0.8.2

- renamed par_map_args to `par_convert_f`
- clip_*_ext functions are removed
- vect_validate function is removed
- Description update for ellipsis arguments in documentation

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: chopin
 Title: Computation of Spatial Data by Hierarchical and Objective Partitioning of Inputs for Parallel Processing
-Version: 0.8.1
+Version: 0.8.2
 Authors@R: c(
     person("Insang", "Song", , "geoissong@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8732-3256")),
@@ -25,7 +25,7 @@ URL: https://github.com/NIEHS/chopin
 BugReports: https://github.com/NIEHS/chopin/issues
 Depends: 
     R (>= 4.1)
-SystemRequirements: NetCDF4
+SystemRequirements: netcdf
 Encoding: UTF-8
 LazyData: true
 LazyDataCompression: xz

NAMESPACE

@@ -2,9 +2,9 @@
 
 export(extract_at)
 export(kernelfunction)
+export(par_convert_f)
 export(par_grid)
 export(par_hierarchy)
-export(par_map_args)
 export(par_merge_grid)
 export(par_multirasters)
 export(par_pad_balanced)
@@ -54,11 +54,9 @@ importFrom(sf,st_coordinates)
 importFrom(sf,st_crs)
 importFrom(sf,st_geometry_type)
 importFrom(sf,st_interpolate_aw)
-importFrom(sf,st_intersection)
 importFrom(sf,st_intersects)
 importFrom(sf,st_length)
 importFrom(sf,st_make_grid)
-importFrom(sf,st_make_valid)
 importFrom(sf,st_read)
 importFrom(sf,st_relate)
 importFrom(sf,st_set_crs)
@@ -74,15 +72,13 @@ importFrom(terra,area)
 importFrom(terra,as.polygons)
 importFrom(terra,buffer)
 importFrom(terra,crds)
-importFrom(terra,crop)
 importFrom(terra,crs)
 importFrom(terra,distance)
 importFrom(terra,expanse)
 importFrom(terra,ext)
 importFrom(terra,geom)
 importFrom(terra,geomtype)
 importFrom(terra,intersect)
-importFrom(terra,makeValid)
 importFrom(terra,nearby)
 importFrom(terra,project)
 importFrom(terra,rast)

NEWS.md

@@ -1,14 +1,14 @@
-# 0.7.8
-- `.check_package` refactoring: no `library()` call is required
+# 0.8
+- Bumped version from 0.7.8 to 0.8.0: improving package coverage
+- README.md: two mermaid plots are pre-generated as png files
+- Internal `clip_*()` functions are removed
+- `par_map_args()` is renamed to `par_convert_f()`
 
-# 0.7.7
-- Documentation is revised
 
-# 0.7.6
+# 0.7
+- `.check_package` refactoring: no `library()` call is required
 - Internal function .check_par_spatraster is added to main `par_*` functions
-
-# 0.7.5
-- Internal: Preprocessing "dot-functions" -- universally usable functions are plain S3, whereas others that are class-specific were implemented in S4
+- Internal preprocessing "dot-functions" -- universally usable functions are plain S3, whereas others that are class-specific were implemented in S4
 - Added
   - CITATION.cff
   - `par_*`: argument `pad_y` to enable applying padded extent to x or y (e.g., y in raster-vector overlay and x otherwise)
@@ -20,69 +20,54 @@
   - `any_class_args`, `is_within_ref`, `par_fallback`, `check_dist_incorrect`
   - `par_grid` argument: `grids_input_ids`
   - Data: SRTM (TIFF replaces RDS)
-
-# 0.7.4
 - Data preprocessing parts are separated into internal functions
 - Name change
   - `check_subject` to `.check_vector`
   - `reproject_b2r` to `reproject_to_raster`
   - `vect_valid_repair` to `vect_validate`
 - targets-friendly helper function: `par_split_list`
   - Vignette for `par_split_list`
-
-# 0.7.3
-- BREAKING
-  - `par_*` family naming hierarchy: `par_make_*` to `par_pad_*`
-    - Plain gridding (`par_make_grid`) and clustering (`par_make_balanced`) functions are internal
-  - Main `par_*` runners (par_grid, par_hierarchy, par_multirasters) are kept
+- `par_*` family naming hierarchy: `par_make_*` to `par_pad_*`
+  - Plain gridding (`par_make_grid`) and clustering (`par_make_balanced`) functions are internal
+- Main `par_*` runners (par_grid, par_hierarchy, par_multirasters) are kept
 - `extract_at` is redesigned as a S4 method
 - All messaging is managed by `cli` package
 - Added zzz.R for startup message
-
-# 0.7.2
 - `summarize_aw` gets generic argument names `x` and `y`
 - `mirai` backend is introduced
 - Internal functions are not exported
-
-# 0.7.0
 - Type check function `check_subject` is added. This function is internal.
 - `vapply` argument `FUN.VALUE` fixed
 
