example: `c(xmin=0, ymin=0, xmax=10, ymax=10)`
-- Make list objects with: 
-    - An extent vector in each element
-    - Preprocessed vector objects with respect to each extent vector in the first list
-    - Preferably all lists are named 
-- Write a `future.apply` script running through the extent list object
-- Run a small amount of data to estimate the total computational demand
-- Submit a job with a proper amount of computational assets
diff --git a/scomps.Rcheck/00_pkg_src/scomps/vignettes/v01_generate_computational_grid.Rmd b/scomps.Rcheck/00_pkg_src/scomps/vignettes/v01_generate_computational_grid.Rmd
deleted file mode 100644
index 4bc1aaf2..00000000
--- a/scomps.Rcheck/00_pkg_src/scomps/vignettes/v01_generate_computational_grid.Rmd
+++ /dev/null
@@ -1,46 +0,0 @@
----
-title: "Generate computational grids"
-date: "`r Sys.Date()`"
-output: rmarkdown::html_vignette
-vignette: >
-  %\VignetteIndexEntry{computational_grids}
-  %\VignetteEngine{knitr::rmarkdown}
-  %\VignetteEncoding{UTF-8}
----
-
-
-```{r}
-knitr::opts_chunk$set(warning = FALSE, message = FALSE)
-
-```
-
-
-## Prepare input data
-```{r}
-library(scomps)
-library(sf)
-library(terra)
-library(stars)
-library(dplyr)
-
-```
-
-## Computational grids
-```{r}
-# your_grid = scomps::sp_index_grid()
-
-```
-
-
-## Visualize computational grids
-```{r}
-# library(mapsf)
-# mf_map(your_grid$geometry)
-
-
-```
-
-
-
-## Notes
-- Computational grids are the exhaustive split of the entire study region. You should take a square buffer of each grid to clip the target raster or vector.
diff --git a/scomps.Rcheck/00check.log b/scomps.Rcheck/00check.log
deleted file mode 100644
index 2fc32c95..00000000
--- a/scomps.Rcheck/00check.log
+++ /dev/null
@@ -1,79 +0,0 @@
-* using log directory ‘/Users/songi2/Documents/GitHub/Scalable_GIS/scomps.Rcheck’
-* using R version 4.3.1 (2023-06-16)
-* using platform: aarch64-apple-darwin20 (64-bit)
-* R was compiled by
-    Apple clang version 14.0.0 (clang-1400.0.29.202)
-    GNU Fortran (GCC) 12.2.0
-* running under: macOS Ventura 13.6
-* using session charset: UTF-8
-* checking for file ‘scomps/DESCRIPTION’ ... OK
-* this is package ‘scomps’ version ‘0.0.3.10042023’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... OK
-* checking if this is a source package ... OK
-* checking if there is a namespace ... OK
-* checking for executable files ... OK
-* checking for hidden files and directories ... OK
-* checking for portable file names ... OK
-* checking for sufficient/correct file permissions ... OK
-* checking whether package ‘scomps’ can be installed ... OK
-* checking installed package size ... OK
-* checking package directory ... OK
-* checking DESCRIPTION meta-information ... NOTE
-Malformed Description field: should contain one or more complete sentences.
-* checking top-level files ... OK
-* checking for left-over files ... OK
-* checking index information ... OK
-* checking package subdirectories ... OK
-* checking R files for non-ASCII characters ... OK
-* checking R files for syntax errors ... OK
-* checking whether the package can be loaded ... OK
-* checking whether the package can be loaded with stated dependencies ... OK
-* checking whether the package can be unloaded cleanly ... OK
-* checking whether the namespace can be loaded with stated dependencies ... OK
-* checking whether the namespace can be unloaded cleanly ... OK
-* checking loading without being on the library search path ... OK
-* checking dependencies in R code ... NOTE
-Namespaces in Imports field not imported from:
-  ‘covr’ ‘future’ ‘testthat’ ‘units’
-  All declared Imports should be used.
-* checking S3 generic/method consistency ... OK
-* checking replacement functions ... OK
-* checking foreign function calls ... OK
-* checking R code for possible problems ... NOTE
-calculate_sedc: no visible binding for global variable ‘dist’
-check_within_reference: no visible binding for global variable ‘x’
-extract_with_buffer.flat: no visible binding for global variable ‘ID’
-extract_with_buffer.kernel: no visible binding for global variable ‘ID’
-get_computational_regions: no visible binding for global variable ‘y’
-sp_indexing: no visible binding for global variable ‘x’
-sp_indexing: no visible binding for global variable ‘y’
-Undefined global functions or variables:
-  ID dist x y
-Consider adding
-  importFrom("stats", "dist")
-to your NAMESPACE file.
-* checking Rd files ... OK
-* checking Rd metadata ... OK
-* checking Rd cross-references ... OK
-* checking for missing documentation entries ... OK
-* checking for code/documentation mismatches ... OK
-* checking Rd \usage sections ... OK
-* checking Rd contents ... OK
-* checking for unstated dependencies in examples ... OK
-* checking installed files from ‘inst/doc’ ... OK
-* checking files in ‘vignettes’ ... OK
-* checking examples ... OK
-* checking for unstated dependencies in ‘tests’ ... OK
-* checking tests ... OK
-  Running ‘testthat.R’
-* checking for unstated dependencies in vignettes ... OK
-* checking package vignettes in ‘inst/doc’ ... OK
-* checking running R code from vignettes ... NONE
-  ‘v00_good_practice_parallelization.Rmd’ using ‘UTF-8’... OK
-  ‘v01_generate_computational_grid.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* checking PDF version of manual ... OK
-* DONE
-Status: 3 NOTEs
diff --git a/scomps.Rcheck/00install.out b/scomps.Rcheck/00install.out
deleted file mode 100644
index 1c871a2e..00000000
--- a/scomps.Rcheck/00install.out
+++ /dev/null
@@ -1,13 +0,0 @@
-* installing *source* package ‘scomps’ ...
-** using staged installation
-** R
-** inst
-** byte-compile and prepare package for lazy loading
-** help
-*** installing help indices
-** building package indices
-** installing vignettes
-** testing if installed package can be loaded from temporary location
-** testing if installed package can be loaded from final location
-** testing if installed package keeps a record of temporary installation path
-* DONE (scomps)
diff --git a/scomps.Rcheck/Rdlatex.log b/scomps.Rcheck/Rdlatex.log
deleted file mode 100644
index bb0bdaa0..00000000
--- a/scomps.Rcheck/Rdlatex.log
+++ /dev/null
@@ -1,564 +0,0 @@
-Hmm ... looks like a package
-Converting parsed Rd's to LaTeX ..
-Creating pdf output from LaTeX ...
-
-This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Homebrew) (preloaded format=pdflatex)
- restricted \write18 enabled.
-entering extended mode
-LaTeX2e <2022-11-01> patch level 1
-L3 programming layer <2023-02-22> (./Rd2.tex
-
-(/opt/homebrew/Cellar/texlive/20230313_2/share/texmf-dist/tex/latex/base/book.c
-ls
-Document Class: book 2022/07/02 v1.4n Standard LaTeX document class
-
-(/opt/homebrew/Cellar/texlive/20230313_2/share/texmf-dist/tex/latex/base/bk10.c
-lo)) (/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
-(/opt/homebrew/Cellar/texlive/20230313_2/share/texmf-dist/tex/latex/base/ifthen
-.sty)
-(/opt/homebrew/Cellar/texlive/20230313_2/share/texmf-dist/tex/latex/tools/longt
-able.sty)
-(/opt/homebrew/Cellar/texlive/20230313_2/share/texmf-dist/tex/latex/tools/bm.st
-y)
-(/opt/homebrew/Cellar/texlive/20230313_2/share/texmf-dist/tex/latex/base/alltt.
-sty)
-(/opt/homebrew/Cellar/texlive/20230313_2/share/texmf-dist/tex/latex/tools/verba
-tim.sty)
-(/opt/homebrew/Cellar/texlive/20230313_2/share/texmf-dist/tex/latex/url/url.sty
-)
-(/opt/homebrew/Cellar/texlive/20230313_2/share/texmf-dist/tex/latex/base/textco
-mp.sty)
-(/opt/homebrew/Cellar/texlive/20230313_2/share/texmf-dist/tex/latex/amsmath/ams
-math.sty
-For additional information on amsmath, use the `?' option.
-
-(/opt/homebrew/Cellar/texlive/20230313_2/share/texmf-dist/tex/latex/amsmath/ams
-text.sty
-(/opt/homebrew/Cellar/texlive/20230313_2/share/texmf-dist/tex/latex/amsmath/ams
-gen.sty))
-(/opt/homebrew/Cellar/texlive/20230313_2/share/texmf-dist/tex/latex/amsmath/ams
-bsy.sty)
-(/opt/homebrew/Cellar/texlive/20230313_2/share/texmf-dist/tex/latex/amsmath/ams
-opn.sty))
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-/zi4.sty
-`inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe)
-(/opt/homebrew/Cellar/texlive/20230313_2/share/texmf-dist/tex/latex/xkeyval/xke
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-[]\T1/ptm/m/n/10 sf*/stars/SpatVector/SpatRaster ob-ject or a named nu-meric ve
-c-tor with four names
-[4] [5] [6] [7]
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-[]\T1/zi4/m/n/10 "id_from:id_to" []\T1/ptm/m/n/10 for-mat or []\T1/zi4/m/n/10 c
-(unique(grid_id)[id_from], unique(grid_id)[id_to]) 
-[8] [9] [10] [11] [12] [13] [14] [15]
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-56e679a5/Rd2.aux) )
-(see the transcript file for additional information)
-Output written on Rd2.pdf (17 pages, 116155 bytes).
-Transcript written on Rd2.log.
-Saving output to ‘scomps-manual.pdf’ ...
-Done
-You may want to clean up by 'rm -Rf /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmpOaxUwq/Rd2pdff3c856e679a5'
diff --git a/scomps.Rcheck/scomps-Ex.R b/scomps.Rcheck/scomps-Ex.R
deleted file mode 100644
index 4c502e90..00000000
--- a/scomps.Rcheck/scomps-Ex.R
+++ /dev/null
@@ -1,121 +0,0 @@
-pkgname <- "scomps"
-source(file.path(R.home("share"), "R", "examples-header.R"))
-options(warn = 1)
-library('scomps')
-
-base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
-base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
-cleanEx()
-nameEx("aw_covariates")
-### * aw_covariates
-
-flush(stderr()); flush(stdout())
-
-### Name: aw_covariates
-### Title: Computing area weighted covariates using two polygon sf or
-###   SpatVector objects
-### Aliases: aw_covariates
-
-### ** Examples
-
-# package
-library(sf)
-
-# run
-nc = sf::st_read(system.file("shape/nc.shp", package="sf"))
-nc = sf::st_transform(nc, 5070)
-pp = sf::st_sample(nc, size = 300)
-pp = sf::st_as_sf(pp)
-pp[["id"]] = seq(1, nrow(pp))
-sf::st_crs(pp) = "EPSG:5070"
-ppb = sf::st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
-
-system.time({ppb_nc_aw = aw_covariates(ppb, nc, 'id')})
-summary(ppb_nc_aw)
-#### Example of aw_covariates ends ####
-
-
-
-cleanEx()
-nameEx("check_crs")
-### * check_crs
-
-flush(stderr()); flush(stdout())
-
-### Name: check_crs
-### Title: Check Coordinate Reference System
-### Aliases: check_crs
-
-### ** Examples
-
-# data
-library(sf)
-ncpath = system.file("shape/nc.shp", package = "sf")
-nc = read_sf(ncpath)
-check_crs(nc)
-
-
-
-
-cleanEx()
-nameEx("get_computational_regions")
-### * get_computational_regions
-
-flush(stderr()); flush(stdout())
-
-### Name: get_computational_regions
-### Title: Get a set of computational regions
-### Aliases: get_computational_regions
-
-### ** Examples
-
-# data
-library(sf)
-ncpath = system.file("shape/nc.shp", package = "sf")
-nc = read_sf(ncpath)
-nc = st_transform(nc, "EPSG:5070")
-# run
-# nc_comp_region = get_computational_regions(nc, nx = 12, ny = 8)
-
-
-
-
-cleanEx()
-nameEx("grid_merge")
-### * grid_merge
-
-flush(stderr()); flush(stdout())
-
-### Name: grid_merge
-### Title: grid_merge: Merge grid polygons with given rules
-### Aliases: grid_merge
-
-### ** Examples
-
-# library(sf)
-# library(igraph)
-# ligrary(dplyr)
-# dg = sf::st_as_sfc(st_bbox(c(xmin = 0, ymin = 0, xmax = 8e5, ymax = 6e5)))
-# sf::st_crs(dg) = 5070
-# dgs = sf::st_as_sf(st_make_grid(dg, n = c(20, 15)))
-# dgs$CGRIDID = seq(1, nrow(dgs))
-#
-# dg_sample = st_sample(dg, kappa = 5e-9, mu = 15, scale = 20000, type = "Thomas")
-# sf::st_crs(dg_sample) = sf::st_crs(dg)
-# dg_merged = grid_merge(sf::st_as_sf(sss), dgs, 100)
-#### NOT RUN ####
-
-
-
-### * 

-###
-cleanEx()
-options(digits = 7L)
-base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-grDevices::dev.off()
-###
-### Local variables: ***
-### mode: outline-minor ***
-### outline-regexp: "\\(> \\)?### [*]+" ***
-### End: ***
-quit('no')
diff --git a/scomps.Rcheck/scomps-Ex.Rout b/scomps.Rcheck/scomps-Ex.Rout
deleted file mode 100644
index 68d31f33..00000000
--- a/scomps.Rcheck/scomps-Ex.Rout
+++ /dev/null
@@ -1,212 +0,0 @@
-
-R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
-Copyright (C) 2023 The R Foundation for Statistical Computing
-Platform: aarch64-apple-darwin20 (64-bit)
-
-R is free software and comes with ABSOLUTELY NO WARRANTY.
-You are welcome to redistribute it under certain conditions.
-Type 'license()' or 'licence()' for distribution details.
-
-  Natural language support but running in an English locale
-
-R is a collaborative project with many contributors.
-Type 'contributors()' for more information and
-'citation()' on how to cite R or R packages in publications.
-
-Type 'demo()' for some demos, 'help()' for on-line help, or
-'help.start()' for an HTML browser interface to help.
-Type 'q()' to quit R.
-
-> pkgname <- "scomps"
-> source(file.path(R.home("share"), "R", "examples-header.R"))
-> options(warn = 1)
-> library('scomps')
-> 
-> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
-> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
-> cleanEx()
-> nameEx("aw_covariates")
-> ### * aw_covariates
-> 
-> flush(stderr()); flush(stdout())
-> 
-> ### Name: aw_covariates
-> ### Title: Computing area weighted covariates using two polygon sf or
-> ###   SpatVector objects
-> ### Aliases: aw_covariates
-> 
-> ### ** Examples
-> 
-> # package
-> library(sf)
-Linking to GEOS 3.11.0, GDAL 3.5.3, PROJ 9.1.0; sf_use_s2() is TRUE
-> 
-> # run
-> nc = sf::st_read(system.file("shape/nc.shp", package="sf"))
-Reading layer `nc' from data source 
-  `/Users/songi2/Library/R/arm64/4.3/library/sf/shape/nc.shp' 
-  using driver `ESRI Shapefile'
-Simple feature collection with 100 features and 14 fields
-Geometry type: MULTIPOLYGON
-Dimension:     XY
-Bounding box:  xmin: -84.32385 ymin: 33.88199 xmax: -75.45698 ymax: 36.58965
-Geodetic CRS:  NAD27
-> nc = sf::st_transform(nc, 5070)
-> pp = sf::st_sample(nc, size = 300)
-> pp = sf::st_as_sf(pp)
-> pp[["id"]] = seq(1, nrow(pp))
-> sf::st_crs(pp) = "EPSG:5070"
-> ppb = sf::st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
-> 
-> system.time({ppb_nc_aw = aw_covariates(ppb, nc, 'id')})
-Warning in st_interpolate_aw.sf(poly_weight[, index_numeric], poly_in, extensive = FALSE) :
-  st_interpolate_aw assumes attributes are constant or uniform over areas of x
-   user  system elapsed 
-  0.180   0.003   0.183 
-> summary(ppb_nc_aw)
-      AREA           PERIMETER         CNTY_         CNTY_ID    
- Min.   :0.06133   Min.   :1.114   Min.   :1825   Min.   :1825  
- 1st Qu.:0.12008   1st Qu.:1.549   1st Qu.:1917   1st Qu.:1917  
- Median :0.13834   Median :1.685   Median :2000   Median :2000  
- Mean   :0.14702   Mean   :1.777   Mean   :2004   Mean   :2004  
- 3rd Qu.:0.17292   3rd Qu.:1.978   3rd Qu.:2078   3rd Qu.:2078  
- Max.   :0.24000   Max.   :3.588   Max.   :2241   Max.   :2241  
-     FIPSNO         CRESS_ID          BIR74             SID74       
- Min.   :37009   Min.   : 5.042   Min.   :  315.1   Min.   : 0.000  
- 1st Qu.:37075   1st Qu.:38.024   1st Qu.: 1955.4   1st Qu.: 4.015  
- Median :37104   Median :52.610   Median : 3124.2   Median : 6.867  
- Mean   :37103   Mean   :51.798   Mean   : 3977.7   Mean   : 8.529  
- 3rd Qu.:37131   3rd Qu.:65.974   3rd Qu.: 4639.0   3rd Qu.:10.591  
- Max.   :37191   Max.   :95.910   Max.   :18561.5   Max.   :36.075  
-    NWBIR74             BIR79             SID79           NWBIR79        
- Min.   :   6.222   Min.   :  403.3   Min.   : 0.000   Min.   :   4.222  
- 1st Qu.: 458.022   1st Qu.: 2393.5   1st Qu.: 4.990   1st Qu.: 589.223  
- Median : 955.882   Median : 3903.2   Median : 8.036   Median :1189.908  
- Mean   :1285.378   Mean   : 5092.6   Mean   :10.052   Mean   :1655.747  
- 3rd Qu.:1669.800   3rd Qu.: 5904.1   3rd Qu.:13.890   3rd Qu.:2127.972  
- Max.   :6467.572   Max.   :26115.7   Max.   :34.448   Max.   :9367.957  
-          geometry  
- POLYGON      :300  
- epsg:5070    :  0  
- +proj=aea ...:  0  
-                    
-                    
-                    
-> #### Example of aw_covariates ends ####
-> 
-> 
-> 
-> cleanEx()
-
-detaching ‘package:sf’
-
-> nameEx("check_crs")
-> ### * check_crs
-> 
-> flush(stderr()); flush(stdout())
-> 
-> ### Name: check_crs
-> ### Title: Check Coordinate Reference System
-> ### Aliases: check_crs
-> 
-> ### ** Examples
-> 
-> # data
-> library(sf)
-Linking to GEOS 3.11.0, GDAL 3.5.3, PROJ 9.1.0; sf_use_s2() is TRUE
-> ncpath = system.file("shape/nc.shp", package = "sf")
-> nc = read_sf(ncpath)
-> check_crs(nc)
-Coordinate Reference System:
-  User input: NAD27 
-  wkt:
-GEOGCRS["NAD27",
-    DATUM["North American Datum 1927",
-        ELLIPSOID["Clarke 1866",6378206.4,294.978698213898,
-            LENGTHUNIT["metre",1]]],
-    PRIMEM["Greenwich",0,
-        ANGLEUNIT["degree",0.0174532925199433]],
-    CS[ellipsoidal,2],
-        AXIS["latitude",north,
-            ORDER[1],
-            ANGLEUNIT["degree",0.0174532925199433]],
-        AXIS["longitude",east,
-            ORDER[2],
-            ANGLEUNIT["degree",0.0174532925199433]],
-    ID["EPSG",4267]]
-> 
-> 
-> 
-> 
-> cleanEx()
-
-detaching ‘package:sf’
-
-> nameEx("get_computational_regions")
-> ### * get_computational_regions
-> 
-> flush(stderr()); flush(stdout())
-> 
-> ### Name: get_computational_regions
-> ### Title: Get a set of computational regions
-> ### Aliases: get_computational_regions
-> 
-> ### ** Examples
-> 
-> # data
-> library(sf)
-Linking to GEOS 3.11.0, GDAL 3.5.3, PROJ 9.1.0; sf_use_s2() is TRUE
-> ncpath = system.file("shape/nc.shp", package = "sf")
-> nc = read_sf(ncpath)
-> nc = st_transform(nc, "EPSG:5070")
-> # run
-> # nc_comp_region = get_computational_regions(nc, nx = 12, ny = 8)
-> 
-> 
-> 
-> 
-> cleanEx()
-
-detaching ‘package:sf’
-
-> nameEx("grid_merge")
-> ### * grid_merge
-> 
-> flush(stderr()); flush(stdout())
-> 
-> ### Name: grid_merge
-> ### Title: grid_merge: Merge grid polygons with given rules
-> ### Aliases: grid_merge
-> 
-> ### ** Examples
-> 
-> # library(sf)
-> # library(igraph)
-> # ligrary(dplyr)
-> # dg = sf::st_as_sfc(st_bbox(c(xmin = 0, ymin = 0, xmax = 8e5, ymax = 6e5)))
-> # sf::st_crs(dg) = 5070
-> # dgs = sf::st_as_sf(st_make_grid(dg, n = c(20, 15)))
-> # dgs$CGRIDID = seq(1, nrow(dgs))
-> #
-> # dg_sample = st_sample(dg, kappa = 5e-9, mu = 15, scale = 20000, type = "Thomas")
-> # sf::st_crs(dg_sample) = sf::st_crs(dg)
-> # dg_merged = grid_merge(sf::st_as_sf(sss), dgs, 100)
-> #### NOT RUN ####
-> 
-> 
-> 
-> ### * 

-> ###
-> cleanEx()
-> options(digits = 7L)
-> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  0.684 0.035 0.72 0 0 
-> grDevices::dev.off()
-null device 
-          1 
-> ###
-> ### Local variables: ***
-> ### mode: outline-minor ***
-> ### outline-regexp: "\\(> \\)?### [*]+" ***
-> ### End: ***
-> quit('no')
diff --git a/scomps.Rcheck/scomps-Ex.pdf b/scomps.Rcheck/scomps-Ex.pdf
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diff --git a/scomps.Rcheck/scomps/DESCRIPTION b/scomps.Rcheck/scomps/DESCRIPTION
deleted file mode 100644
index 737d2c62..00000000
--- a/scomps.Rcheck/scomps/DESCRIPTION
+++ /dev/null
@@ -1,22 +0,0 @@
-Package: scomps
-Title: Scalable R geospatial computation
-Version: 0.0.3.10042023
-Authors@R: 
-    person("Insang", "Song", , "geoissong@gmail.com", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0001-8732-3256"))
-Description: A package for scalable geospatial computation for
-    environmental health research
-License: MIT + file LICENSE
-Encoding: UTF-8
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
-Imports: covr, dplyr, future, future.apply, methods, rlang, sf, stars,
-        terra, testthat, units
-Suggests: future.batchtools, igraph, knitr, logr, rmarkdown, withr
-VignetteBuilder: knitr
-Config/testthat/edition: 3
-NeedsCompilation: no
-Packaged: 2023-10-04 15:41:03 UTC; songi2
-Author: Insang Song [aut, cre] ()
-Maintainer: Insang Song 
-Built: R 4.3.1; ; 2023-10-04 15:41:20 UTC; unix
diff --git a/scomps.Rcheck/scomps/INDEX b/scomps.Rcheck/scomps/INDEX
deleted file mode 100644
index 80dc13d3..00000000
--- a/scomps.Rcheck/scomps/INDEX
+++ /dev/null
@@ -1,39 +0,0 @@
-aw_covariates           Computing area weighted covariates using two
-                        polygon sf or SpatVector objects
-calculate_sedc          Calculate SEDC covariates
-check_bbox              Check if the data extent is inside the
-                        reference bounding box
-check_crs               Check Coordinate Reference System
-check_crs2              check_crs2: Coordinate system checker
-check_packbound         Return the package the input object is based on
-check_within_reference
-                        Check if the boundary of the vector/raster
-                        object is inside the reference
-clip_as_extent          Extent clipping
-clip_as_extent_ras      clip_as_extent_ras: Clip input raster.
-clip_as_extent_ras2     clip_as_extent_ras2: Clip input raster (version
-                        2).
-distribute_process      Process a given function in the entire or
-                        partial computational grids (under
-                        construction)
-estimate_demands        Estimate computational demands from inputs (to
-                        be written)
-extent_to_polygon       Generate a rectangular polygon from extent
-extract_with            Extract raster values with point buffers or
-                        polygons
-extract_with_buffer     Extract summarized values from raster with
-                        points and a buffer radius (to be written)
-extract_with_polygons   Extract summarized values from raster with
-                        generic polygons
-get_computational_regions
-                        Get a set of computational regions
-grid_merge              grid_merge: Merge grid polygons with given
-                        rules
-initate_log             Turn on logging
-rast_short              Quick call for SpatRaster with a window
-set_clip_extent         Setting the clipping extent
-sp_index_grid           sp_index_grid: Generate grid polygons
-sp_indexing             Create integer indices for grid
-switch_packbound        Switch spatial data class
-validate_and_repair_vectors
-                        Validate and repair input vector data
diff --git a/scomps.Rcheck/scomps/LICENSE b/scomps.Rcheck/scomps/LICENSE
deleted file mode 100644
index 74e6421f..00000000
--- a/scomps.Rcheck/scomps/LICENSE
+++ /dev/null
@@ -1,2 +0,0 @@
-YEAR: 2023
-COPYRIGHT HOLDER: I. Song
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diff --git a/scomps.Rcheck/scomps/NAMESPACE b/scomps.Rcheck/scomps/NAMESPACE
deleted file mode 100644
index b8f3fc6a..00000000
--- a/scomps.Rcheck/scomps/NAMESPACE
+++ /dev/null
@@ -1,27 +0,0 @@
-# Generated by roxygen2: do not edit by hand
-
-export(aw_covariates)
-export(calculate_sedc)
-export(check_bbox)
-export(check_crs)
-export(check_crs2)
-export(check_packbound)
-export(check_within_reference)
-export(clip_as_extent)
-export(clip_as_extent_ras)
-export(clip_as_extent_ras2)
-export(distribute_process)
-export(estimate_demands)
-export(extent_to_polygon)
-export(extract_with)
-export(extract_with_buffer)
-export(extract_with_polygons)
-export(get_computational_regions)
-export(grid_merge)
-export(initate_log)
-export(rast_short)
-export(set_clip_extent)
-export(sp_index_grid)
-export(sp_indexing)
-export(switch_packbound)
-export(validate_and_repair_vectors)
diff --git a/scomps.Rcheck/scomps/R/scomps b/scomps.Rcheck/scomps/R/scomps
deleted file mode 100644
index 66861563..00000000
--- a/scomps.Rcheck/scomps/R/scomps
+++ /dev/null
@@ -1,27 +0,0 @@
-#  File share/R/nspackloader.R
-#  Part of the R package, https://www.R-project.org
-#
-#  Copyright (C) 1995-2012 The R Core Team
-#
-#  This program is free software; you can redistribute it and/or modify
-#  it under the terms of the GNU General Public License as published by
-#  the Free Software Foundation; either version 2 of the License, or
-#  (at your option) any later version.
-#
-#  This program is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#  GNU General Public License for more details.
-#
-#  A copy of the GNU General Public License is available at
-#  https://www.r-project.org/Licenses/
-
-local({
-    info <- loadingNamespaceInfo()
-    pkg <- info$pkgname
-    ns <- .getNamespace(as.name(pkg))
-    if (is.null(ns))
-        stop("cannot find namespace environment for ", pkg, domain = NA);
-    dbbase <- file.path(info$libname, pkg, "R", pkg)
-    lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
-})
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-R: Vignettes and other documentation
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 Vignettes and other documentation
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Vignettes from package 'scomps'

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scomps::v00_good_practice_parallelizationgood_practice_hpcHTMLsourceR code
scomps::v01_generate_computational_gridcomputational_gridsHTMLsourceR code

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diff --git a/scomps.Rcheck/scomps/doc/v00_good_practice_parallelization.R b/scomps.Rcheck/scomps/doc/v00_good_practice_parallelization.R
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--- a/scomps.Rcheck/scomps/doc/v00_good_practice_parallelization.R
+++ /dev/null
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-## -----------------------------------------------------------------------------
-knitr::opts_chunk$set(warning = FALSE, message = FALSE)
-
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diff --git a/scomps.Rcheck/scomps/doc/v00_good_practice_parallelization.Rmd b/scomps.Rcheck/scomps/doc/v00_good_practice_parallelization.Rmd
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--- a/scomps.Rcheck/scomps/doc/v00_good_practice_parallelization.Rmd
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----
-title: "Good practice of scomps with HPC"
-date: "`r Sys.Date()`"
-output: rmarkdown::html_vignette
-vignette: >
-  %\VignetteIndexEntry{good_practice_hpc}
-  %\VignetteEngine{knitr::rmarkdown}
-  %\VignetteEncoding{UTF-8}
----
-
-
-```{r}
-knitr::opts_chunk$set(warning = FALSE, message = FALSE)
-
-```
-
-## Assumptions
-- Users have an accessible HPC at your work
-- Data are stored in distributed file systems (usually incorporated into the HPC system)
-
-
-## Basic workflow
-
-### Practice for minimizing errors
-- Consider using `try()` or `tryCatch()` not to a tiny error will halt all the work without any results 
-    - Especially with the higher-level functions
-- "IPDE -- Inspect, Predict, Decide, Execute" all the time
-
-### Raster-Vector overlay
-- Make `sp_index_grid()` to get padded grid objects
-- Convert sf/SpatVector objects into `terra::ext()` compatible named numeric vector
-    - For example: `c(xmin=0, ymin=0, xmax=10, ymax=10)`
-- Make list objects with: 
-    - An extent vector in each element
-    - Preprocessed vector objects with respect to each extent vector in the first list
-    - Preferably all lists are named 
-- Write a `future.apply` script running through the extent list object
-- Run a small amount of data to estimate the total computational demand
-- Submit a job with a proper amount of computational assets
diff --git a/scomps.Rcheck/scomps/doc/v00_good_practice_parallelization.html b/scomps.Rcheck/scomps/doc/v00_good_practice_parallelization.html
deleted file mode 100644
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Good practice of scomps with HPC

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2023-10-04

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knitr::opts_chunk$set(warning = FALSE, message = FALSE)

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Assumptions

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  • Users have an accessible HPC at your work
    • 
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  • Data are stored in distributed file systems (usually incorporated
-into the HPC system)
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Basic workflow

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Practice for minimizing errors

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  • Consider using try() or tryCatch() not to
-a tiny error will halt all the work without any results
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    • Especially with the higher-level functions
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  • “IPDE – Inspect, Predict, Decide, Execute” all the time
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Raster-Vector overlay

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  • Make sp_index_grid() to get padded grid objects
    • 
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  • Convert sf/SpatVector objects into terra::ext()
-compatible named numeric vector
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    • For example: c(xmin=0, ymin=0, xmax=10, ymax=10)
      • 
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  • Make list objects with:
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-the first list
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    • Preferably all lists are named
      • 
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    • 
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  • Write a future.apply script running through the extent
-list object
    • 
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  • Run a small amount of data to estimate the total computational
-demand
    • 
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  • Submit a job with a proper amount of computational assets
    • 
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diff --git a/scomps.Rcheck/scomps/doc/v01_generate_computational_grid.R b/scomps.Rcheck/scomps/doc/v01_generate_computational_grid.R
deleted file mode 100644
index aa3d29fc..00000000
--- a/scomps.Rcheck/scomps/doc/v01_generate_computational_grid.R
+++ /dev/null
@@ -1,22 +0,0 @@
-## -----------------------------------------------------------------------------
-knitr::opts_chunk$set(warning = FALSE, message = FALSE)
-
-
-## -----------------------------------------------------------------------------
-library(scomps)
-library(sf)
-library(terra)
-library(stars)
-library(dplyr)
-
-
-## -----------------------------------------------------------------------------
-# your_grid = scomps::sp_index_grid()
-
-
-## -----------------------------------------------------------------------------
-# library(mapsf)
-# mf_map(your_grid$geometry)
-
-
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diff --git a/scomps.Rcheck/scomps/doc/v01_generate_computational_grid.Rmd b/scomps.Rcheck/scomps/doc/v01_generate_computational_grid.Rmd
deleted file mode 100644
index 4bc1aaf2..00000000
--- a/scomps.Rcheck/scomps/doc/v01_generate_computational_grid.Rmd
+++ /dev/null
@@ -1,46 +0,0 @@
----
-title: "Generate computational grids"
-date: "`r Sys.Date()`"
-output: rmarkdown::html_vignette
-vignette: >
-  %\VignetteIndexEntry{computational_grids}
-  %\VignetteEngine{knitr::rmarkdown}
-  %\VignetteEncoding{UTF-8}
----
-
-
-```{r}
-knitr::opts_chunk$set(warning = FALSE, message = FALSE)
-
-```
-
-
-## Prepare input data
-```{r}
-library(scomps)
-library(sf)
-library(terra)
-library(stars)
-library(dplyr)
-
-```
-
-## Computational grids
-```{r}
-# your_grid = scomps::sp_index_grid()
-
-```
-
-
-## Visualize computational grids
-```{r}
-# library(mapsf)
-# mf_map(your_grid$geometry)
-
-
-```
-
-
-
-## Notes
-- Computational grids are the exhaustive split of the entire study region. You should take a square buffer of each grid to clip the target raster or vector.
diff --git a/scomps.Rcheck/scomps/doc/v01_generate_computational_grid.html b/scomps.Rcheck/scomps/doc/v01_generate_computational_grid.html
deleted file mode 100644
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@@ -1,388 +0,0 @@
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Generate computational grids

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2023-10-04

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knitr::opts_chunk$set(warning = FALSE, message = FALSE)

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Prepare input data

-
library(scomps)
-library(sf)
-library(terra)
-library(stars)
-library(dplyr)

-

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Computational grids

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# your_grid = scomps::sp_index_grid()

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Visualize computational grids

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# library(mapsf)
-# mf_map(your_grid$geometry)

-

-

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Notes

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  • Computational grids are the exhaustive split of the entire study
-region. You should take a square buffer of each grid to clip the target
-raster or vector.
    • 
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diff --git a/scomps.Rcheck/scomps/help/AnIndex b/scomps.Rcheck/scomps/help/AnIndex
deleted file mode 100644
index a7b8aefb..00000000
--- a/scomps.Rcheck/scomps/help/AnIndex
+++ /dev/null
@@ -1,25 +0,0 @@
-aw_covariates	aw_covariates
-calculate_sedc	calculate_sedc
-check_bbox	check_bbox
-check_crs	check_crs
-check_crs2	check_crs2
-check_packbound	check_packbound
-check_within_reference	check_within_reference
-clip_as_extent	clip_as_extent
-clip_as_extent_ras	clip_as_extent_ras
-clip_as_extent_ras2	clip_as_extent_ras2
-distribute_process	distribute_process
-estimate_demands	estimate_demands
-extent_to_polygon	extent_to_polygon
-extract_with	extract_with
-extract_with_buffer	extract_with_buffer
-extract_with_polygons	extract_with_polygons
-get_computational_regions	get_computational_regions
-grid_merge	grid_merge
-initate_log	initate_log
-rast_short	rast_short
-set_clip_extent	set_clip_extent
-sp_indexing	sp_indexing
-sp_index_grid	sp_index_grid
-switch_packbound	switch_packbound
-validate_and_repair_vectors	validate_and_repair_vectors
diff --git a/scomps.Rcheck/scomps/help/aliases.rds b/scomps.Rcheck/scomps/help/aliases.rds
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--- a/scomps.Rcheck/scomps/html/00Index.html
+++ /dev/null
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-R: Scalable R geospatial computation
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 Scalable R geospatial computation
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Documentation for package ‘scomps’ version 0.0.3.10042023

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Help Pages

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aw_covariatesComputing area weighted covariates using two polygon sf or SpatVector objects
calculate_sedcCalculate SEDC covariates
check_bboxCheck if the data extent is inside the reference bounding box
check_crsCheck Coordinate Reference System
check_crs2check_crs2: Coordinate system checker
check_packboundReturn the package the input object is based on
check_within_referenceCheck if the boundary of the vector/raster object is inside the reference
clip_as_extentExtent clipping
clip_as_extent_rasclip_as_extent_ras: Clip input raster.
clip_as_extent_ras2clip_as_extent_ras2: Clip input raster (version 2).
distribute_processProcess a given function in the entire or partial computational grids (under construction)
estimate_demandsEstimate computational demands from inputs (to be written)
extent_to_polygonGenerate a rectangular polygon from extent
extract_withExtract raster values with point buffers or polygons
extract_with_bufferExtract summarized values from raster with points and a buffer radius (to be written)
extract_with_polygonsExtract summarized values from raster with generic polygons
get_computational_regionsGet a set of computational regions
grid_mergegrid_merge: Merge grid polygons with given rules
initate_logTurn on logging
rast_shortQuick call for SpatRaster with a window
set_clip_extentSetting the clipping extent
sp_indexingCreate integer indices for grid
sp_index_gridsp_index_grid: Generate grid polygons
switch_packboundSwitch spatial data class
validate_and_repair_vectorsValidate and repair input vector data