-# 0.6.4
-- FIX: `grid_target_id` in `par_grid` accepts numeric or character input to filter grids
+# 0.6
+- Fixed: `grid_target_id` in `par_grid` accepts numeric or character input to filter grids
 - `par_fallback` is returning error_message field with actual error messages
 - `collapse` package is added to Imports (i.e., `rowbind` function is used in place of `dplyr::bind_rows`)
 - Tests were fixed following refactoring/updating `par_*` functions
 - `chopin` processing functions now support file path input with extents in `par_grid`
-
-# 0.6.3
-- FIX: Missing argument passing in `par_pad_grid` with `mode = "grid_advanced"`
+- Fixed: Missing argument passing in `par_pad_grid` with `mode = "grid_advanced"`
 - Vignette update: v01
-
-# 0.6.2
-- FIX: align input-output classes in `par_merge_grid`
-- IMPROVE: grid_advanced mode supports the maximum of merged unit grids
+- Fixed: align input-output classes in `par_merge_grid`
+- Improved: grid_advanced mode supports the maximum of merged unit grids
 - Added the balanced number mode of splitting input points (`par_pad_balanced`; thanks to comments of Dr. Michael Fessler)
 - Added function of the balanced mode for `par_grid` (`par_group_grid`)
 - All internal `sapply` is changed to `vapply`
 - Added a diagram for guiding users' choice for `par_*` functions for parallelization considering raster/vector data situations
 - litr R Markdown file is moved to the archive
 
-# 0.5.0
+# 0.5
 - `par_grid` unifies the classes of grid inputs
 - `par_cut_coords`: a supplementary function effectively operating with `par_def_q` for `mode = "grid_quantile"` in `par_pad_grid`. X- and Y-coordinates (of centroids for polygon inputs) are split into quantile groups to balance the number of features in each grid; does not account for geometric complexity (i.e., number of vertices)
 - Padded grid generation in `par_pad_grid` is done only by `terra::buffer`
 - `extract_at*` functions get `max_cells`, which is passed to `exactextractr::exact_extract` for speedup in expense of memory pressure
 - Added a new vignette on the demonstration of climate/weather data extraction
 
-# 0.4.0
+# 0.4
 - `surf` argument in `extract_at*()` accepts file paths
 - Raster cropping is now optional
 
-# 0.3.1
+# 0.3
 - Dropped `rast_short`
 - Added examples
-
-# 0.3.0
 - README.md is replaced by README.Rmd
 - Documentation is clarified about the second argument in `...` in `par_*` functions

R/check.R

@@ -221,7 +221,7 @@ reproject_std <-
 
 #' @title Align vector CRS to raster's
 #' @family Helper functions
-#' @keywords internal soft-deprecated
+#' @keywords internal
 #' @param vector `sf`/`stars`/`SpatVector`/`SpatRaster` object
 #' @param raster `SpatRaster` object
 #' @returns Reprojected object in the same class as \code{vector}
@@ -254,43 +254,6 @@ reproject_to_raster <-
 
 
 
-#' Validate and repair input vector data
-#' @family Helper functions
-#' @keywords internal soft-deprecated
-#' @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.
-#' @returns A repaired `sf` or `SpatVector` object depending on
-#' the class of input_vector.
-#' @note This function works with GEOS (>=3.8).
-#' @examples
-#' \dontrun{
-#' library(terra)
-#' library(sf)
-#' ncpath <- system.file("gpkg/nc.gpkg", package = "sf")
-#' nc <- terra::vect(ncpath)
-#'
-#' nc_valid <- vect_validate(nc)
-#' }
-#' @importFrom terra makeValid
-#' @importFrom sf st_make_valid
-vect_validate <- function(input_vector) {
-  detected <- dep_check(input_vector)
-
-  validated <- switch(detected,
-    terra = terra::makeValid(input_vector),
-    sf = sf::st_make_valid(input_vector)
-  )
-
-  return(validated)
-}
-
 
 # ## .intersect_extent ####
 #' Get intersection extent

R/gridding.R

@@ -34,7 +34,6 @@
 #' @description Using input points, the bounding box is split to
 #'  the predefined numbers of columns and rows.
 #'  Each grid will be buffered by the radius.
-#' @seealso [`par_merge_grid`]
 #' @author Insang Song
 #' @examples
 #' # data