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diff --git a/scomps.Rcheck/scomps/html/R.css b/scomps.Rcheck/scomps/html/R.css
deleted file mode 100644
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-@media screen {
-    .container {
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-	padding-left: 10px;
-	margin-right: auto;
-	margin-left: auto;
-	max-width: 900px;
-    }
-}
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-.rimage img { /* from knitr - for examples and demos */
-    width: 96%;
-    margin-left: 2%;
-} 	
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-.katex { font-size: 1.1em; }
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-code {
-    color: inherit;
-    background: inherit;
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-body {
-    line-height: 1.4;
-    background: white;
-    color: black;
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-a:link {
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-    font-size: 1.4em; /* x-large; */
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diff --git a/scomps.Rcheck/tests/startup.Rs b/scomps.Rcheck/tests/startup.Rs
deleted file mode 100644
index 8ad6d250..00000000
--- a/scomps.Rcheck/tests/startup.Rs
+++ /dev/null
@@ -1,4 +0,0 @@
-## A custom startup file for tests
-## Run as if a system Rprofile, so no packages, no assignments
-options(useFancyQuotes = FALSE)
-
diff --git a/scomps.Rcheck/tests/testthat.R b/scomps.Rcheck/tests/testthat.R
deleted file mode 100644
index b465b524..00000000
--- a/scomps.Rcheck/tests/testthat.R
+++ /dev/null
@@ -1,12 +0,0 @@
-# This file is part of the standard setup for testthat.
-# It is recommended that you do not modify it.
-#
-# Where should you do additional test configuration?
-# Learn more about the roles of various files in:
-# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
-# * https://testthat.r-lib.org/articles/special-files.html
-
-library(testthat)
-library(scomps)
-
-test_check("scomps")
diff --git a/scomps.Rcheck/tests/testthat.Rout b/scomps.Rcheck/tests/testthat.Rout
deleted file mode 100644
index dfb13fbb..00000000
--- a/scomps.Rcheck/tests/testthat.Rout
+++ /dev/null
@@ -1,37 +0,0 @@
-
-R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
-Copyright (C) 2023 The R Foundation for Statistical Computing
-Platform: aarch64-apple-darwin20 (64-bit)
-
-R is free software and comes with ABSOLUTELY NO WARRANTY.
-You are welcome to redistribute it under certain conditions.
-Type 'license()' or 'licence()' for distribution details.
-
-R is a collaborative project with many contributors.
-Type 'contributors()' for more information and
-'citation()' on how to cite R or R packages in publications.
-
-Type 'demo()' for some demos, 'help()' for on-line help, or
-'help.start()' for an HTML browser interface to help.
-Type 'q()' to quit R.
-
-> # This file is part of the standard setup for testthat.
-> # It is recommended that you do not modify it.
-> #
-> # Where should you do additional test configuration?
-> # Learn more about the roles of various files in:
-> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
-> # * https://testthat.r-lib.org/articles/special-files.html
-> 
-> library(testthat)
-> library(scomps)
-> 
-> test_check("scomps")
-pr, tas, 
-pr, tas, 
-pr, tas, 
-[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
-> 
-> proc.time()
-   user  system elapsed 
-  1.703   0.063   1.763 
diff --git a/scomps.Rcheck/tests/testthat/tests.R b/scomps.Rcheck/tests/testthat/tests.R
deleted file mode 100644
index 6efa4142..00000000
--- a/scomps.Rcheck/tests/testthat/tests.R
+++ /dev/null
@@ -1,65 +0,0 @@
-# Generated from scomps_rmarkdown_litr.rmd: do not edit by hand  
-testthat::test_that("What package does the input object belong?",
-{
-    withr::local_package("stars")
-    withr::local_package("terra")
-    withr::local_options(list(sf_use_s2 = FALSE))
-    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
-    bcsd_stars = stars::read_stars(bcsd_path)
-
-    packbound_stars = check_packbound(bcsd_stars)
-    sprast_bcsd = terra::rast(bcsd_path)
-    packbound_terra = check_packbound(sprast_bcsd)
-
-    testthat::expect_equal(packbound_stars, "sf")
-    testthat::expect_equal(packbound_terra, "terra")
-})
-
-
-testthat::test_that("What package does the input object belong?",
-{
-    withr::local_package("stars")
-    withr::local_package("terra")
-    withr::local_options(list(sf_use_s2 = FALSE))
-    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
-    bcsd_stars = stars::read_stars(bcsd_path)
-
-    nc = system.file(package = "sf", "shape/nc.shp")
-    nc = sf::read_sf(nc)
-
-    datatype_stars = check_datatype(bcsd_stars)
-    datatype_sf = check_datatype(nc)
-
-    testthat::expect_equal(datatype_stars, "raster")
-    testthat::expect_equal(datatype_sf, "vector")
-})
-
-
-testthat::test_that("Format is well converted",
-{
-    withr::local_package("stars")
-    withr::local_package("terra")
-    withr::local_options(list(sf_use_s2 = FALSE))
-
-    # starts from sf/stars
-    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
-    bcsd_stars = stars::read_stars(bcsd_path)
-    nc = system.file(package = "sf", "shape/nc.shp")
-    nc = sf::read_sf(nc)
-
-    stars_bcsd_tr = switch_packbound(bcsd_stars)
-    sf_nc_tr = switch_packbound(nc)
-
-    testthat::expect_equal(check_packbound(stars_bcsd_tr), "terra")
-    testthat::expect_equal(check_packbound(sf_nc_tr), "terra")
-
-    stars_bcsd_trb = switch_packbound(stars_bcsd_tr)
-    sf_nc_trb = switch_packbound(sf_nc_tr)
-
-    testthat::expect_equal(check_packbound(stars_bcsd_trb), "sf")
-    testthat::expect_equal(check_packbound(sf_nc_trb), "sf")
-
-})
-
-
-
diff --git a/scomps/DESCRIPTION b/scomps/DESCRIPTION
index acb3b95d..8858880b 100644
--- a/scomps/DESCRIPTION
+++ b/scomps/DESCRIPTION
@@ -32,4 +32,4 @@ Suggests:
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 LitrVersionUsed: 0.9.0
-LitrId: 27d90205fd42be403e707a6a559e8eae
+LitrId: b724f15aefeda747a5a888516d5c7129
diff --git a/scomps/R/check.R b/scomps/R/check.R
index 2e1bbcf2..3b30feda 100644
--- a/scomps/R/check.R
+++ b/scomps/R/check.R
@@ -32,8 +32,11 @@ check_datatype <- function(input) {
 #' @return A (reprojected) sf or SpatVector object.
 #' @export
 check_crs2 <- function(input, crs_standard = "EPSG:4326") {
-  check_crs.sf <- function(input){
-    if (is.na(sf::st_crs(input))){cat('Please check the coordinate system or its EPSG code of your input object.'); return(NULL)}
+  check_crs_sf <- function(input) {
+    if (is.na(sf::st_crs(input))) {
+      cat('Please check the coordinate system or its EPSG code of your input object.')
+      return(NULL)
+    }
     if (sf::st_crs(input)$epsg == crs_standard ) {
       return(input)
     } 
@@ -41,17 +44,17 @@ check_crs2 <- function(input, crs_standard = "EPSG:4326") {
     return(input_transformed)
   }
 
-  check_crs.terra <- function(input) {
+  check_crs_terra <- function(input) {
     if (terra::crs(input, describe = TRUE)$code == crs_standard) {
       return(input)
     }
-    input_transformed = terra::project(input, terra::crs(crs_standard))
+    input_transformed <- terra::project(input, terra::crs(crs_standard))
     return(input_transformed)
   }
-    detected = check_packbound(input)
+    detected <- check_packbound(input)
     switch(detected,
-          terra = check_crs.terra(input),
-          sf = check_crs.sf(input))
+          terra = check_crs_terra(input),
+          sf = check_crs_sf(input))
   }
 
 #' Generate a rectangular polygon from extent
@@ -69,20 +72,20 @@ extent_to_polygon <- function(extent, output_class = "terra", crs = "EPSG:4326")
     if (is.null(attr(extent, "names"))) {
       stop("Your extent is an unnamed numeric vector. Please define names xmin/xmax/ymin/ymax explicitly.\n")
     }
-    extent = switch(
+    extent <- switch(
       output_class,
       sf = sf::st_bbox(extent),
       terra = terra::ext(extent)
     )
   }
 
-  extent_polygon = switch(
+  extent_polygon <- switch(
     output_class,
     sf = sf::st_as_sfc(extent),
     terra = terra::vect(extent)
   )
 
-  extent_polygon = switch(
+  extent_polygon <- switch(
     output_class,
     sf = sf::st_set_crs(extent_polygon, sf::st_crs(crs)),
     terra = terra::set.crs(extent_polygon, terra::crs(crs))
@@ -110,18 +113,18 @@ check_bbox <- function(
     stop("CRS should be entered when the reference extent is a vector.\n")
   }
   if (is.numeric(reference) && !is.null(reference_crs)) {
-    reference = sf::st_as_sfc(sf::st_bbox(reference), crs = reference_crs)
+    reference <- sf::st_as_sfc(sf::st_bbox(reference), crs = reference_crs)
   }
-  query_crs = check_crs(data_query)
-  ref_crs = check_crs(reference)
+  query_crs <- check_crs(data_query)
+  ref_crs <- check_crs(reference)
   if (is.na(query_crs) || is.null(query_crs)) {
     stop("The dataset you queried has no CRS. Please make sure your dataset has the correct CRS.\n")
   }
-  query_matched = sf::st_transform(data_query, sf::st_crs(ref_crs))
+  query_matched <- sf::st_transform(data_query, sf::st_crs(ref_crs))
 
 
 
-  check_result = sf::st_within()
+  check_result <- sf::st_within()
   return(check_result)
 }
 
@@ -144,12 +147,14 @@ check_crs <- function(x) {
     stopifnot("Input is invalid.\n" = (methods::is(x, "sf") || methods::is(x, "stars") || methods::is(x, "SpatVector") || methods::is(x, "SpatRaster")))
     
     if (methods::is(x, "sf") || methods::is(x, "stars")) {
-        crs_wkt = sf::st_crs(x)
+        crs_wkt <- sf::st_crs(x)
     } else {
-        crs_wkt = terra::crs(x)
+        crs_wkt <- terra::crs(x)
     }
 
-    stopifnot("No CRS is defined in the input. Please consult the metadata or the data source.\n" = !is.na(crs_wkt) || crs_wkt != "")
+    stopifnot(
+      "No CRS is defined in the input. Please consult the metadata or the data source.\n" =
+      !is.na(crs_wkt) || crs_wkt != "")
     return(crs_wkt)
 }
 
@@ -160,20 +165,20 @@ check_crs <- function(x) {
 #' @author Insang Song \email{geoissong@@gmail.com}
 #' @export 
 check_within_reference <- function(input_object, reference) {
-    stopifnot("Input is invalid.\n" = (methods::is(x, "sf") || methods::is(x, "stars") || methods::is(x, "SpatVector") || methods::is(x, "SpatRaster")))
-    stopifnot("Reference is invalid.\n" = (methods::is(x, "sf") || methods::is(x, "stars") || methods::is(x, "SpatVector") || methods::is(x, "SpatRaster")))
+    stopifnot("Input is invalid.\n" = (methods::is(input_object, "sf") || methods::is(input_object, "stars") || methods::is(input_object, "SpatVector") || methods::is(input_object, "SpatRaster")))
+    stopifnot("Reference is invalid.\n" = (methods::is(input_object, "sf") || methods::is(input_object, "stars") || methods::is(input_object, "SpatVector") || methods::is(input_object, "SpatRaster")))
 
   bbox_input <- input_object
     sf::st_bbox() |>
     sf::st_as_sfc()
   
-  bbox_reference = reference |>
+  bbox_reference <- reference |>
     sf::st_bbox() |>
     sf::st_as_sfc()
 
-  iswithin = sf::st_covered_by(bbox_input, bbox_reference)
-  iswithin = length(iswithin[[1]])
-  iswithin = (iswithin == 1)
+  iswithin <- sf::st_covered_by(bbox_input, bbox_reference)
+  iswithin <- length(iswithin[[1]])
+  iswithin <- (iswithin == 1)
   invisible(iswithin)
 }
 
diff --git a/scomps/R/estimate_demands.R b/scomps/R/estimate_demands.R
index 0c0bf6d7..02dcb346 100644
--- a/scomps/R/estimate_demands.R
+++ b/scomps/R/estimate_demands.R
@@ -2,7 +2,7 @@
 
 #' Estimate computational demands from inputs (to be written)
 #' 
-#' @param inputs a list of sf/Spat* objects or file paths
+#' @param inputs character vector of file paths
 #' @param nx integer(1). 
 #' @param ny integer(1). 
 #' @param padding numeric(1). Extrusion factor 
diff --git a/scomps/R/indexing.R b/scomps/R/indexing.R
index 7555a3f9..bfd3cf8b 100644
--- a/scomps/R/indexing.R
+++ b/scomps/R/indexing.R
@@ -7,7 +7,7 @@
 #' @param ncutsx integer(1). The number of splits along x-axis.
 #' @param ncutsy integer(1). The number of splits along y-axis.
 #' @export
-sp_indexing <- function(points_in, ncutsx, ncutsy){
+sp_indexing <- function(points_in, ncutsx, ncutsy) {
   # pts <- data.table(pnts)
   points_in <- points_in |>
     dplyr::mutate(or_id = seq(1, dim(points_in)[1]))
diff --git a/scomps/R/interpret_computational_domain.R b/scomps/R/interpret_computational_domain.R
index 90132a7f..f1a565fb 100644
--- a/scomps/R/interpret_computational_domain.R
+++ b/scomps/R/interpret_computational_domain.R
@@ -16,16 +16,24 @@
 #' @examples 
 #' # data
 #' library(sf)
-#' ncpath = system.file("shape/nc.shp", package = "sf")
-#' nc = read_sf(ncpath)
-#' nc = st_transform(nc, "EPSG:5070")
+#' ncpath <- system.file("shape/nc.shp", package = "sf")
+#' nc <- read_sf(ncpath)
+#' nc <- st_transform(nc, "EPSG:5070")
 #' # run
-#' # nc_comp_region = get_computational_regions(nc, nx = 12, ny = 8)
+#' # nc_comp_region <- get_computational_regions(nc, nx = 12, ny = 8)
 #' 
 #' @export 
-get_computational_regions <- function(input, mode = "grid", nx = 10, ny = 10, grid_min_features = 30, padding = NULL, unit = NULL, ...) {
+get_computational_regions <- function(
+  input, 
+  mode = "grid", 
+  nx = 10, 
+  ny = 10, 
+  grid_min_features = 30, 
+  padding = NULL, 
+  unit = NULL, 
+  ...) {
   # type check
-  package_detected = check_packbound(input)
+  package_detected <- check_packbound(input)
   # stopifnot("Invalid input.\n" = !any(grepl("^(sf|Spat)", class(input))))
   stopifnot("Argument mode should be one of 'grid', 'grid_advanced', or 'density'.\n" = !mode %in% c("grid", "grid_advanced", "density"))
   stopifnot("Ensure that nx, ny, and grid_min_features are all integer.\n" = all(is.integer(nx), is.integer(y), is.integer(grid_min_features)))
@@ -48,25 +56,25 @@ get_computational_regions <- function(input, mode = "grid", nx = 10, ny = 10, gr
 #' @return A sf or SpatVector object of computation grids with unique grid id (CGRIDID).
 #' @export
 sp_index_grid <- function(points_in, ncutsx, ncutsy){
-  package_detected = check_packbound(points_in)
+  package_detected <- check_packbound(points_in)
 
-  sp_index_grid.sf = function(points_in, ncutsx, ncutsy) {
+  sp_index_grid_sf <- function(points_in, ncutsx, ncutsy) {
     grid1 <- sf::st_make_grid(points_in, n = c(ncutsx, ncutsy)) |> 
       as.data.frame() |> 
       sf::st_as_sf()
     grid1 <- grid1[points_in, ]
     return(grid1)
   }
-  sp_index_grid.terra = function(points_in, ncutsx, ncutsy) {
+  sp_index_grid_terra <- function(points_in, ncutsx, ncutsy) {
     grid1 <- terra::rast(points_in, nrows = ncutsy, ncols = ncutsx)
     grid1 <- terra::as.polygons(grid1)
     return(grid1)
   }
-  grid_out = switch(package_detected,
-        sf = sp_index_grid.sf(points_in, ncutsx, ncutsy),
-        terra = sp_index_grid.terra(points_in, ncutsx, ncutsy))
+  grid_out <- switch(package_detected,
+        sf = sp_index_grid_sf(points_in, ncutsx, ncutsy),
+        terra = sp_index_grid_terra(points_in, ncutsx, ncutsy))
     
-  grid_out$CGRIDID = seq(1, nrow(x = grid_out)) 
+  grid_out$CGRIDID <- seq(1, nrow(x = grid_out)) 
   return(grid_out)
 
 }
@@ -93,28 +101,28 @@ sp_index_grid <- function(points_in, ncutsx, ncutsy){
 #' # dg_merged = grid_merge(sf::st_as_sf(sss), dgs, 100)
 #' #### NOT RUN ####
 #' @export
-grid_merge <- function(points_in, grid_in, grid_min_features){
-  package_detected = check_packbound(points_in)
+grid_merge <- function(points_in, grid_in, grid_min_features) {
+  package_detected <- check_packbound(points_in)
   if (package_detected == "terra") {
-    points_in = sf::st_as_sf(points_in)
-    grid_in = sf::st_as_sf(grid_in)
+    points_in <- sf::st_as_sf(points_in)
+    grid_in <- sf::st_as_sf(grid_in)
   }
 
-  n_points_in_grid = lengths(sf::st_intersects(grid_in, points_in))
-  grid_self = sf::st_relate(grid_in, grid_in, pattern = "2********")
-  grid_rook = sf::st_relate(grid_in, grid_in, pattern = "F***1****")
-  grid_rooks = mapply(c, grid_self, grid_rook, SIMPLIFY = FALSE)
-  grid_lt_threshold = (n_points_in_grid < grid_min_features)
+  n_points_in_grid <- lengths(sf::st_intersects(grid_in, points_in))
+  grid_self <- sf::st_relate(grid_in, grid_in, pattern = "2********")
+  grid_rook <- sf::st_relate(grid_in, grid_in, pattern = "F***1****")
+  grid_rooks <- mapply(c, grid_self, grid_rook, SIMPLIFY = FALSE)
+  grid_lt_threshold <- (n_points_in_grid < grid_min_features)
   stopifnot("Threshold is too low. Please try higher threshold.\n" = sum(grid_lt_threshold) != 0)
-  grid_lt_threshold = seq(1, nrow(grid_in))[grid_lt_threshold]
+  grid_lt_threshold <- seq(1, nrow(grid_in))[grid_lt_threshold]
 
   # This part does not work as expected. Should investigate edge list and actual row index of the grid object; 
-  identified = lapply(grid_rooks, \(x) sort(x[which(x %in% grid_lt_threshold)]))
-  identified = identified[grid_lt_threshold]
-  identified = unique(identified)
-  identified = identified[sapply(identified, length) > 1]
+  identified <- lapply(grid_rooks, \(x) sort(x[which(x %in% grid_lt_threshold)]))
+  identified <- identified[grid_lt_threshold]
+  identified <- unique(identified)
+  identified <- identified[sapply(identified, length) > 1]
 
-  identified_graph = lapply(identified, \(x) t(utils::combn(x, 2))) |>
+  identified_graph <- lapply(identified, \(x) t(utils::combn(x, 2))) |>
     Reduce(f = rbind, x = _) |>
     unique() |>
     apply(X = _, 2, as.character) |>
@@ -123,30 +131,30 @@ grid_merge <- function(points_in, grid_in, grid_min_features){
     igraph::components()
   # return(identified_graph)
 
-  identified_graph_member = identified_graph$membership
+  identified_graph_member <- identified_graph$membership
 
-  merge_idx = as.integer(names(identified_graph_member))
-  merge_member = split(merge_idx, identified_graph_member)
-  merge_member_label = unlist(lapply(merge_member, \(x) paste(x, collapse = "_")))
-  merge_member_label = merge_member_label[identified_graph_member]
+  merge_idx <- as.integer(names(identified_graph_member))
+  merge_member <- split(merge_idx, identified_graph_member)
+  merge_member_label <- unlist(lapply(merge_member, \(x) paste(x, collapse = "_")))
+  merge_member_label <- merge_member_label[identified_graph_member]
 
   # sf object manipulation
-  grid_out = grid_in
-  grid_out[["CGRIDID"]][merge_idx] = merge_member_label
+  grid_out <- grid_in
+  grid_out[["CGRIDID"]][merge_idx] <- merge_member_label
   # for (k in seq_along(merge_member_label)) {
   #   target_idx = merge_member_label[[k]]
   #   grid_out[["CGRIDID"]][target_idx] = paste("M_", paste(target_idx, collapse = "_"), sep = "")
   # }
-  grid_out = grid_out |>
+  grid_out <- grid_out |>
     dplyr::group_by(!!rlang::sym("CGRIDID")) |>
     dplyr::summarize(n_merged = dplyr::n()) |>
     dplyr::ungroup() 
 
   ## polsby-popper test for shape compactness
-  grid_merged = grid_out[which(grid_out$n_merged > 1),]
-  grid_merged_area = as.numeric(sf::st_area(grid_merged))
-  grid_merged_perimeter = as.numeric(sf::st_length(sf::st_cast(grid_merged, "LINESTRING")))
-  grid_merged_pptest = (4 * pi * grid_merged_area) / (grid_merged_perimeter ^ 2)
+  grid_merged <- grid_out[which(grid_out$n_merged > 1),]
+  grid_merged_area <- as.numeric(sf::st_area(grid_merged))
+  grid_merged_perimeter <- as.numeric(sf::st_length(sf::st_cast(grid_merged, "LINESTRING")))
+  grid_merged_pptest <- (4 * pi * grid_merged_area) / (grid_merged_perimeter ^ 2)
 
   # pptest value is bounded [0,1]; 0.3 threshold is groundless at this moment, possibly will make it defined by users.
   if (max(unique(identified_graph_member)) > floor(0.1 * nrow(grid_in)) || any(grid_merged_pptest < 0.3)) {
@@ -188,23 +196,23 @@ distribute_process <- function(grids, grid_id = NULL, fun, ...) {
     # subset using grids and grid_id
     if (!is.null(grid_id)) {
         if (is.character(grid_id)) {
-            grid_id_parsed = strsplit(grid_id, ":", fixed = TRUE)[[1]]
-            grid_ids = c(which(unique(grids[["CGRIDID"]]) == grid_id_parsed[1]),
+            grid_id_parsed <- strsplit(grid_id, ":", fixed = TRUE)[[1]]
+            grid_ids <- c(which(unique(grids[["CGRIDID"]]) == grid_id_parsed[1]),
                          which(unique(grids[["CGRIDID"]]) == grid_id_parsed[2]))
         }
         if (is.numeric(grid_id)) {
-            grid_ids = unique(grids[["CGRIDID"]])[grid_id]
+            grid_ids <- unique(grids[["CGRIDID"]])[grid_id]
         }
     }
-    grids_target = grids[grid_ids,]
-    grids_target_list = split(grids_target, grids_target[["CGRIDID"]])
+    grids_target <- grids[grid_ids,]
+    grids_target_list <- split(grids_target, grids_target[["CGRIDID"]])
 
-    results_distributed = future.apply::future_lapply(
+    results_distributed <- future.apply::future_lapply(
         \(x, ...) {
             fun(...)
         }, grids_target_list, 
         future.seed = TRUE)
-    results_distributed = do.call(rbind, results_distributed)
+    results_distributed <- do.call(rbind, results_distributed)
     return(results_distributed)
 }
 
diff --git a/scomps/R/preprocessing.R b/scomps/R/preprocessing.R
index 93b3ad93..093186bc 100644
--- a/scomps/R/preprocessing.R
+++ b/scomps/R/preprocessing.R
@@ -8,11 +8,11 @@
 #' @return A terra::ext or sfc_POLYGON object of the computation extent.
 #' @export
 set_clip_extent <- function(pnts, buffer_r) {
-  detected = check_packbound(pnts)
+  detected <- check_packbound(pnts)
   if (detected == "terra") {
-    ext_input = terra::ext(pnts)
+    ext_input <- terra::ext(pnts)
     # Note that `+` operation on terra::ext output accounts for the operand as it is.
-    ext_input = ext_input + (1.1 * buffer_r + 30)
+    ext_input <- ext_input + (1.1 * buffer_r + 30)
   }
   if (detected == "sf") {
     ext_input <- pnts |> sf::st_bbox()
diff --git a/scomps/R/processing.R b/scomps/R/processing.R
index 00b3e1d3..d53b8f59 100644
--- a/scomps/R/processing.R
+++ b/scomps/R/processing.R
@@ -9,28 +9,28 @@
 #' @param target_input sf or SpatVector object to be clipped
 #' @return A clipped sf or SpatVector object.
 #' @export
-clip_as_extent <- function(pnts, buffer_r, nqsegs=NULL, target_input){
+clip_as_extent <- function(pnts, buffer_r, nqsegs=NULL, target_input) {
   if (any(sapply(list(pnts, buffer_r, target_input), is.null))) {
     stop("One or more required arguments are NULL. Please check.\n")
   }
-  detected_pnts = check_packbound(pnts)
-  detected_target = check_packbound(target_input)
+  detected_pnts <- check_packbound(pnts)
+  detected_target <- check_packbound(target_input)
 
   if (detected_pnts != detected_target) {
     warning("Inputs are not the same class.\n")
-    target_input = switch(detected_target,
+    target_input <- switch(detected_target,
         sf = terra::vect(target_input),
         terra = sf::st_as_sf(target_input))
   }
   
-  ext_input = set_clip_extent(pnts, buffer_r)
+  ext_input <- set_clip_extent(pnts, buffer_r)
   cat("Clip target features with the input feature extent...\n")
   if (detected_pnts == "sf") {
-    cae = ext_input |>
+    cae <- ext_input |>
       sf::st_intersection(x = target_input)
   }
   if (detected_pnts == "terra") {
-    cae = terra::intersect(target_input, ext_input)
+    cae <- terra::intersect(target_input, ext_input)
   }
    
   return(cae)
@@ -44,11 +44,11 @@ clip_as_extent <- function(pnts, buffer_r, nqsegs=NULL, target_input){
 #' @param nqsegs integer(1). the number of points per a quarter circle
 #' @param ras SpatRaster object to be clipped
 #' @export
-clip_as_extent_ras <- function(pnts, buffer_r, nqsegs = 180, ras){
+clip_as_extent_ras <- function(pnts, buffer_r, nqsegs = 180, ras) {
   if (any(sapply(list(pnts, buffer_r, ras), is.null))) {
     stop("Any of required arguments are NULL. Please check.\n")
   }
-  ext_input = set_clip_extent(pnts, buffer_r) |>
+  ext_input <- set_clip_extent(pnts, buffer_r) |>
     terra::ext()
 
   cae <- terra::crop(ras, ext_input, snap = 'out')
@@ -63,11 +63,11 @@ clip_as_extent_ras <- function(pnts, buffer_r, nqsegs = 180, ras){
 #' @param nqsegs integer(1). the number of points per a quarter circle
 #' @param ras SpatRaster object to be clipped
 #' @export
-clip_as_extent_ras2 <- function(points_in, buffer_r, nqsegs=180, ras){
+clip_as_extent_ras2 <- function(points_in, buffer_r, nqsegs=180, ras) {
   if (any(sapply(list(points_in, buffer_r, ras), is.null))) {
     stop("Any of required arguments are NULL. Please check.\n")
   }
-  ext_input = set_clip_extent(points_in, buffer_r) |>
+  ext_input <- set_clip_extent(points_in, buffer_r) |>
     terra::ext()
 
   cae <- terra::crop(ras, ext_input, snap = 'out')
@@ -94,15 +94,15 @@ extract_with_polygons <- function(
     stopifnot("Check class of the input raster.\n" = any(methods::is(surf, "stars"), methods::is(surf, "SpatRaster")))
     stopifnot(is.character(id))
 
-    cls_polys = check_packbound(polys)
-    cls_surf = check_packbound(surf)
+    cls_polys <- check_packbound(polys)
+    cls_surf <- check_packbound(surf)
 
     if (cls_polys != cls_surf) {
-      polys = switch_packbound(polys)
+      polys <- switch_packbound(polys)
     }
 
-    extract_with_polygons.sf = function(polys, surf, id, func) {
-        extracted = stars::st_extract(x = surf, at = polys, FUN = func)
+    extract_with_polygons_sf <- function(polys, surf, id, func) {
+        extracted <- stars::st_extract(x = surf, at = polys, FUN = func)
         # extracted = extracted |>
         #   group_by(!!sym(id)) |>
         #   summarize(across(-!!sym(id), ~func)) |>
@@ -110,19 +110,19 @@ extract_with_polygons <- function(
         return(extracted)
     }
 
-    extract_with_polygons.terra = function(polys, surf, id, func) {
-        extracted = terra::extract(surf, polys)
-        extracted = extracted |>
+    extract_with_polygons_terra <- function(polys, surf, id, func) {
+        extracted <- terra::extract(surf, polys)
+        extracted <- extracted |>
           dplyr::group_by(!!rlang::sym(id)) |>
           dplyr::summarize(dplyr::across(-!!rlang::sym(id), ~func)) |>
           dplyr::ungroup()
         return(extracted)
     }
 
-    extracted_poly = switch(
+    extracted_poly <- switch(
         cls_surf,
-        sf = extract_with_polygons.sf(polys = polys, surf = surf, id = id, func = func),
-        terra = extract_with_polygons.terra(polys = polys, surf = surf, id = id, func = func)
+        sf = extract_with_polygons_sf(polys = polys, surf = surf, id = id, func = func),
+        terra = extract_with_polygons_terra(polys = polys, surf = surf, id = id, func = func)
     )
     return(extracted_poly)
 }
@@ -146,7 +146,7 @@ extract_with <- function(raster, vector, id, func = mean, mode = "polygon", ...)
     stopifnot(is.character(id))
     stopifnot(id %in% names(vector))
 
-    extracted = 
+    extracted <- 
       switch(mode,
         polygon = extract_with_polygons(vector, raster, id, func),
         buffer = extract_with_buffer(vector, raster, id = id, func = func, ...))
@@ -166,26 +166,26 @@ extract_with <- function(raster, vector, id, func = mean, mode = "polygon", ...)
 #' @export
 calculate_sedc <- function(point_from, point_to, id, sedc_bandwidth, threshold, target_fields) {
   # define sources, set SEDC exponential decay range
-  len_point_from = seq_len(nrow(point_from))
-  len_point_to = seq_len(nrow(point_to))
+  len_point_from <- seq_len(nrow(point_from))
+  len_point_to <- seq_len(nrow(point_to))
 
-  point_from$from_id = len_point_from
+  point_from$from_id <- len_point_from
   # select egrid_v only if closer than 3e5 meters from each aqs
-  point_from_buf = terra::buffer(point_from_buf, threshold = threshold, quadsegs = 90)
-  point_to = point_to[point_from_buf,]
-  point_to$to_id = len_point_to
+  point_from_buf <- terra::buffer(point_from_buf, threshold = threshold, quadsegs = 90)
+  point_to <- point_to[point_from_buf,]
+  point_to$to_id <- len_point_to
 
   # near features with distance argument: only returns integer indices
-  near_from_to = terra::nearby(point_from, point_to, distance = threshold)
+  near_from_to <- terra::nearby(point_from, point_to, distance = threshold)
   # attaching actual distance
-  dist_near_to = terra::distance(point_from, point_to)
-  dist_near_to_df = as.vector(dist_near_to)
+  dist_near_to <- terra::distance(point_from, point_to)
+  dist_near_to_df <- as.vector(dist_near_to)
   # adding integer indices
-  dist_near_to_tdf = expand.grid(from_id = len_point_from, to_id = len_point_to)
-  dist_near_to_df = cbind(dist_near_to_tdf, dist = dist_near_to_df)
+  dist_near_to_tdf <- expand.grid(from_id = len_point_from, to_id = len_point_to)
+  dist_near_to_df <- cbind(dist_near_to_tdf, dist = dist_near_to_df)
 
   # summary
-  near_from_to = near_from_to |>
+  near_from_to <- near_from_to |>
     dplyr::as_tibble() |>
     dplyr::left_join(data.frame(point_from)) |>
     dplyr::left_join(data.frame(point_to)) |>
@@ -214,15 +214,15 @@ calculate_sedc <- function(point_from, point_to, id, sedc_bandwidth, threshold,
 #' library(sf)
 #' 
 #' # run
-#' nc = sf::st_read(system.file("shape/nc.shp", package="sf"))
-#' nc = sf::st_transform(nc, 5070)
-#' pp = sf::st_sample(nc, size = 300)
-#' pp = sf::st_as_sf(pp)
-#' pp[["id"]] = seq(1, nrow(pp))
-#' sf::st_crs(pp) = "EPSG:5070"
-#' ppb = sf::st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
+#' nc <- sf::st_read(system.file("shape/nc.shp", package="sf"))
+#' nc <- sf::st_transform(nc, 5070)
+#' pp <- sf::st_sample(nc, size = 300)
+#' pp <- sf::st_as_sf(pp)
+#' pp[["id"]] <- seq(1, nrow(pp))
+#' sf::st_crs(pp) <- "EPSG:5070"
+#' ppb <- sf::st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
 #' 
-#' system.time({ppb_nc_aw = aw_covariates(ppb, nc, 'id')})
+#' system.time({ppb_nc_aw <- aw_covariates(ppb, nc, 'id')})
 #' summary(ppb_nc_aw)
 #' #### Example of aw_covariates ends ####
 #' @export
@@ -232,13 +232,13 @@ aw_covariates <- function(poly_in, poly_weight, id_poly_in = "ID") {
     #check_crs()
 
     ## distinguish numeric and nonnumeric columns
-    index_numeric = grep("(integer|numeric)", unlist(sapply(poly_weight, class)))
+    index_numeric <- grep("(integer|numeric)", unlist(sapply(poly_weight, class)))
     
     aw_covariates.terra = function(poly_in, poly_weight, id_poly_in = id_poly_in) {
         
-        poly_intersected = terra::intersect(poly_in, poly_weight)
-        poly_intersected[["area_segment_"]] = terra::expanse(poly_intersected)
-        poly_intersected = data.frame(poly_intersected) |>
+        poly_intersected <- terra::intersect(poly_in, poly_weight)
+        poly_intersected[["area_segment_"]] <- terra::expanse(poly_intersected)
+        poly_intersected <- data.frame(poly_intersected) |>
             dplyr::group_by(!!rlang::sym(id_poly_in)) |>
             dplyr::summarize(dplyr::across(is.numeric,
                         ~stats::weighted.mean(., w = area_segment_))) |>
@@ -246,11 +246,11 @@ aw_covariates <- function(poly_in, poly_weight, id_poly_in = "ID") {
         return(poly_intersected)
     }
 
-    class_poly_in = check_packbound(poly_in)
-    class_poly_weight = check_packbound(poly_weight)
+    class_poly_in <- check_packbound(poly_in)
+    class_poly_weight <- check_packbound(poly_weight)
 
     if (class_poly_in != class_poly_weight) {
-      class_poly_weight = switch_packbound(class_poly_weight)
+      class_poly_weight <- switch_packbound(class_poly_weight)
     }
     
     switch(class_poly_in,
@@ -296,7 +296,7 @@ extract_with_buffer <- function(
     stopifnot(is.integer(qsegs))
 
     if (!is.null(kernel)) {
-        extracted = extract_with_buffer.flat(points = points,
+        extracted <- extract_with_buffer.flat(points = points,
                                       surf = surf,
                                       radius = radius,
                                       id = id,
@@ -305,7 +305,7 @@ extract_with_buffer <- function(
         return(extracted)
     }
 
-    extracted = extract_with_buffer.kernel(points = points,
+    extracted <- extract_with_buffer.kernel(points = points,
                                            surf = surf,
                                            radius = radius,
                                            id = id,
@@ -322,17 +322,17 @@ extract_with_buffer.flat <- function(
         points, surf, radius, id, qsegs, func = mean, kernel = NULL, bandwidth = NULL
     ) {
     # generate buffers
-    bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
+    bufs <- terra::buffer(points, width = radius, quadsegs = qsegs)
     # crop raster
-    bufs_extent = terra::ext(bufs)
-    surf_cropped = terra::crop(surf, bufs_extent)
-    name_surf_val = names(surf)
+    bufs_extent <- terra::ext(bufs)
+    surf_cropped <- terra::crop(surf, bufs_extent)
+    name_surf_val <- names(surf)
     # extract raster values
-    surf_at_bufs = terra::extract(surf_cropped, bufs)
-    surf_at_bufs_summary = 
+    surf_at_bufs <- terra::extract(surf_cropped, bufs)
+    surf_at_bufs_summary <- 
         surf_at_bufs |> 
             dplyr::group_by(ID) |> 
-            dplyr::summarize(dplyr::across(dplyr::all_of(name_surf_val), ~mean, na.rm=T)) |> 
+            dplyr::summarize(dplyr::across(dplyr::all_of(name_surf_val), ~mean, na.rm = TRUE)) |> 
             dplyr::ungroup()
     return(surf_at_bufs_summary)
 }
@@ -343,18 +343,18 @@ extract_with_buffer.kernel <- function(
         points, surf, radius, id, qsegs, func = mean, kernel, bandwidth
     ) {
         # generate buffers
-        bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
+        bufs <- terra::buffer(points, width = radius, quadsegs = qsegs)
         # crop raster
-        bufs_extent = terra::ext(bufs)
-        surf_cropped = terra::crop(surf, bufs_extent)
-        name_surf_val = names(surf)
+        bufs_extent <- terra::ext(bufs)
+        surf_cropped <- terra::crop(surf, bufs_extent)
+        name_surf_val <- names(surf)
 
         # TODO: kernel implementation
 
 
         # extract raster values
-        surf_at_bufs = terra::extract(surf_cropped, bufs)
-        surf_at_bufs_summary = 
+        surf_at_bufs <- terra::extract(surf_cropped, bufs)
+        surf_at_bufs_summary <- 
             surf_at_bufs |> 
                 dplyr::group_by(ID) |> 
                 dplyr::summarize(dplyr::across(dplyr::all_of(name_surf_val), ~mean, na.rm=T)) |> 
diff --git a/scomps/R/switch_format.R b/scomps/R/switch_format.R
index a0c38e8f..868c3da5 100644
--- a/scomps/R/switch_format.R
+++ b/scomps/R/switch_format.R
@@ -8,10 +8,10 @@
 #' @export
 switch_packbound <- function(input) {
   stopifnot("Input should be one of sf or Spat* object.\n" = any(methods::is(input, "sf"), methods::is(input, "stars"), methods::is(input, "SpatVector"), methods::is(input, "SpatRaster")))
-  cls_input = check_packbound(input)
-  type_input = check_datatype(input)
+  cls_input <- check_packbound(input)
+  type_input <- check_datatype(input)
 
-  switched = 
+  switched <- 
   switch(cls_input,
     sf = switch(type_input,
       vector = terra::vect(input),
diff --git a/scomps/R/validate.R b/scomps/R/validate.R
index 545869c2..43ea82b2 100644
--- a/scomps/R/validate.R
+++ b/scomps/R/validate.R
@@ -7,9 +7,9 @@
 #' @return A repaired sf or SpatVector object depending on the class of input_vector.
 #' @export
 validate_and_repair_vectors <- function(input_vector) {
-  detected = check_packbound(input_vector)
+  detected <- check_packbound(input_vector)
 
-  validated = switch(detected,
+  validated <- switch(detected,
     terra = terra::makeValid(input_vector),
     sf = sf::st_make_valid(input_vector))
 
diff --git a/scomps/man/aw_covariates.Rd b/scomps/man/aw_covariates.Rd
index ca836de6..9743d66a 100644
--- a/scomps/man/aw_covariates.Rd
+++ b/scomps/man/aw_covariates.Rd
@@ -24,15 +24,15 @@ When poly_in and poly_weight are different classes, poly_weight will be converte
 library(sf)
 
 # run
-nc = sf::st_read(system.file("shape/nc.shp", package="sf"))
-nc = sf::st_transform(nc, 5070)
-pp = sf::st_sample(nc, size = 300)
-pp = sf::st_as_sf(pp)
-pp[["id"]] = seq(1, nrow(pp))
-sf::st_crs(pp) = "EPSG:5070"
-ppb = sf::st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
+nc <- sf::st_read(system.file("shape/nc.shp", package="sf"))
+nc <- sf::st_transform(nc, 5070)
+pp <- sf::st_sample(nc, size = 300)
+pp <- sf::st_as_sf(pp)
+pp[["id"]] <- seq(1, nrow(pp))
+sf::st_crs(pp) <- "EPSG:5070"
+ppb <- sf::st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
 
-system.time({ppb_nc_aw = aw_covariates(ppb, nc, 'id')})
+system.time({ppb_nc_aw <- aw_covariates(ppb, nc, 'id')})
 summary(ppb_nc_aw)
 #### Example of aw_covariates ends ####
 }
diff --git a/scomps/man/estimate_demands.Rd b/scomps/man/estimate_demands.Rd
index 787ad77f..a22698fc 100644
--- a/scomps/man/estimate_demands.Rd
+++ b/scomps/man/estimate_demands.Rd
@@ -7,7 +7,7 @@
 estimate_demands(inputs, nx, ny, padding)
 }
 \arguments{
-\item{inputs}{a list of sf/Spat* objects or file paths}
+\item{inputs}{character vector of file paths}
 
 \item{nx}{integer(1).}
 
diff --git a/scomps/man/get_computational_regions.Rd b/scomps/man/get_computational_regions.Rd
index 6a864a55..5cd1bb49 100644
--- a/scomps/man/get_computational_regions.Rd
+++ b/scomps/man/get_computational_regions.Rd
@@ -41,11 +41,11 @@ TODO. Using input points, the bounding box is split to the predefined numbers of
 \examples{
 # data
 library(sf)
-ncpath = system.file("shape/nc.shp", package = "sf")
-nc = read_sf(ncpath)
-nc = st_transform(nc, "EPSG:5070")
+ncpath <- system.file("shape/nc.shp", package = "sf")
+nc <- read_sf(ncpath)
+nc <- st_transform(nc, "EPSG:5070")
 # run
-# nc_comp_region = get_computational_regions(nc, nx = 12, ny = 8)
+# nc_comp_region <- get_computational_regions(nc, nx = 12, ny = 8)
 
 }
 \author{
diff --git a/scomps/tests/testthat/tests.R b/scomps/tests/testthat/tests.R
index 6efa4142..a0674e10 100644
--- a/scomps/tests/testthat/tests.R
+++ b/scomps/tests/testthat/tests.R
@@ -4,12 +4,12 @@ testthat::test_that("What package does the input object belong?",
     withr::local_package("stars")
     withr::local_package("terra")
     withr::local_options(list(sf_use_s2 = FALSE))
-    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
-    bcsd_stars = stars::read_stars(bcsd_path)
+    bcsd_path <- system.file(package = "stars", "nc/bcsd_obs_1999.nc")
+    bcsd_stars <- stars::read_stars(bcsd_path)
 
-    packbound_stars = check_packbound(bcsd_stars)
-    sprast_bcsd = terra::rast(bcsd_path)
-    packbound_terra = check_packbound(sprast_bcsd)
+    packbound_stars <- check_packbound(bcsd_stars)
+    sprast_bcsd <- terra::rast(bcsd_path)
+    packbound_terra <- check_packbound(sprast_bcsd)
 
     testthat::expect_equal(packbound_stars, "sf")
     testthat::expect_equal(packbound_terra, "terra")
@@ -21,14 +21,14 @@ testthat::test_that("What package does the input object belong?",
     withr::local_package("stars")
     withr::local_package("terra")
     withr::local_options(list(sf_use_s2 = FALSE))
-    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
-    bcsd_stars = stars::read_stars(bcsd_path)
+    bcsd_path <- system.file(package = "stars", "nc/bcsd_obs_1999.nc")
+    bcsd_stars <- stars::read_stars(bcsd_path)
 
-    nc = system.file(package = "sf", "shape/nc.shp")
-    nc = sf::read_sf(nc)
+    nc <- system.file(package = "sf", "shape/nc.shp")
+    nc <- sf::read_sf(nc)
 
-    datatype_stars = check_datatype(bcsd_stars)
-    datatype_sf = check_datatype(nc)
+    datatype_stars <- check_datatype(bcsd_stars)
+    datatype_sf <- check_datatype(nc)
 
     testthat::expect_equal(datatype_stars, "raster")
     testthat::expect_equal(datatype_sf, "vector")
@@ -42,19 +42,19 @@ testthat::test_that("Format is well converted",
     withr::local_options(list(sf_use_s2 = FALSE))
 
     # starts from sf/stars
-    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
-    bcsd_stars = stars::read_stars(bcsd_path)
-    nc = system.file(package = "sf", "shape/nc.shp")
-    nc = sf::read_sf(nc)
+    bcsd_path <- system.file(package = "stars", "nc/bcsd_obs_1999.nc")
+    bcsd_stars <- stars::read_stars(bcsd_path)
+    nc <- system.file(package = "sf", "shape/nc.shp")
+    nc <- sf::read_sf(nc)
 
-    stars_bcsd_tr = switch_packbound(bcsd_stars)
-    sf_nc_tr = switch_packbound(nc)
+    stars_bcsd_tr <- switch_packbound(bcsd_stars)
+    sf_nc_tr <- switch_packbound(nc)
 
     testthat::expect_equal(check_packbound(stars_bcsd_tr), "terra")
     testthat::expect_equal(check_packbound(sf_nc_tr), "terra")
 
-    stars_bcsd_trb = switch_packbound(stars_bcsd_tr)
-    sf_nc_trb = switch_packbound(sf_nc_tr)
+    stars_bcsd_trb <- switch_packbound(stars_bcsd_tr)
+    sf_nc_trb <- switch_packbound(sf_nc_tr)
 
     testthat::expect_equal(check_packbound(stars_bcsd_trb), "sf")
     testthat::expect_equal(check_packbound(sf_nc_trb), "sf")
diff --git a/scomps_coverage_report.html b/scomps_coverage_report.html
index 60117c09..95ef497a 100644
--- a/scomps_coverage_report.html
+++ b/scomps_coverage_report.html
@@ -545,14 +545,14 @@ 
scomps coverage - 6.75%

                     62
                     !
                     