R/preprocessing.R

@@ -8,7 +8,7 @@
 #' @param extrusion numeric(1). The extent extrusion factor.
 #'   Default is 1.1, meaning that the actual padding is 10 percent
 #'   wider than `radius`.
-#' @returns A `terra::ext` or sfc_POLYGON object of the computation extent.
+#' @returns A [`terra::ext`] or sfc_POLYGON object of the computation extent.
 #' @examples
 #' \dontrun{
 #' library(sf)
@@ -47,110 +47,3 @@ get_clip_ext <- function(
   }
   return(ext_input)
 }
-
-
-#' Clip to the buffered extent of input vector
-#' @family Helper functions
-#' @description Clip input vector by
-#'  the expected maximum extent of computation.
-#' @keywords internal
-#' @author Insang Song
-#' @param x `sf` or `SpatVector` object to be clipped
-#' @param y `sf` or `SpatVector` object
-#' @param radius `numeric(1)`. Circular buffer radius.
-#'  this value will be automatically multiplied by 1.1
-#' @returns A clipped `sf` or `SpatVector` object.
-#' @examples
-#' \dontrun{
-#' library(sf)
-#' library(stars)
-#' library(terra)
-#' options(sf_use_s2 = FALSE)
-#'
-#' bcsd_path <- system.file(package = "stars", "nc/bcsd_obs_1999.nc")
-#' bcsd <- stars::read_stars(bcsd_path)
-#' bcsd <- sf::st_as_sf(bcsd)
-#' bcsd_rpnt <- sf::st_as_sf(sf::st_sample(bcsd, 4L))
-#' bcsd_rpntm <- sf::st_as_sf(sf::st_sample(bcsd, 1000L))
-#' clip_vec_ext(bcsd_rpntm, 1000, bcsd_rpnt)
-#' }
-#' @importFrom sf st_intersection
-#' @importFrom terra intersect
-clip_vec_ext <- function(
-  x,
-  y,
-  radius
-) {
-  if (any(
-    vapply(
-      list(x, y, radius),
-      FUN = is.null,
-      FUN.VALUE = logical(1)
-    )
-  )) {
-    cli::cli_abort(
-      c("x" = "One or more required arguments are NULL. Please check.\n")
-    )
-  }
-  detected_pnts <- dep_check(y)
-  detected_target <- dep_check(x)
-
-  if (detected_pnts != detected_target) {
-    cli::cli_warn(c("Inputs are not the same class.\n"))
-    x <- dep_switch(x)
-  }
-
-  ext_input <- get_clip_ext(y, radius)
-
-  cli::cli_inform(
-    c("i" = "Clip target features with the input feature extent...\n")
-  )
-  if (detected_pnts == "sf") {
-    cae <-
-      sf::st_intersection(x = x, y = ext_input)
-  }
-  if (detected_pnts == "terra") {
-    cae <- terra::intersect(x, ext_input)
-  }
-
-  return(cae)
-}
-
-#' Clip input raster with a buffered vector extent.
-#' @family Helper functions
-#' @keywords internal soft-deprecated
-#' @description Clip input raster by the expected maximum extent of
-#' computation.
-#' @param x `SpatRaster` object to be clipped
-#' @param y `sf` or `SpatVector` object
-#' @param radius numeric(1). buffer radius.
-#' This value will be automatically multiplied by `extrusion`
-#' @param nqsegs integer(1). the number of points per a quarter circle.
-#'   Default is 180L.
-#' @param extrusion numeric(1). Extrusion factor for the extent. Default is 1.1.
-#' @returns A clipped `SpatRaster` object.
-#' @author Insang Song
-#' @importFrom terra vect crop
-clip_ras_ext <- function(
-  x = NULL,
-  y = NULL,
-  radius = NULL,
-  nqsegs = 180L,
-  extrusion = 1.1
-) {
-  if (any(
-    vapply(list(y, radius, x),
-           FUN = is.null,
-           FUN.VALUE = logical(1))
-  )) {
-    cli::cli_abort(
-      c("x" = "Any of required arguments are NULL. Please check.\n")
-    )
-  }
-  radius <- extrusion * radius
-  ext_input <- get_clip_ext(y, radius)
-  ext_input <- terra::vect(ext_input)
-
-  cae <- terra::crop(x, ext_input, snap = "out")
-  return(cae)
-}

R/processing.R

@@ -707,7 +707,7 @@ summarize_sedc <-
 #' It only works with `x` of character(1) file path.
 #' See [`terra::ext`] for more details. Coordinate systems should match.
 #' @param out_class character(1). "sf" or "terra". Output class.
-#' @param ... Placeholder.
+#' @param ... Additional arguments depending on class of `x` and `y`.
 #' @returns A data.frame with all numeric fields of area-weighted means.
 #' @description When `x` and `y` are different classes,
 #'  `poly_weight` will be converted to the class of `x`.