-                      
        sf = sp_index_grid.sf(points_in, ncutsx, ncutsy),

+                      
        sf = sp_index_grid.sf(points_in, ncutsx, ncutsy),

                     
                   
                   
                     63
                     !
                     
-                      
        terra = sp_index_grid.terra(points_in, ncutsx, ncutsy))

+                      
        terra = sp_index_grid.terra(points_in, ncutsx, ncutsy))

                     
                   
                   
@@ -2427,14 +2427,14 @@ 
scomps coverage - 6.75%

                     124
                     !
                     
-                      
        sf = extract_with_polygons.sf(polys = polys, surf = surf, id = id, func = func),

+                      
        sf = extract_with_polygons.sf(polys = polys, surf = surf, id = id, func = func),

                     
                   
                   
                     125
                     !
                     
-                      
        terra = extract_with_polygons.terra(polys = polys, surf = surf, id = id, func = func)

+                      
        terra = extract_with_polygons.terra(polys = polys, surf = surf, id = id, func = func)

                     
                   
                   
diff --git a/scomps_rmarkdown_litr.html b/scomps_rmarkdown_litr.html
index 44adce73..3bc16cb8 100644
--- a/scomps_rmarkdown_litr.html
+++ b/scomps_rmarkdown_litr.html
@@ -449,12 +449,12 @@ 
Create functions

     withr::local_package("stars")
     withr::local_package("terra")
     withr::local_options(list(sf_use_s2 = FALSE))
-    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
-    bcsd_stars = stars::read_stars(bcsd_path)
+    bcsd_path <- system.file(package = "stars", "nc/bcsd_obs_1999.nc")
+    bcsd_stars <- stars::read_stars(bcsd_path)
 
-    packbound_stars = check_packbound(bcsd_stars)
-    sprast_bcsd = terra::rast(bcsd_path)
-    packbound_terra = check_packbound(sprast_bcsd)
+    packbound_stars <- check_packbound(bcsd_stars)
+    sprast_bcsd <- terra::rast(bcsd_path)
+    packbound_terra <- check_packbound(sprast_bcsd)
 
     testthat::expect_equal(packbound_stars, "sf")
     testthat::expect_equal(packbound_terra, "terra")
@@ -466,14 +466,14 @@ 
Create functions

     withr::local_package("stars")
     withr::local_package("terra")
     withr::local_options(list(sf_use_s2 = FALSE))
-    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
-    bcsd_stars = stars::read_stars(bcsd_path)
+    bcsd_path <- system.file(package = "stars", "nc/bcsd_obs_1999.nc")
+    bcsd_stars <- stars::read_stars(bcsd_path)
 
-    nc = system.file(package = "sf", "shape/nc.shp")
-    nc = sf::read_sf(nc)
+    nc <- system.file(package = "sf", "shape/nc.shp")
+    nc <- sf::read_sf(nc)
 
-    datatype_stars = check_datatype(bcsd_stars)
-    datatype_sf = check_datatype(nc)
+    datatype_stars <- check_datatype(bcsd_stars)
+    datatype_sf <- check_datatype(nc)
 
     testthat::expect_equal(datatype_stars, "raster")
     testthat::expect_equal(datatype_sf, "vector")
@@ -490,10 +490,10 @@ 
Create functions

 #' @export
 switch_packbound <- function(input) {
   stopifnot("Input should be one of sf or Spat* object.\n" = any(methods::is(input, "sf"), methods::is(input, "stars"), methods::is(input, "SpatVector"), methods::is(input, "SpatRaster")))
-  cls_input = check_packbound(input)
-  type_input = check_datatype(input)
+  cls_input <- check_packbound(input)
+  type_input <- check_datatype(input)
 
-  switched = 
+  switched <- 
   switch(cls_input,
     sf = switch(type_input,
       vector = terra::vect(input),
@@ -513,19 +513,19 @@ 
Create functions

     withr::local_options(list(sf_use_s2 = FALSE))
 
     # starts from sf/stars
-    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
-    bcsd_stars = stars::read_stars(bcsd_path)
-    nc = system.file(package = "sf", "shape/nc.shp")
-    nc = sf::read_sf(nc)
+    bcsd_path <- system.file(package = "stars", "nc/bcsd_obs_1999.nc")
+    bcsd_stars <- stars::read_stars(bcsd_path)
+    nc <- system.file(package = "sf", "shape/nc.shp")
+    nc <- sf::read_sf(nc)
 
-    stars_bcsd_tr = switch_packbound(bcsd_stars)
-    sf_nc_tr = switch_packbound(nc)
+    stars_bcsd_tr <- switch_packbound(bcsd_stars)
+    sf_nc_tr <- switch_packbound(nc)
 
     testthat::expect_equal(check_packbound(stars_bcsd_tr), "terra")
     testthat::expect_equal(check_packbound(sf_nc_tr), "terra")
 
-    stars_bcsd_trb = switch_packbound(stars_bcsd_tr)
-    sf_nc_trb = switch_packbound(sf_nc_tr)
+    stars_bcsd_trb <- switch_packbound(stars_bcsd_tr)
+    sf_nc_trb <- switch_packbound(sf_nc_tr)
 
     testthat::expect_equal(check_packbound(stars_bcsd_trb), "sf")
     testthat::expect_equal(check_packbound(sf_nc_trb), "sf")
@@ -542,8 +542,11 @@ 
Create functions

 #' @return A (reprojected) sf or SpatVector object.
 #' @export
 check_crs2 <- function(input, crs_standard = "EPSG:4326") {
-  check_crs.sf <- function(input){
-    if (is.na(sf::st_crs(input))){cat('Please check the coordinate system or its EPSG code of your input object.'); return(NULL)}
+  check_crs_sf <- function(input) {
+    if (is.na(sf::st_crs(input))) {
+      cat('Please check the coordinate system or its EPSG code of your input object.')
+      return(NULL)
+    }
     if (sf::st_crs(input)$epsg == crs_standard ) {
       return(input)
     } 
@@ -551,17 +554,17 @@ 
Create functions

     return(input_transformed)
   }
 
-  check_crs.terra <- function(input) {
+  check_crs_terra <- function(input) {
     if (terra::crs(input, describe = TRUE)$code == crs_standard) {
       return(input)
     }
-    input_transformed = terra::project(input, terra::crs(crs_standard))
+    input_transformed <- terra::project(input, terra::crs(crs_standard))
     return(input_transformed)
   }
-    detected = check_packbound(input)
+    detected <- check_packbound(input)
     switch(detected,
-          terra = check_crs.terra(input),
-          sf = check_crs.sf(input))
+          terra = check_crs_terra(input),
+          sf = check_crs_sf(input))
   }

 
#' Validate and repair input vector data
 #' @description It tries repairing input vector data. Vector validity violation usually appears in polygon data with self-crossing or hole orders. This function will pass the input_vector object to sf::st_make_valid() (if input_vector is sf) or terra::makeValid() (if input_vector is SpatVector). May take some time depending on the geometry complexity.
@@ -570,9 +573,9 @@ 
Create functions

 #' @return A repaired sf or SpatVector object depending on the class of input_vector.
 #' @export
 validate_and_repair_vectors <- function(input_vector) {
-  detected = check_packbound(input_vector)
+  detected <- check_packbound(input_vector)
 
-  validated = switch(detected,
+  validated <- switch(detected,
     terra = terra::makeValid(input_vector),
     sf = sf::st_make_valid(input_vector))
 
@@ -605,11 +608,11 @@ 
Create functions

 #' @return A terra::ext or sfc_POLYGON object of the computation extent.
 #' @export
 set_clip_extent <- function(pnts, buffer_r) {
-  detected = check_packbound(pnts)
+  detected <- check_packbound(pnts)
   if (detected == "terra") {
-    ext_input = terra::ext(pnts)
+    ext_input <- terra::ext(pnts)
     # Note that `+` operation on terra::ext output accounts for the operand as it is.
-    ext_input = ext_input + (1.1 * buffer_r + 30)
+    ext_input <- ext_input + (1.1 * buffer_r + 30)
   }
   if (detected == "sf") {
     ext_input <- pnts |> sf::st_bbox()
@@ -628,28 +631,28 @@ 
Create functions

 #' @param target_input sf or SpatVector object to be clipped
 #' @return A clipped sf or SpatVector object.
 #' @export
-clip_as_extent <- function(pnts, buffer_r, nqsegs=NULL, target_input){
+clip_as_extent <- function(pnts, buffer_r, nqsegs=NULL, target_input) {
   if (any(sapply(list(pnts, buffer_r, target_input), is.null))) {
     stop("One or more required arguments are NULL. Please check.\n")
   }
-  detected_pnts = check_packbound(pnts)
-  detected_target = check_packbound(target_input)
+  detected_pnts <- check_packbound(pnts)
+  detected_target <- check_packbound(target_input)
 
   if (detected_pnts != detected_target) {
     warning("Inputs are not the same class.\n")
-    target_input = switch(detected_target,
+    target_input <- switch(detected_target,
         sf = terra::vect(target_input),
         terra = sf::st_as_sf(target_input))
   }
   
-  ext_input = set_clip_extent(pnts, buffer_r)
+  ext_input <- set_clip_extent(pnts, buffer_r)
   cat("Clip target features with the input feature extent...\n")
   if (detected_pnts == "sf") {
-    cae = ext_input |>
+    cae <- ext_input |>
       sf::st_intersection(x = target_input)
   }
   if (detected_pnts == "terra") {
-    cae = terra::intersect(target_input, ext_input)
+    cae <- terra::intersect(target_input, ext_input)
   }
    
   return(cae)
@@ -662,11 +665,11 @@ 
Create functions

 #' @param nqsegs integer(1). the number of points per a quarter circle
 #' @param ras SpatRaster object to be clipped
 #' @export
-clip_as_extent_ras <- function(pnts, buffer_r, nqsegs = 180, ras){
+clip_as_extent_ras <- function(pnts, buffer_r, nqsegs = 180, ras) {
   if (any(sapply(list(pnts, buffer_r, ras), is.null))) {
     stop("Any of required arguments are NULL. Please check.\n")
   }
-  ext_input = set_clip_extent(pnts, buffer_r) |>
+  ext_input <- set_clip_extent(pnts, buffer_r) |>
     terra::ext()
 
   cae <- terra::crop(ras, ext_input, snap = 'out')
@@ -680,11 +683,11 @@ 
Create functions

 #' @param nqsegs integer(1). the number of points per a quarter circle
 #' @param ras SpatRaster object to be clipped
 #' @export
-clip_as_extent_ras2 <- function(points_in, buffer_r, nqsegs=180, ras){
+clip_as_extent_ras2 <- function(points_in, buffer_r, nqsegs=180, ras) {
   if (any(sapply(list(points_in, buffer_r, ras), is.null))) {
     stop("Any of required arguments are NULL. Please check.\n")
   }
-  ext_input = set_clip_extent(points_in, buffer_r) |>
+  ext_input <- set_clip_extent(points_in, buffer_r) |>
     terra::ext()
 
   cae <- terra::crop(ras, ext_input, snap = 'out')
@@ -697,7 +700,7 @@ 
Create functions

 #' @param ncutsx integer(1). The number of splits along x-axis.
 #' @param ncutsy integer(1). The number of splits along y-axis.
 #' @export
-sp_indexing <- function(points_in, ncutsx, ncutsy){
+sp_indexing <- function(points_in, ncutsx, ncutsy) {
   # pts <- data.table(pnts)
   points_in <- points_in |>
     dplyr::mutate(or_id = seq(1, dim(points_in)[1]))
@@ -726,7 +729,7 @@ 
Create functions

 

 
#' Estimate computational demands from inputs (to be written)
 #' 
-#' @param inputs a list of sf/Spat* objects or file paths
+#' @param inputs character vector of file paths
 #' @param nx integer(1). 
 #' @param ny integer(1). 
 #' @param padding numeric(1). Extrusion factor 
@@ -762,16 +765,24 @@ 
Create functions

 #' @examples 
 #' # data
 #' library(sf)
-#' ncpath = system.file("shape/nc.shp", package = "sf")
-#' nc = read_sf(ncpath)
-#' nc = st_transform(nc, "EPSG:5070")
+#' ncpath <- system.file("shape/nc.shp", package = "sf")
+#' nc <- read_sf(ncpath)
+#' nc <- st_transform(nc, "EPSG:5070")
 #' # run
-#' # nc_comp_region = get_computational_regions(nc, nx = 12, ny = 8)
+#' # nc_comp_region <- get_computational_regions(nc, nx = 12, ny = 8)
 #' 
 #' @export 
-get_computational_regions <- function(input, mode = "grid", nx = 10, ny = 10, grid_min_features = 30, padding = NULL, unit = NULL, ...) {
+get_computational_regions <- function(
+  input, 
+  mode = "grid", 
+  nx = 10, 
+  ny = 10, 
+  grid_min_features = 30, 
+  padding = NULL, 
+  unit = NULL, 
+  ...) {
   # type check
-  package_detected = check_packbound(input)
+  package_detected <- check_packbound(input)
   # stopifnot("Invalid input.\n" = !any(grepl("^(sf|Spat)", class(input))))
   stopifnot("Argument mode should be one of 'grid', 'grid_advanced', or 'density'.\n" = !mode %in% c("grid", "grid_advanced", "density"))
   stopifnot("Ensure that nx, ny, and grid_min_features are all integer.\n" = all(is.integer(nx), is.integer(y), is.integer(grid_min_features)))
@@ -794,25 +805,25 @@ 
Create functions

 #' @return A sf or SpatVector object of computation grids with unique grid id (CGRIDID).
 #' @export
 sp_index_grid <- function(points_in, ncutsx, ncutsy){
-  package_detected = check_packbound(points_in)
+  package_detected <- check_packbound(points_in)
 
-  sp_index_grid.sf = function(points_in, ncutsx, ncutsy) {
+  sp_index_grid_sf <- function(points_in, ncutsx, ncutsy) {
     grid1 <- sf::st_make_grid(points_in, n = c(ncutsx, ncutsy)) |> 
       as.data.frame() |> 
       sf::st_as_sf()
     grid1 <- grid1[points_in, ]
     return(grid1)
   }
-  sp_index_grid.terra = function(points_in, ncutsx, ncutsy) {
+  sp_index_grid_terra <- function(points_in, ncutsx, ncutsy) {
     grid1 <- terra::rast(points_in, nrows = ncutsy, ncols = ncutsx)
     grid1 <- terra::as.polygons(grid1)
     return(grid1)
   }
-  grid_out = switch(package_detected,
-        sf = sp_index_grid.sf(points_in, ncutsx, ncutsy),
-        terra = sp_index_grid.terra(points_in, ncutsx, ncutsy))
+  grid_out <- switch(package_detected,
+        sf = sp_index_grid_sf(points_in, ncutsx, ncutsy),
+        terra = sp_index_grid_terra(points_in, ncutsx, ncutsy))
     
-  grid_out$CGRIDID = seq(1, nrow(x = grid_out)) 
+  grid_out$CGRIDID <- seq(1, nrow(x = grid_out)) 
   return(grid_out)
 
 }
@@ -839,28 +850,28 @@ 
Create functions

 #' # dg_merged = grid_merge(sf::st_as_sf(sss), dgs, 100)
 #' #### NOT RUN ####
 #' @export
-grid_merge <- function(points_in, grid_in, grid_min_features){
-  package_detected = check_packbound(points_in)
+grid_merge <- function(points_in, grid_in, grid_min_features) {
+  package_detected <- check_packbound(points_in)
   if (package_detected == "terra") {
-    points_in = sf::st_as_sf(points_in)
-    grid_in = sf::st_as_sf(grid_in)
+    points_in <- sf::st_as_sf(points_in)
+    grid_in <- sf::st_as_sf(grid_in)
   }
 
-  n_points_in_grid = lengths(sf::st_intersects(grid_in, points_in))
-  grid_self = sf::st_relate(grid_in, grid_in, pattern = "2********")
-  grid_rook = sf::st_relate(grid_in, grid_in, pattern = "F***1****")
-  grid_rooks = mapply(c, grid_self, grid_rook, SIMPLIFY = FALSE)
-  grid_lt_threshold = (n_points_in_grid < grid_min_features)
+  n_points_in_grid <- lengths(sf::st_intersects(grid_in, points_in))
+  grid_self <- sf::st_relate(grid_in, grid_in, pattern = "2********")
+  grid_rook <- sf::st_relate(grid_in, grid_in, pattern = "F***1****")
+  grid_rooks <- mapply(c, grid_self, grid_rook, SIMPLIFY = FALSE)
+  grid_lt_threshold <- (n_points_in_grid < grid_min_features)
   stopifnot("Threshold is too low. Please try higher threshold.\n" = sum(grid_lt_threshold) != 0)
-  grid_lt_threshold = seq(1, nrow(grid_in))[grid_lt_threshold]
+  grid_lt_threshold <- seq(1, nrow(grid_in))[grid_lt_threshold]
 
   # This part does not work as expected. Should investigate edge list and actual row index of the grid object; 
-  identified = lapply(grid_rooks, \(x) sort(x[which(x %in% grid_lt_threshold)]))
-  identified = identified[grid_lt_threshold]
-  identified = unique(identified)
-  identified = identified[sapply(identified, length) > 1]
+  identified <- lapply(grid_rooks, \(x) sort(x[which(x %in% grid_lt_threshold)]))
+  identified <- identified[grid_lt_threshold]
+  identified <- unique(identified)
+  identified <- identified[sapply(identified, length) > 1]
 
-  identified_graph = lapply(identified, \(x) t(utils::combn(x, 2))) |>
+  identified_graph <- lapply(identified, \(x) t(utils::combn(x, 2))) |>
     Reduce(f = rbind, x = _) |>
     unique() |>
     apply(X = _, 2, as.character) |>
@@ -869,30 +880,30 @@ 
Create functions

     igraph::components()
   # return(identified_graph)
 
-  identified_graph_member = identified_graph$membership
+  identified_graph_member <- identified_graph$membership
 
-  merge_idx = as.integer(names(identified_graph_member))
-  merge_member = split(merge_idx, identified_graph_member)
-  merge_member_label = unlist(lapply(merge_member, \(x) paste(x, collapse = "_")))
-  merge_member_label = merge_member_label[identified_graph_member]
+  merge_idx <- as.integer(names(identified_graph_member))
+  merge_member <- split(merge_idx, identified_graph_member)
+  merge_member_label <- unlist(lapply(merge_member, \(x) paste(x, collapse = "_")))
+  merge_member_label <- merge_member_label[identified_graph_member]
 
   # sf object manipulation
-  grid_out = grid_in
-  grid_out[["CGRIDID"]][merge_idx] = merge_member_label
+  grid_out <- grid_in
+  grid_out[["CGRIDID"]][merge_idx] <- merge_member_label
   # for (k in seq_along(merge_member_label)) {
   #   target_idx = merge_member_label[[k]]
   #   grid_out[["CGRIDID"]][target_idx] = paste("M_", paste(target_idx, collapse = "_"), sep = "")
   # }
-  grid_out = grid_out |>
+  grid_out <- grid_out |>
     dplyr::group_by(!!rlang::sym("CGRIDID")) |>
     dplyr::summarize(n_merged = dplyr::n()) |>
     dplyr::ungroup() 
 
   ## polsby-popper test for shape compactness
-  grid_merged = grid_out[which(grid_out$n_merged > 1),]
-  grid_merged_area = as.numeric(sf::st_area(grid_merged))
-  grid_merged_perimeter = as.numeric(sf::st_length(sf::st_cast(grid_merged, "LINESTRING")))
-  grid_merged_pptest = (4 * pi * grid_merged_area) / (grid_merged_perimeter ^ 2)
+  grid_merged <- grid_out[which(grid_out$n_merged > 1),]
+  grid_merged_area <- as.numeric(sf::st_area(grid_merged))
+  grid_merged_perimeter <- as.numeric(sf::st_length(sf::st_cast(grid_merged, "LINESTRING")))
+  grid_merged_pptest <- (4 * pi * grid_merged_area) / (grid_merged_perimeter ^ 2)
 
   # pptest value is bounded [0,1]; 0.3 threshold is groundless at this moment, possibly will make it defined by users.
   if (max(unique(identified_graph_member)) > floor(0.1 * nrow(grid_in)) || any(grid_merged_pptest < 0.3)) {
@@ -932,20 +943,20 @@ 
Create functions

     if (is.null(attr(extent, "names"))) {
       stop("Your extent is an unnamed numeric vector. Please define names xmin/xmax/ymin/ymax explicitly.\n")
     }
-    extent = switch(
+    extent <- switch(
       output_class,
       sf = sf::st_bbox(extent),
       terra = terra::ext(extent)
     )
   }
 
-  extent_polygon = switch(
+  extent_polygon <- switch(
     output_class,
     sf = sf::st_as_sfc(extent),
     terra = terra::vect(extent)
   )
 
-  extent_polygon = switch(
+  extent_polygon <- switch(
     output_class,
     sf = sf::st_set_crs(extent_polygon, sf::st_crs(crs)),
     terra = terra::set.crs(extent_polygon, terra::crs(crs))
@@ -972,18 +983,18 @@ 
Create functions

     stop("CRS should be entered when the reference extent is a vector.\n")
   }
   if (is.numeric(reference) && !is.null(reference_crs)) {
-    reference = sf::st_as_sfc(sf::st_bbox(reference), crs = reference_crs)
+    reference <- sf::st_as_sfc(sf::st_bbox(reference), crs = reference_crs)
   }
-  query_crs = check_crs(data_query)
-  ref_crs = check_crs(reference)
+  query_crs <- check_crs(data_query)
+  ref_crs <- check_crs(reference)
   if (is.na(query_crs) || is.null(query_crs)) {
     stop("The dataset you queried has no CRS. Please make sure your dataset has the correct CRS.\n")
   }
-  query_matched = sf::st_transform(data_query, sf::st_crs(ref_crs))
+  query_matched <- sf::st_transform(data_query, sf::st_crs(ref_crs))
 
 
 
-  check_result = sf::st_within()
+  check_result <- sf::st_within()
   return(check_result)
 }
 
@@ -1008,15 +1019,15 @@ 
Create functions

     stopifnot("Check class of the input raster.\n" = any(methods::is(surf, "stars"), methods::is(surf, "SpatRaster")))
     stopifnot(is.character(id))
 
-    cls_polys = check_packbound(polys)
-    cls_surf = check_packbound(surf)
+    cls_polys <- check_packbound(polys)
+    cls_surf <- check_packbound(surf)
 
     if (cls_polys != cls_surf) {
-      polys = switch_packbound(polys)
+      polys <- switch_packbound(polys)
     }
 
-    extract_with_polygons.sf = function(polys, surf, id, func) {
-        extracted = stars::st_extract(x = surf, at = polys, FUN = func)
+    extract_with_polygons_sf <- function(polys, surf, id, func) {
+        extracted <- stars::st_extract(x = surf, at = polys, FUN = func)
         # extracted = extracted |>
         #   group_by(!!sym(id)) |>
         #   summarize(across(-!!sym(id), ~func)) |>
@@ -1024,19 +1035,19 @@ 
Create functions

         return(extracted)
     }
 
-    extract_with_polygons.terra = function(polys, surf, id, func) {
-        extracted = terra::extract(surf, polys)
-        extracted = extracted |>
+    extract_with_polygons_terra <- function(polys, surf, id, func) {
+        extracted <- terra::extract(surf, polys)
+        extracted <- extracted |>
           dplyr::group_by(!!rlang::sym(id)) |>
           dplyr::summarize(dplyr::across(-!!rlang::sym(id), ~func)) |>
           dplyr::ungroup()
         return(extracted)
     }
 
-    extracted_poly = switch(
+    extracted_poly <- switch(
         cls_surf,
-        sf = extract_with_polygons.sf(polys = polys, surf = surf, id = id, func = func),
-        terra = extract_with_polygons.terra(polys = polys, surf = surf, id = id, func = func)
+        sf = extract_with_polygons_sf(polys = polys, surf = surf, id = id, func = func),
+        terra = extract_with_polygons_terra(polys = polys, surf = surf, id = id, func = func)
     )
     return(extracted_poly)
 }
@@ -1059,7 +1070,7 @@ 
Create functions

     stopifnot(is.character(id))
     stopifnot(id %in% names(vector))
 
-    extracted = 
+    extracted <- 
       switch(mode,
         polygon = extract_with_polygons(vector, raster, id, func),
         buffer = extract_with_buffer(vector, raster, id = id, func = func, ...))
@@ -1083,12 +1094,14 @@ 
Create functions

     stopifnot("Input is invalid.\n" = (methods::is(x, "sf") || methods::is(x, "stars") || methods::is(x, "SpatVector") || methods::is(x, "SpatRaster")))
     
     if (methods::is(x, "sf") || methods::is(x, "stars")) {
-        crs_wkt = sf::st_crs(x)
+        crs_wkt <- sf::st_crs(x)
     } else {
-        crs_wkt = terra::crs(x)
+        crs_wkt <- terra::crs(x)
     }
 
-    stopifnot("No CRS is defined in the input. Please consult the metadata or the data source.\n" = !is.na(crs_wkt) || crs_wkt != "")
+    stopifnot(
+      "No CRS is defined in the input. Please consult the metadata or the data source.\n" =
+      !is.na(crs_wkt) || crs_wkt != "")
     return(crs_wkt)
 }

 
#' Check if the boundary of the vector/raster object is inside the reference
@@ -1098,20 +1111,20 @@ 
Create functions

 #' @author Insang Song \email{geoissong@@gmail.com}
 #' @export 
 check_within_reference <- function(input_object, reference) {
-    stopifnot("Input is invalid.\n" = (methods::is(x, "sf") || methods::is(x, "stars") || methods::is(x, "SpatVector") || methods::is(x, "SpatRaster")))
-    stopifnot("Reference is invalid.\n" = (methods::is(x, "sf") || methods::is(x, "stars") || methods::is(x, "SpatVector") || methods::is(x, "SpatRaster")))
+    stopifnot("Input is invalid.\n" = (methods::is(input_object, "sf") || methods::is(input_object, "stars") || methods::is(input_object, "SpatVector") || methods::is(input_object, "SpatRaster")))
+    stopifnot("Reference is invalid.\n" = (methods::is(input_object, "sf") || methods::is(input_object, "stars") || methods::is(input_object, "SpatVector") || methods::is(input_object, "SpatRaster")))
 
   bbox_input <- input_object
     sf::st_bbox() |>
     sf::st_as_sfc()
   
-  bbox_reference = reference |>
+  bbox_reference <- reference |>
     sf::st_bbox() |>
     sf::st_as_sfc()
 
-  iswithin = sf::st_covered_by(bbox_input, bbox_reference)
-  iswithin = length(iswithin[[1]])
-  iswithin = (iswithin == 1)
+  iswithin <- sf::st_covered_by(bbox_input, bbox_reference)
+  iswithin <- length(iswithin[[1]])
+  iswithin <- (iswithin == 1)
   invisible(iswithin)
 }
 
@@ -1128,26 +1141,26 @@ 
Create functions

 #' @export
 calculate_sedc <- function(point_from, point_to, id, sedc_bandwidth, threshold, target_fields) {
   # define sources, set SEDC exponential decay range
-  len_point_from = seq_len(nrow(point_from))
-  len_point_to = seq_len(nrow(point_to))
+  len_point_from <- seq_len(nrow(point_from))
+  len_point_to <- seq_len(nrow(point_to))
 
-  point_from$from_id = len_point_from
+  point_from$from_id <- len_point_from
   # select egrid_v only if closer than 3e5 meters from each aqs
-  point_from_buf = terra::buffer(point_from_buf, threshold = threshold, quadsegs = 90)
-  point_to = point_to[point_from_buf,]
-  point_to$to_id = len_point_to
+  point_from_buf <- terra::buffer(point_from_buf, threshold = threshold, quadsegs = 90)
+  point_to <- point_to[point_from_buf,]
+  point_to$to_id <- len_point_to
 
   # near features with distance argument: only returns integer indices
-  near_from_to = terra::nearby(point_from, point_to, distance = threshold)
+  near_from_to <- terra::nearby(point_from, point_to, distance = threshold)
   # attaching actual distance
-  dist_near_to = terra::distance(point_from, point_to)
-  dist_near_to_df = as.vector(dist_near_to)
+  dist_near_to <- terra::distance(point_from, point_to)
+  dist_near_to_df <- as.vector(dist_near_to)
   # adding integer indices
-  dist_near_to_tdf = expand.grid(from_id = len_point_from, to_id = len_point_to)
-  dist_near_to_df = cbind(dist_near_to_tdf, dist = dist_near_to_df)
+  dist_near_to_tdf <- expand.grid(from_id = len_point_from, to_id = len_point_to)
+  dist_near_to_df <- cbind(dist_near_to_tdf, dist = dist_near_to_df)
 
   # summary
-  near_from_to = near_from_to |>
+  near_from_to <- near_from_to |>
     dplyr::as_tibble() |>
     dplyr::left_join(data.frame(point_from)) |>
     dplyr::left_join(data.frame(point_to)) |>
@@ -1175,15 +1188,15 @@ 
Create functions

 #' library(sf)
 #' 
 #' # run
-#' nc = sf::st_read(system.file("shape/nc.shp", package="sf"))
-#' nc = sf::st_transform(nc, 5070)
-#' pp = sf::st_sample(nc, size = 300)
-#' pp = sf::st_as_sf(pp)
-#' pp[["id"]] = seq(1, nrow(pp))
-#' sf::st_crs(pp) = "EPSG:5070"
-#' ppb = sf::st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
+#' nc <- sf::st_read(system.file("shape/nc.shp", package="sf"))
+#' nc <- sf::st_transform(nc, 5070)
+#' pp <- sf::st_sample(nc, size = 300)
+#' pp <- sf::st_as_sf(pp)
+#' pp[["id"]] <- seq(1, nrow(pp))
+#' sf::st_crs(pp) <- "EPSG:5070"
+#' ppb <- sf::st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
 #' 
-#' system.time({ppb_nc_aw = aw_covariates(ppb, nc, 'id')})
+#' system.time({ppb_nc_aw <- aw_covariates(ppb, nc, 'id')})
 #' summary(ppb_nc_aw)
 #' #### Example of aw_covariates ends ####
 #' @export
@@ -1193,13 +1206,13 @@ 
Create functions

     #check_crs()
 
     ## distinguish numeric and nonnumeric columns
-    index_numeric = grep("(integer|numeric)", unlist(sapply(poly_weight, class)))
+    index_numeric <- grep("(integer|numeric)", unlist(sapply(poly_weight, class)))
     
     aw_covariates.terra = function(poly_in, poly_weight, id_poly_in = id_poly_in) {
         
-        poly_intersected = terra::intersect(poly_in, poly_weight)
-        poly_intersected[["area_segment_"]] = terra::expanse(poly_intersected)
-        poly_intersected = data.frame(poly_intersected) |>
+        poly_intersected <- terra::intersect(poly_in, poly_weight)
+        poly_intersected[["area_segment_"]] <- terra::expanse(poly_intersected)
+        poly_intersected <- data.frame(poly_intersected) |>
             dplyr::group_by(!!rlang::sym(id_poly_in)) |>
             dplyr::summarize(dplyr::across(is.numeric,
                         ~stats::weighted.mean(., w = area_segment_))) |>
@@ -1207,11 +1220,11 @@ 
Create functions

         return(poly_intersected)
     }
 
-    class_poly_in = check_packbound(poly_in)
-    class_poly_weight = check_packbound(poly_weight)
+    class_poly_in <- check_packbound(poly_in)
+    class_poly_weight <- check_packbound(poly_weight)
 
     if (class_poly_in != class_poly_weight) {
-      class_poly_weight = switch_packbound(class_poly_weight)
+      class_poly_weight <- switch_packbound(class_poly_weight)
     }
     
     switch(class_poly_in,
@@ -1256,7 +1269,7 @@ 
Create functions

     stopifnot(is.integer(qsegs))
 
     if (!is.null(kernel)) {
-        extracted = extract_with_buffer.flat(points = points,
+        extracted <- extract_with_buffer.flat(points = points,
                                       surf = surf,
                                       radius = radius,
                                       id = id,
@@ -1265,7 +1278,7 @@ 
Create functions

         return(extracted)
     }
 
-    extracted = extract_with_buffer.kernel(points = points,
+    extracted <- extract_with_buffer.kernel(points = points,
                                            surf = surf,
                                            radius = radius,
                                            id = id,
@@ -1282,17 +1295,17 @@ 
Create functions

         points, surf, radius, id, qsegs, func = mean, kernel = NULL, bandwidth = NULL
     ) {
     # generate buffers
-    bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
+    bufs <- terra::buffer(points, width = radius, quadsegs = qsegs)
     # crop raster
-    bufs_extent = terra::ext(bufs)
-    surf_cropped = terra::crop(surf, bufs_extent)
-    name_surf_val = names(surf)
+    bufs_extent <- terra::ext(bufs)
+    surf_cropped <- terra::crop(surf, bufs_extent)
+    name_surf_val <- names(surf)
     # extract raster values
-    surf_at_bufs = terra::extract(surf_cropped, bufs)
-    surf_at_bufs_summary = 
+    surf_at_bufs <- terra::extract(surf_cropped, bufs)
+    surf_at_bufs_summary <- 
         surf_at_bufs |> 
             dplyr::group_by(ID) |> 
-            dplyr::summarize(dplyr::across(dplyr::all_of(name_surf_val), ~mean, na.rm=T)) |> 
+            dplyr::summarize(dplyr::across(dplyr::all_of(name_surf_val), ~mean, na.rm = TRUE)) |> 
             dplyr::ungroup()
     return(surf_at_bufs_summary)
 }
@@ -1303,18 +1316,18 @@ 
Create functions

         points, surf, radius, id, qsegs, func = mean, kernel, bandwidth
     ) {
         # generate buffers
-        bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
+        bufs <- terra::buffer(points, width = radius, quadsegs = qsegs)
         # crop raster
-        bufs_extent = terra::ext(bufs)
-        surf_cropped = terra::crop(surf, bufs_extent)
-        name_surf_val = names(surf)
+        bufs_extent <- terra::ext(bufs)
+        surf_cropped <- terra::crop(surf, bufs_extent)
+        name_surf_val <- names(surf)
 
         # TODO: kernel implementation
 
 
         # extract raster values
-        surf_at_bufs = terra::extract(surf_cropped, bufs)
-        surf_at_bufs_summary = 
+        surf_at_bufs <- terra::extract(surf_cropped, bufs)
+        surf_at_bufs_summary <- 
             surf_at_bufs |> 
                 dplyr::group_by(ID) |> 
                 dplyr::summarize(dplyr::across(dplyr::all_of(name_surf_val), ~mean, na.rm=T)) |> 
@@ -1338,23 +1351,23 @@ 
Create functions

     # subset using grids and grid_id
     if (!is.null(grid_id)) {
         if (is.character(grid_id)) {
-            grid_id_parsed = strsplit(grid_id, ":", fixed = TRUE)[[1]]
-            grid_ids = c(which(unique(grids[["CGRIDID"]]) == grid_id_parsed[1]),
+            grid_id_parsed <- strsplit(grid_id, ":", fixed = TRUE)[[1]]
+            grid_ids <- c(which(unique(grids[["CGRIDID"]]) == grid_id_parsed[1]),
                          which(unique(grids[["CGRIDID"]]) == grid_id_parsed[2]))
         }
         if (is.numeric(grid_id)) {
-            grid_ids = unique(grids[["CGRIDID"]])[grid_id]
+            grid_ids <- unique(grids[["CGRIDID"]])[grid_id]
         }
     }
-    grids_target = grids[grid_ids,]
-    grids_target_list = split(grids_target, grids_target[["CGRIDID"]])
+    grids_target <- grids[grid_ids,]
+    grids_target_list <- split(grids_target, grids_target[["CGRIDID"]])
 
-    results_distributed = future.apply::future_lapply(
+    results_distributed <- future.apply::future_lapply(
         \(x, ...) {
             fun(...)
         }, grids_target_list, 
         future.seed = TRUE)
-    results_distributed = do.call(rbind, results_distributed)
+    results_distributed <- do.call(rbind, results_distributed)
     return(results_distributed)
 }
 

@@ -1368,12 +1381,12 @@ 
Documenting the package and building

 devtools::document(".")
 devtools::test()
 devtools::build()
-devtools::install(dependencies = F, build_vignettes = TRUE)
+devtools::install(dependencies = FALSE, build_vignettes = TRUE)
 # devtools::check(document = FALSE)
 

 
## ℹ Updating scomps documentation
 ## ℹ Loading scomps

-
## Warning: [check.R:133] @description requires a value

+
## Warning: [check.R:136] @description requires a value

 
## Warning: [processing.R:139] @return requires a value

 
## Writing 'NAMESPACE'
 ## Writing 'check_packbound.Rd'
@@ -1441,7 +1454,7 @@ 
Documenting the package and building

 ## Warning: invalid gid value replaced by that for user 'nobody'
 ## 
 ## Running /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL \
-##   /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmpdIhnyr/scomps_0.0.3.10042023.tar.gz \
+##   /var/folders/58/7rn_bn5d6k3_cxwnzdhswpz4n0z2n9/T//RtmpXO9KMG/scomps_0.0.3.10042023.tar.gz \
 ##   --install-tests 
 ## * installing to library ‘/Users/songi2/Library/R/arm64/4.3/library’
 ## * installing *source* package ‘scomps’ ...
diff --git a/scomps_rmarkdown_litr.rmd b/scomps_rmarkdown_litr.rmd
index 854d21e4..c7ddd025 100644
--- a/scomps_rmarkdown_litr.rmd
+++ b/scomps_rmarkdown_litr.rmd
@@ -115,12 +115,12 @@ testthat::test_that("What package does the input object belong?",
     withr::local_package("stars")
     withr::local_package("terra")
     withr::local_options(list(sf_use_s2 = FALSE))
-    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
-    bcsd_stars = stars::read_stars(bcsd_path)
+    bcsd_path <- system.file(package = "stars", "nc/bcsd_obs_1999.nc")
+    bcsd_stars <- stars::read_stars(bcsd_path)
 
-    packbound_stars = check_packbound(bcsd_stars)
-    sprast_bcsd = terra::rast(bcsd_path)
-    packbound_terra = check_packbound(sprast_bcsd)
+    packbound_stars <- check_packbound(bcsd_stars)
+    sprast_bcsd <- terra::rast(bcsd_path)
+    packbound_terra <- check_packbound(sprast_bcsd)
 
     testthat::expect_equal(packbound_stars, "sf")
     testthat::expect_equal(packbound_terra, "terra")
@@ -132,14 +132,14 @@ testthat::test_that("What package does the input object belong?",
     withr::local_package("stars")
     withr::local_package("terra")
     withr::local_options(list(sf_use_s2 = FALSE))
-    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
-    bcsd_stars = stars::read_stars(bcsd_path)
+    bcsd_path <- system.file(package = "stars", "nc/bcsd_obs_1999.nc")
+    bcsd_stars <- stars::read_stars(bcsd_path)
 
-    nc = system.file(package = "sf", "shape/nc.shp")
-    nc = sf::read_sf(nc)
+    nc <- system.file(package = "sf", "shape/nc.shp")
+    nc <- sf::read_sf(nc)
 
-    datatype_stars = check_datatype(bcsd_stars)
-    datatype_sf = check_datatype(nc)
+    datatype_stars <- check_datatype(bcsd_stars)
+    datatype_sf <- check_datatype(nc)
 
     testthat::expect_equal(datatype_stars, "raster")
     testthat::expect_equal(datatype_sf, "vector")
@@ -155,10 +155,10 @@ testthat::test_that("What package does the input object belong?",
 #' @export
 switch_packbound <- function(input) {
   stopifnot("Input should be one of sf or Spat* object.\n" = any(methods::is(input, "sf"), methods::is(input, "stars"), methods::is(input, "SpatVector"), methods::is(input, "SpatRaster")))
-  cls_input = check_packbound(input)
-  type_input = check_datatype(input)
+  cls_input <- check_packbound(input)
+  type_input <- check_datatype(input)
 
-  switched = 
+  switched <- 
   switch(cls_input,
     sf = switch(type_input,
       vector = terra::vect(input),
@@ -182,19 +182,19 @@ testthat::test_that("Format is well converted",
     withr::local_options(list(sf_use_s2 = FALSE))
 
     # starts from sf/stars
-    bcsd_path = system.file(package = "stars", "nc/bcsd_obs_1999.nc")
-    bcsd_stars = stars::read_stars(bcsd_path)
-    nc = system.file(package = "sf", "shape/nc.shp")
-    nc = sf::read_sf(nc)
+    bcsd_path <- system.file(package = "stars", "nc/bcsd_obs_1999.nc")
+    bcsd_stars <- stars::read_stars(bcsd_path)
+    nc <- system.file(package = "sf", "shape/nc.shp")
+    nc <- sf::read_sf(nc)
 
-    stars_bcsd_tr = switch_packbound(bcsd_stars)
-    sf_nc_tr = switch_packbound(nc)
+    stars_bcsd_tr <- switch_packbound(bcsd_stars)
+    sf_nc_tr <- switch_packbound(nc)
 
     testthat::expect_equal(check_packbound(stars_bcsd_tr), "terra")
     testthat::expect_equal(check_packbound(sf_nc_tr), "terra")
 
-    stars_bcsd_trb = switch_packbound(stars_bcsd_tr)
-    sf_nc_trb = switch_packbound(sf_nc_tr)
+    stars_bcsd_trb <- switch_packbound(stars_bcsd_tr)
+    sf_nc_trb <- switch_packbound(sf_nc_tr)
 
     testthat::expect_equal(check_packbound(stars_bcsd_trb), "sf")
     testthat::expect_equal(check_packbound(sf_nc_trb), "sf")
@@ -212,8 +212,11 @@ testthat::test_that("Format is well converted",
 #' @return A (reprojected) sf or SpatVector object.
 #' @export
 check_crs2 <- function(input, crs_standard = "EPSG:4326") {
-  check_crs.sf <- function(input){
-    if (is.na(sf::st_crs(input))){cat('Please check the coordinate system or its EPSG code of your input object.'); return(NULL)}
+  check_crs_sf <- function(input) {
+    if (is.na(sf::st_crs(input))) {
+      cat('Please check the coordinate system or its EPSG code of your input object.')
+      return(NULL)
+    }
     if (sf::st_crs(input)$epsg == crs_standard ) {
       return(input)
     } 
@@ -221,17 +224,17 @@ check_crs2 <- function(input, crs_standard = "EPSG:4326") {
     return(input_transformed)
   }
 
-  check_crs.terra <- function(input) {
+  check_crs_terra <- function(input) {
     if (terra::crs(input, describe = TRUE)$code == crs_standard) {
       return(input)
     }
-    input_transformed = terra::project(input, terra::crs(crs_standard))
+    input_transformed <- terra::project(input, terra::crs(crs_standard))
     return(input_transformed)
   }
-    detected = check_packbound(input)
+    detected <- check_packbound(input)
     switch(detected,
-          terra = check_crs.terra(input),
-          sf = check_crs.sf(input))
+          terra = check_crs_terra(input),
+          sf = check_crs_sf(input))
   }
 ```
 
@@ -243,9 +246,9 @@ check_crs2 <- function(input, crs_standard = "EPSG:4326") {
 #' @return A repaired sf or SpatVector object depending on the class of input_vector.
 #' @export
 validate_and_repair_vectors <- function(input_vector) {
-  detected = check_packbound(input_vector)
+  detected <- check_packbound(input_vector)
 
-  validated = switch(detected,
+  validated <- switch(detected,
     terra = terra::makeValid(input_vector),
     sf = sf::st_make_valid(input_vector))
 
@@ -285,11 +288,11 @@ initate_log <- function(expr, dolog = FALSE, logpath) {
 #' @return A terra::ext or sfc_POLYGON object of the computation extent.
 #' @export
 set_clip_extent <- function(pnts, buffer_r) {
-  detected = check_packbound(pnts)
+  detected <- check_packbound(pnts)
   if (detected == "terra") {
-    ext_input = terra::ext(pnts)
+    ext_input <- terra::ext(pnts)
     # Note that `+` operation on terra::ext output accounts for the operand as it is.
-    ext_input = ext_input + (1.1 * buffer_r + 30)
+    ext_input <- ext_input + (1.1 * buffer_r + 30)
   }
   if (detected == "sf") {
     ext_input <- pnts |> sf::st_bbox()
@@ -312,28 +315,28 @@ set_clip_extent <- function(pnts, buffer_r) {
 #' @param target_input sf or SpatVector object to be clipped
 #' @return A clipped sf or SpatVector object.
 #' @export
-clip_as_extent <- function(pnts, buffer_r, nqsegs=NULL, target_input){
+clip_as_extent <- function(pnts, buffer_r, nqsegs=NULL, target_input) {
   if (any(sapply(list(pnts, buffer_r, target_input), is.null))) {
     stop("One or more required arguments are NULL. Please check.\n")
   }
-  detected_pnts = check_packbound(pnts)
-  detected_target = check_packbound(target_input)
+  detected_pnts <- check_packbound(pnts)
+  detected_target <- check_packbound(target_input)
 
   if (detected_pnts != detected_target) {
     warning("Inputs are not the same class.\n")
-    target_input = switch(detected_target,
+    target_input <- switch(detected_target,
         sf = terra::vect(target_input),
         terra = sf::st_as_sf(target_input))
   }
   
-  ext_input = set_clip_extent(pnts, buffer_r)
+  ext_input <- set_clip_extent(pnts, buffer_r)
   cat("Clip target features with the input feature extent...\n")
   if (detected_pnts == "sf") {
-    cae = ext_input |>
+    cae <- ext_input |>
       sf::st_intersection(x = target_input)
   }
   if (detected_pnts == "terra") {
-    cae = terra::intersect(target_input, ext_input)
+    cae <- terra::intersect(target_input, ext_input)
   }
    
   return(cae)
@@ -350,11 +353,11 @@ clip_as_extent <- function(pnts, buffer_r, nqsegs=NULL, target_input){
 #' @param nqsegs integer(1). the number of points per a quarter circle
 #' @param ras SpatRaster object to be clipped
 #' @export
-clip_as_extent_ras <- function(pnts, buffer_r, nqsegs = 180, ras){
+clip_as_extent_ras <- function(pnts, buffer_r, nqsegs = 180, ras) {
   if (any(sapply(list(pnts, buffer_r, ras), is.null))) {
     stop("Any of required arguments are NULL. Please check.\n")
   }
-  ext_input = set_clip_extent(pnts, buffer_r) |>
+  ext_input <- set_clip_extent(pnts, buffer_r) |>
     terra::ext()
 
   cae <- terra::crop(ras, ext_input, snap = 'out')
@@ -372,11 +375,11 @@ clip_as_extent_ras <- function(pnts, buffer_r, nqsegs = 180, ras){
 #' @param nqsegs integer(1). the number of points per a quarter circle
 #' @param ras SpatRaster object to be clipped
 #' @export
-clip_as_extent_ras2 <- function(points_in, buffer_r, nqsegs=180, ras){
+clip_as_extent_ras2 <- function(points_in, buffer_r, nqsegs=180, ras) {
   if (any(sapply(list(points_in, buffer_r, ras), is.null))) {
     stop("Any of required arguments are NULL. Please check.\n")
   }
-  ext_input = set_clip_extent(points_in, buffer_r) |>
+  ext_input <- set_clip_extent(points_in, buffer_r) |>
     terra::ext()
 
   cae <- terra::crop(ras, ext_input, snap = 'out')
@@ -393,7 +396,7 @@ clip_as_extent_ras2 <- function(points_in, buffer_r, nqsegs=180, ras){
 #' @param ncutsx integer(1). The number of splits along x-axis.
 #' @param ncutsy integer(1). The number of splits along y-axis.
 #' @export
-sp_indexing <- function(points_in, ncutsx, ncutsy){
+sp_indexing <- function(points_in, ncutsx, ncutsy) {
   # pts <- data.table(pnts)
   points_in <- points_in |>
     dplyr::mutate(or_id = seq(1, dim(points_in)[1]))
@@ -430,7 +433,7 @@ rast_short <- function(rasterpath, win) {
 ```{r}
 #' Estimate computational demands from inputs (to be written)
 #' 
-#' @param inputs a list of sf/Spat* objects or file paths
+#' @param inputs character vector of file paths
 #' @param nx integer(1). 
 #' @param ny integer(1). 
 #' @param padding numeric(1). Extrusion factor 
@@ -470,16 +473,24 @@ estimate_demands <- function(
 #' @examples 
 #' # data
 #' library(sf)
-#' ncpath = system.file("shape/nc.shp", package = "sf")
-#' nc = read_sf(ncpath)
-#' nc = st_transform(nc, "EPSG:5070")
+#' ncpath <- system.file("shape/nc.shp", package = "sf")
+#' nc <- read_sf(ncpath)
+#' nc <- st_transform(nc, "EPSG:5070")
 #' # run
-#' # nc_comp_region = get_computational_regions(nc, nx = 12, ny = 8)
+#' # nc_comp_region <- get_computational_regions(nc, nx = 12, ny = 8)
 #' 
 #' @export 
-get_computational_regions <- function(input, mode = "grid", nx = 10, ny = 10, grid_min_features = 30, padding = NULL, unit = NULL, ...) {
+get_computational_regions <- function(
+  input, 
+  mode = "grid", 
+  nx = 10, 
+  ny = 10, 
+  grid_min_features = 30, 
+  padding = NULL, 
+  unit = NULL, 
+  ...) {
   # type check
-  package_detected = check_packbound(input)
+  package_detected <- check_packbound(input)
   # stopifnot("Invalid input.\n" = !any(grepl("^(sf|Spat)", class(input))))
   stopifnot("Argument mode should be one of 'grid', 'grid_advanced', or 'density'.\n" = !mode %in% c("grid", "grid_advanced", "density"))
   stopifnot("Ensure that nx, ny, and grid_min_features are all integer.\n" = all(is.integer(nx), is.integer(y), is.integer(grid_min_features)))
@@ -502,25 +513,25 @@ get_computational_regions <- function(input, mode = "grid", nx = 10, ny = 10, gr
 #' @return A sf or SpatVector object of computation grids with unique grid id (CGRIDID).
 #' @export
 sp_index_grid <- function(points_in, ncutsx, ncutsy){
-  package_detected = check_packbound(points_in)
+  package_detected <- check_packbound(points_in)
 
-  sp_index_grid.sf = function(points_in, ncutsx, ncutsy) {
+  sp_index_grid_sf <- function(points_in, ncutsx, ncutsy) {
     grid1 <- sf::st_make_grid(points_in, n = c(ncutsx, ncutsy)) |> 
       as.data.frame() |> 
       sf::st_as_sf()
     grid1 <- grid1[points_in, ]
     return(grid1)
   }
-  sp_index_grid.terra = function(points_in, ncutsx, ncutsy) {
+  sp_index_grid_terra <- function(points_in, ncutsx, ncutsy) {
     grid1 <- terra::rast(points_in, nrows = ncutsy, ncols = ncutsx)
     grid1 <- terra::as.polygons(grid1)
     return(grid1)
   }
-  grid_out = switch(package_detected,
-        sf = sp_index_grid.sf(points_in, ncutsx, ncutsy),
-        terra = sp_index_grid.terra(points_in, ncutsx, ncutsy))
+  grid_out <- switch(package_detected,
+        sf = sp_index_grid_sf(points_in, ncutsx, ncutsy),
+        terra = sp_index_grid_terra(points_in, ncutsx, ncutsy))
     
-  grid_out$CGRIDID = seq(1, nrow(x = grid_out)) 
+  grid_out$CGRIDID <- seq(1, nrow(x = grid_out)) 
   return(grid_out)
 
 }
@@ -547,28 +558,28 @@ sp_index_grid <- function(points_in, ncutsx, ncutsy){
 #' # dg_merged = grid_merge(sf::st_as_sf(sss), dgs, 100)
 #' #### NOT RUN ####
 #' @export
-grid_merge <- function(points_in, grid_in, grid_min_features){
-  package_detected = check_packbound(points_in)
+grid_merge <- function(points_in, grid_in, grid_min_features) {
+  package_detected <- check_packbound(points_in)
   if (package_detected == "terra") {
-    points_in = sf::st_as_sf(points_in)
-    grid_in = sf::st_as_sf(grid_in)
+    points_in <- sf::st_as_sf(points_in)
+    grid_in <- sf::st_as_sf(grid_in)
   }
 
-  n_points_in_grid = lengths(sf::st_intersects(grid_in, points_in))
-  grid_self = sf::st_relate(grid_in, grid_in, pattern = "2********")
-  grid_rook = sf::st_relate(grid_in, grid_in, pattern = "F***1****")
-  grid_rooks = mapply(c, grid_self, grid_rook, SIMPLIFY = FALSE)
-  grid_lt_threshold = (n_points_in_grid < grid_min_features)
+  n_points_in_grid <- lengths(sf::st_intersects(grid_in, points_in))
+  grid_self <- sf::st_relate(grid_in, grid_in, pattern = "2********")
+  grid_rook <- sf::st_relate(grid_in, grid_in, pattern = "F***1****")
+  grid_rooks <- mapply(c, grid_self, grid_rook, SIMPLIFY = FALSE)
+  grid_lt_threshold <- (n_points_in_grid < grid_min_features)
   stopifnot("Threshold is too low. Please try higher threshold.\n" = sum(grid_lt_threshold) != 0)
-  grid_lt_threshold = seq(1, nrow(grid_in))[grid_lt_threshold]
+  grid_lt_threshold <- seq(1, nrow(grid_in))[grid_lt_threshold]
 
   # This part does not work as expected. Should investigate edge list and actual row index of the grid object; 
-  identified = lapply(grid_rooks, \(x) sort(x[which(x %in% grid_lt_threshold)]))
-  identified = identified[grid_lt_threshold]
-  identified = unique(identified)
-  identified = identified[sapply(identified, length) > 1]
+  identified <- lapply(grid_rooks, \(x) sort(x[which(x %in% grid_lt_threshold)]))
+  identified <- identified[grid_lt_threshold]
+  identified <- unique(identified)
+  identified <- identified[sapply(identified, length) > 1]
 
-  identified_graph = lapply(identified, \(x) t(utils::combn(x, 2))) |>
+  identified_graph <- lapply(identified, \(x) t(utils::combn(x, 2))) |>
     Reduce(f = rbind, x = _) |>
     unique() |>
     apply(X = _, 2, as.character) |>
@@ -577,30 +588,30 @@ grid_merge <- function(points_in, grid_in, grid_min_features){
     igraph::components()
   # return(identified_graph)
 
-  identified_graph_member = identified_graph$membership
+  identified_graph_member <- identified_graph$membership
 
-  merge_idx = as.integer(names(identified_graph_member))
-  merge_member = split(merge_idx, identified_graph_member)
-  merge_member_label = unlist(lapply(merge_member, \(x) paste(x, collapse = "_")))
-  merge_member_label = merge_member_label[identified_graph_member]
+  merge_idx <- as.integer(names(identified_graph_member))
+  merge_member <- split(merge_idx, identified_graph_member)
+  merge_member_label <- unlist(lapply(merge_member, \(x) paste(x, collapse = "_")))
+  merge_member_label <- merge_member_label[identified_graph_member]
 
   # sf object manipulation
-  grid_out = grid_in
-  grid_out[["CGRIDID"]][merge_idx] = merge_member_label
+  grid_out <- grid_in
+  grid_out[["CGRIDID"]][merge_idx] <- merge_member_label
   # for (k in seq_along(merge_member_label)) {
   #   target_idx = merge_member_label[[k]]
   #   grid_out[["CGRIDID"]][target_idx] = paste("M_", paste(target_idx, collapse = "_"), sep = "")
   # }
-  grid_out = grid_out |>
+  grid_out <- grid_out |>
     dplyr::group_by(!!rlang::sym("CGRIDID")) |>
     dplyr::summarize(n_merged = dplyr::n()) |>
     dplyr::ungroup() 
 
   ## polsby-popper test for shape compactness
-  grid_merged = grid_out[which(grid_out$n_merged > 1),]
-  grid_merged_area = as.numeric(sf::st_area(grid_merged))
-  grid_merged_perimeter = as.numeric(sf::st_length(sf::st_cast(grid_merged, "LINESTRING")))
-  grid_merged_pptest = (4 * pi * grid_merged_area) / (grid_merged_perimeter ^ 2)
+  grid_merged <- grid_out[which(grid_out$n_merged > 1),]
+  grid_merged_area <- as.numeric(sf::st_area(grid_merged))
+  grid_merged_perimeter <- as.numeric(sf::st_length(sf::st_cast(grid_merged, "LINESTRING")))
+  grid_merged_pptest <- (4 * pi * grid_merged_area) / (grid_merged_perimeter ^ 2)
 
   # pptest value is bounded [0,1]; 0.3 threshold is groundless at this moment, possibly will make it defined by users.
   if (max(unique(identified_graph_member)) > floor(0.1 * nrow(grid_in)) || any(grid_merged_pptest < 0.3)) {
@@ -643,20 +654,20 @@ extent_to_polygon <- function(extent, output_class = "terra", crs = "EPSG:4326")
     if (is.null(attr(extent, "names"))) {
       stop("Your extent is an unnamed numeric vector. Please define names xmin/xmax/ymin/ymax explicitly.\n")
     }
-    extent = switch(
+    extent <- switch(
       output_class,
       sf = sf::st_bbox(extent),
       terra = terra::ext(extent)
     )
   }
 
-  extent_polygon = switch(
+  extent_polygon <- switch(
     output_class,
     sf = sf::st_as_sfc(extent),
     terra = terra::vect(extent)
   )
 
-  extent_polygon = switch(
+  extent_polygon <- switch(
     output_class,
     sf = sf::st_set_crs(extent_polygon, sf::st_crs(crs)),
     terra = terra::set.crs(extent_polygon, terra::crs(crs))
@@ -686,18 +697,18 @@ check_bbox <- function(
     stop("CRS should be entered when the reference extent is a vector.\n")
   }
   if (is.numeric(reference) && !is.null(reference_crs)) {
-    reference = sf::st_as_sfc(sf::st_bbox(reference), crs = reference_crs)
+    reference <- sf::st_as_sfc(sf::st_bbox(reference), crs = reference_crs)
   }
-  query_crs = check_crs(data_query)
-  ref_crs = check_crs(reference)
+  query_crs <- check_crs(data_query)
+  ref_crs <- check_crs(reference)
   if (is.na(query_crs) || is.null(query_crs)) {
     stop("The dataset you queried has no CRS. Please make sure your dataset has the correct CRS.\n")
   }
-  query_matched = sf::st_transform(data_query, sf::st_crs(ref_crs))
+  query_matched <- sf::st_transform(data_query, sf::st_crs(ref_crs))
 
 
 
-  check_result = sf::st_within()
+  check_result <- sf::st_within()
   return(check_result)
 }
 
@@ -743,15 +754,15 @@ extract_with_polygons <- function(
     stopifnot("Check class of the input raster.\n" = any(methods::is(surf, "stars"), methods::is(surf, "SpatRaster")))
     stopifnot(is.character(id))
 
-    cls_polys = check_packbound(polys)
-    cls_surf = check_packbound(surf)
+    cls_polys <- check_packbound(polys)
+    cls_surf <- check_packbound(surf)
 
     if (cls_polys != cls_surf) {
-      polys = switch_packbound(polys)
+      polys <- switch_packbound(polys)
     }
 
-    extract_with_polygons.sf = function(polys, surf, id, func) {
-        extracted = stars::st_extract(x = surf, at = polys, FUN = func)
+    extract_with_polygons_sf <- function(polys, surf, id, func) {
+        extracted <- stars::st_extract(x = surf, at = polys, FUN = func)
         # extracted = extracted |>
         #   group_by(!!sym(id)) |>
         #   summarize(across(-!!sym(id), ~func)) |>
@@ -759,19 +770,19 @@ extract_with_polygons <- function(
         return(extracted)
     }
 
-    extract_with_polygons.terra = function(polys, surf, id, func) {
-        extracted = terra::extract(surf, polys)
-        extracted = extracted |>
+    extract_with_polygons_terra <- function(polys, surf, id, func) {
+        extracted <- terra::extract(surf, polys)
+        extracted <- extracted |>
           dplyr::group_by(!!rlang::sym(id)) |>
           dplyr::summarize(dplyr::across(-!!rlang::sym(id), ~func)) |>
           dplyr::ungroup()
         return(extracted)
     }
 
-    extracted_poly = switch(
+    extracted_poly <- switch(
         cls_surf,
-        sf = extract_with_polygons.sf(polys = polys, surf = surf, id = id, func = func),
-        terra = extract_with_polygons.terra(polys = polys, surf = surf, id = id, func = func)
+        sf = extract_with_polygons_sf(polys = polys, surf = surf, id = id, func = func),
+        terra = extract_with_polygons_terra(polys = polys, surf = surf, id = id, func = func)
     )
     return(extracted_poly)
 }
@@ -797,7 +808,7 @@ extract_with <- function(raster, vector, id, func = mean, mode = "polygon", ...)
     stopifnot(is.character(id))
     stopifnot(id %in% names(vector))
 
-    extracted = 
+    extracted <- 
       switch(mode,
         polygon = extract_with_polygons(vector, raster, id, func),
         buffer = extract_with_buffer(vector, raster, id = id, func = func, ...))
@@ -824,12 +835,14 @@ check_crs <- function(x) {
     stopifnot("Input is invalid.\n" = (methods::is(x, "sf") || methods::is(x, "stars") || methods::is(x, "SpatVector") || methods::is(x, "SpatRaster")))
     
     if (methods::is(x, "sf") || methods::is(x, "stars")) {
-        crs_wkt = sf::st_crs(x)
+        crs_wkt <- sf::st_crs(x)
     } else {
-        crs_wkt = terra::crs(x)
+        crs_wkt <- terra::crs(x)
     }
 
-    stopifnot("No CRS is defined in the input. Please consult the metadata or the data source.\n" = !is.na(crs_wkt) || crs_wkt != "")
+    stopifnot(
+      "No CRS is defined in the input. Please consult the metadata or the data source.\n" =
+      !is.na(crs_wkt) || crs_wkt != "")
     return(crs_wkt)
 }
 ```
@@ -843,20 +856,20 @@ check_crs <- function(x) {
 #' @author Insang Song \email{geoissong@@gmail.com}
 #' @export 
 check_within_reference <- function(input_object, reference) {
-    stopifnot("Input is invalid.\n" = (methods::is(x, "sf") || methods::is(x, "stars") || methods::is(x, "SpatVector") || methods::is(x, "SpatRaster")))
-    stopifnot("Reference is invalid.\n" = (methods::is(x, "sf") || methods::is(x, "stars") || methods::is(x, "SpatVector") || methods::is(x, "SpatRaster")))
+    stopifnot("Input is invalid.\n" = (methods::is(input_object, "sf") || methods::is(input_object, "stars") || methods::is(input_object, "SpatVector") || methods::is(input_object, "SpatRaster")))
+    stopifnot("Reference is invalid.\n" = (methods::is(input_object, "sf") || methods::is(input_object, "stars") || methods::is(input_object, "SpatVector") || methods::is(input_object, "SpatRaster")))
 
   bbox_input <- input_object
     sf::st_bbox() |>
     sf::st_as_sfc()
   
-  bbox_reference = reference |>
+  bbox_reference <- reference |>
     sf::st_bbox() |>
     sf::st_as_sfc()
 
-  iswithin = sf::st_covered_by(bbox_input, bbox_reference)
-  iswithin = length(iswithin[[1]])
-  iswithin = (iswithin == 1)
+  iswithin <- sf::st_covered_by(bbox_input, bbox_reference)
+  iswithin <- length(iswithin[[1]])
+  iswithin <- (iswithin == 1)
   invisible(iswithin)
 }
 
@@ -877,26 +890,26 @@ check_within_reference <- function(input_object, reference) {
 #' @export
 calculate_sedc <- function(point_from, point_to, id, sedc_bandwidth, threshold, target_fields) {
   # define sources, set SEDC exponential decay range
-  len_point_from = seq_len(nrow(point_from))
-  len_point_to = seq_len(nrow(point_to))
+  len_point_from <- seq_len(nrow(point_from))
+  len_point_to <- seq_len(nrow(point_to))
 
-  point_from$from_id = len_point_from
+  point_from$from_id <- len_point_from
   # select egrid_v only if closer than 3e5 meters from each aqs
-  point_from_buf = terra::buffer(point_from_buf, threshold = threshold, quadsegs = 90)
-  point_to = point_to[point_from_buf,]
-  point_to$to_id = len_point_to
+  point_from_buf <- terra::buffer(point_from_buf, threshold = threshold, quadsegs = 90)
+  point_to <- point_to[point_from_buf,]
+  point_to$to_id <- len_point_to
 
   # near features with distance argument: only returns integer indices
-  near_from_to = terra::nearby(point_from, point_to, distance = threshold)
+  near_from_to <- terra::nearby(point_from, point_to, distance = threshold)
   # attaching actual distance
-  dist_near_to = terra::distance(point_from, point_to)
-  dist_near_to_df = as.vector(dist_near_to)
+  dist_near_to <- terra::distance(point_from, point_to)
+  dist_near_to_df <- as.vector(dist_near_to)
   # adding integer indices
-  dist_near_to_tdf = expand.grid(from_id = len_point_from, to_id = len_point_to)
-  dist_near_to_df = cbind(dist_near_to_tdf, dist = dist_near_to_df)
+  dist_near_to_tdf <- expand.grid(from_id = len_point_from, to_id = len_point_to)
+  dist_near_to_df <- cbind(dist_near_to_tdf, dist = dist_near_to_df)
 
   # summary
-  near_from_to = near_from_to |>
+  near_from_to <- near_from_to |>
     dplyr::as_tibble() |>
     dplyr::left_join(data.frame(point_from)) |>
     dplyr::left_join(data.frame(point_to)) |>
@@ -927,15 +940,15 @@ calculate_sedc <- function(point_from, point_to, id, sedc_bandwidth, threshold,
 #' library(sf)
 #' 
 #' # run
-#' nc = sf::st_read(system.file("shape/nc.shp", package="sf"))
-#' nc = sf::st_transform(nc, 5070)
-#' pp = sf::st_sample(nc, size = 300)
-#' pp = sf::st_as_sf(pp)
-#' pp[["id"]] = seq(1, nrow(pp))
-#' sf::st_crs(pp) = "EPSG:5070"
-#' ppb = sf::st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
+#' nc <- sf::st_read(system.file("shape/nc.shp", package="sf"))
+#' nc <- sf::st_transform(nc, 5070)
+#' pp <- sf::st_sample(nc, size = 300)
+#' pp <- sf::st_as_sf(pp)
+#' pp[["id"]] <- seq(1, nrow(pp))
+#' sf::st_crs(pp) <- "EPSG:5070"
+#' ppb <- sf::st_buffer(pp, nQuadSegs=180, dist = units::set_units(20, 'km'))
 #' 
-#' system.time({ppb_nc_aw = aw_covariates(ppb, nc, 'id')})
+#' system.time({ppb_nc_aw <- aw_covariates(ppb, nc, 'id')})
 #' summary(ppb_nc_aw)
 #' #### Example of aw_covariates ends ####
 #' @export
@@ -945,13 +958,13 @@ aw_covariates <- function(poly_in, poly_weight, id_poly_in = "ID") {
     #check_crs()
 
     ## distinguish numeric and nonnumeric columns
-    index_numeric = grep("(integer|numeric)", unlist(sapply(poly_weight, class)))
+    index_numeric <- grep("(integer|numeric)", unlist(sapply(poly_weight, class)))
     
     aw_covariates.terra = function(poly_in, poly_weight, id_poly_in = id_poly_in) {
         
-        poly_intersected = terra::intersect(poly_in, poly_weight)
-        poly_intersected[["area_segment_"]] = terra::expanse(poly_intersected)
-        poly_intersected = data.frame(poly_intersected) |>
+        poly_intersected <- terra::intersect(poly_in, poly_weight)
+        poly_intersected[["area_segment_"]] <- terra::expanse(poly_intersected)
+        poly_intersected <- data.frame(poly_intersected) |>
             dplyr::group_by(!!rlang::sym(id_poly_in)) |>
             dplyr::summarize(dplyr::across(is.numeric,
                         ~stats::weighted.mean(., w = area_segment_))) |>
@@ -959,11 +972,11 @@ aw_covariates <- function(poly_in, poly_weight, id_poly_in = "ID") {
         return(poly_intersected)
     }
 
-    class_poly_in = check_packbound(poly_in)
-    class_poly_weight = check_packbound(poly_weight)
+    class_poly_in <- check_packbound(poly_in)
+    class_poly_weight <- check_packbound(poly_weight)
 
     if (class_poly_in != class_poly_weight) {
-      class_poly_weight = switch_packbound(class_poly_weight)
+      class_poly_weight <- switch_packbound(class_poly_weight)
     }
     
     switch(class_poly_in,
@@ -1012,7 +1025,7 @@ extract_with_buffer <- function(
     stopifnot(is.integer(qsegs))
 
     if (!is.null(kernel)) {
-        extracted = extract_with_buffer.flat(points = points,
+        extracted <- extract_with_buffer.flat(points = points,
                                       surf = surf,
                                       radius = radius,
                                       id = id,
@@ -1021,7 +1034,7 @@ extract_with_buffer <- function(
         return(extracted)
     }
 
-    extracted = extract_with_buffer.kernel(points = points,
+    extracted <- extract_with_buffer.kernel(points = points,
                                            surf = surf,
                                            radius = radius,
                                            id = id,
@@ -1038,17 +1051,17 @@ extract_with_buffer.flat <- function(
         points, surf, radius, id, qsegs, func = mean, kernel = NULL, bandwidth = NULL
     ) {
     # generate buffers
-    bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
+    bufs <- terra::buffer(points, width = radius, quadsegs = qsegs)
     # crop raster
-    bufs_extent = terra::ext(bufs)
-    surf_cropped = terra::crop(surf, bufs_extent)
-    name_surf_val = names(surf)
+    bufs_extent <- terra::ext(bufs)
+    surf_cropped <- terra::crop(surf, bufs_extent)
+    name_surf_val <- names(surf)
     # extract raster values
-    surf_at_bufs = terra::extract(surf_cropped, bufs)
-    surf_at_bufs_summary = 
+    surf_at_bufs <- terra::extract(surf_cropped, bufs)
+    surf_at_bufs_summary <- 
         surf_at_bufs |> 
             dplyr::group_by(ID) |> 
-            dplyr::summarize(dplyr::across(dplyr::all_of(name_surf_val), ~mean, na.rm=T)) |> 
+            dplyr::summarize(dplyr::across(dplyr::all_of(name_surf_val), ~mean, na.rm = TRUE)) |> 
             dplyr::ungroup()
     return(surf_at_bufs_summary)
 }
@@ -1059,18 +1072,18 @@ extract_with_buffer.kernel <- function(
         points, surf, radius, id, qsegs, func = mean, kernel, bandwidth
     ) {
         # generate buffers
-        bufs = terra::buffer(points, width = radius, quadsegs = qsegs)
+        bufs <- terra::buffer(points, width = radius, quadsegs = qsegs)
         # crop raster
-        bufs_extent = terra::ext(bufs)
-        surf_cropped = terra::crop(surf, bufs_extent)
-        name_surf_val = names(surf)
+        bufs_extent <- terra::ext(bufs)
+        surf_cropped <- terra::crop(surf, bufs_extent)
+        name_surf_val <- names(surf)
 
         # TODO: kernel implementation
 
 
         # extract raster values
-        surf_at_bufs = terra::extract(surf_cropped, bufs)
-        surf_at_bufs_summary = 
+        surf_at_bufs <- terra::extract(surf_cropped, bufs)
+        surf_at_bufs_summary <- 
             surf_at_bufs |> 
                 dplyr::group_by(ID) |> 
                 dplyr::summarize(dplyr::across(dplyr::all_of(name_surf_val), ~mean, na.rm=T)) |> 
@@ -1098,23 +1111,23 @@ distribute_process <- function(grids, grid_id = NULL, fun, ...) {
     # subset using grids and grid_id
     if (!is.null(grid_id)) {
         if (is.character(grid_id)) {
-            grid_id_parsed = strsplit(grid_id, ":", fixed = TRUE)[[1]]
-            grid_ids = c(which(unique(grids[["CGRIDID"]]) == grid_id_parsed[1]),
+            grid_id_parsed <- strsplit(grid_id, ":", fixed = TRUE)[[1]]
+            grid_ids <- c(which(unique(grids[["CGRIDID"]]) == grid_id_parsed[1]),
                          which(unique(grids[["CGRIDID"]]) == grid_id_parsed[2]))
         }
         if (is.numeric(grid_id)) {
-            grid_ids = unique(grids[["CGRIDID"]])[grid_id]
+            grid_ids <- unique(grids[["CGRIDID"]])[grid_id]
         }
     }
-    grids_target = grids[grid_ids,]
-    grids_target_list = split(grids_target, grids_target[["CGRIDID"]])
+    grids_target <- grids[grid_ids,]
+    grids_target_list <- split(grids_target, grids_target[["CGRIDID"]])
 
-    results_distributed = future.apply::future_lapply(
+    results_distributed <- future.apply::future_lapply(
         \(x, ...) {
             fun(...)
         }, grids_target_list, 
         future.seed = TRUE)
-    results_distributed = do.call(rbind, results_distributed)
+    results_distributed <- do.call(rbind, results_distributed)
     return(results_distributed)
 }
 
@@ -1129,7 +1142,7 @@ We finish by running commands that will document, build, and install the package
 devtools::document(".")
 devtools::test()
 devtools::build()
-devtools::install(dependencies = F, build_vignettes = TRUE)
+devtools::install(dependencies = FALSE, build_vignettes = TRUE)
 # devtools::check(document = FALSE)
 
 ```
\ No newline at end of file
diff --git a/tools/slurm_test/merra1h_aero_extract_local_stars.r b/tools/slurm_test/merra1h_aero_extract_local_stars.r
index 55daf243..2ab335df 100644
--- a/tools/slurm_test/merra1h_aero_extract_local_stars.r
+++ b/tools/slurm_test/merra1h_aero_extract_local_stars.r
@@ -1,8 +1,8 @@
 library(sf)
 library(stars)
 library(dplyr)
-sf_use_s2(F)
-us_extent = 
+sf_use_s2(FALSE)
+us_extent <- 
     sf::st_bbox(c(xmin = -129.5, xmax = -61.1, ymin = 19.5, ymax = 51.8))
 # terra::ext(us_extent)
 
@@ -11,19 +11,19 @@ extract_with_buffer.flat <- function(
         points, surf, radius, id, qsegs, crs_projection = 5070, func = mean, kernel = NULL, bandwidth = NULL
     ) {
     # generate buffers
-    bufs = points |>
+    bufs <- points |>
         sf::st_transform(crs_projection) |>
         sf::st_buffer(dist = radius, nQuadSegs = qsegs) |>
         sf::st_transform(st_crs(points))
     # crop raster
-    bufs_extent = sf::st_bbox(bufs, crs = st_crs(surf))
+    bufs_extent <- sf::st_bbox(bufs, crs = st_crs(surf))
     # surf_cropped = sf::st_crop(surf, bufs_extent)
-    surf_cropped = surf
-    name_surf_val = names(surf)
+    surf_cropped <- surf
+    name_surf_val <- names(surf)
     # extract raster values
-    surf_at_bufs = stars::st_extract(surf_cropped, bufs)
+    surf_at_bufs <- stars::st_extract(surf_cropped, bufs)
     return(surf_at_bufs)
-    surf_at_bufs_summary = 
+    surf_at_bufs_summary <- 
         surf_at_bufs |> 
             st_drop_geometry() |>
             group_by(ID) |> 
@@ -32,12 +32,12 @@ extract_with_buffer.flat <- function(
     return(surf_at_bufs_summary)
 }
 
-pathappend = "/Users/songi2/Documents/GitHub/Scalable_GIS/largedata/"
-merraname = "MERRA2_400.tavg1_2d_aer_Nx.20220820.nc4"
-pointname = "aqs-test-data.gpkg"
+pathappend <- "/Users/songi2/Documents/GitHub/Scalable_GIS/largedata/"
+merraname <- "MERRA2_400.tavg1_2d_aer_Nx.20220820.nc4"
+pointname <- "aqs-test-data.gpkg"
 # pathappend = "/ddn/gs1/home/songi2/covartest/"
-merra = stars::read_ncdf(paste(pathappend, merraname, sep= ""), proxy = TRUE)
-point = sf::read_sf(paste(pathappend, pointname, sep = "")) |>
+merra <- stars::read_ncdf(paste(pathappend, merraname, sep= ""), proxy = TRUE)
+point <- sf::read_sf(paste(pathappend, pointname, sep = "")) |>
     st_transform(4326)
 
 ## I was confused with the notion of time info in SpatRaster.
@@ -53,7 +53,7 @@ point = sf::read_sf(paste(pathappend, pointname, sep = "")) |>
 merra
 
 
-merra_daily = stars::st_apply(merra, MARGIN = 1:2, FUN = mean)
+merra_daily <- stars::st_apply(merra, MARGIN = 1:2, FUN = mean)
 
 # ok
 # timeindex = rep(seq_along(varnames(merra)), each = 24)
@@ -65,7 +65,7 @@ merra_daily = stars::st_apply(merra, MARGIN = 1:2, FUN = mean)
 
 # merra_daily
 
-targ_cols = c("BCCMASS",
+targ_cols <- c("BCCMASS",
 "BCSMASS",
 "DMSCMASS",
 "DMSSMASS",
@@ -83,13 +83,13 @@ targ_cols = c("BCCMASS",
 "SSSMASS",
 "SSCMASS25",
 "SSSMASS25")
-st_crs(merra_daily_t) = "EPSG:4326"
+st_crs(merra_daily_t) <- "EPSG:4326"
 
-st_crs(merra_daily) = st_crs(point)
-merra_daily_t = merra_daily[targ_cols][st_bbox(st_buffer(point, 3e4))]
-merra_daily_t = st_as_stars(merra_daily_t)
+st_crs(merra_daily) <- st_crs(point)
+merra_daily_t <- merra_daily[targ_cols][st_bbox(st_buffer(point, 3e4))]
+merra_daily_t <- st_as_stars(merra_daily_t)
 
-extracted = extract_with_buffer.flat(point, merra_daily_t, "ID.Code", 
+extracted <- extract_with_buffer.flat(point, merra_daily_t, "ID.Code", 
     radius = 20000, qsegs = 90L)
 
 extracted
diff --git a/tools/tarballs/scomps_0.0.3.10042023.tar.gz b/tools/tarballs/scomps_0.0.3.10042023.tar.gz
index 985b79de1e3f2475eff4cb27e057a411db827b1c..fc6fb7f95834551d6b007412582cf4d50a18cda6 100644
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