Merge pull request #9 from Schiano-NOAA/style-doc-code

Style code and document
nmfs-ost · May 6, 2024 · 2403b0d · 2403b0d
2 parents 741650d + 9fc2ed7
commit 2403b0d
Show file tree

Hide file tree

Showing 8 changed files with 66 additions and 50 deletions.
diff --git a/R/add_section.R b/R/add_section.R
@@ -38,14 +38,14 @@ add_section <- function(
   for (i in 1:length(sec_names)) {
     section_i_name <- paste0(gsub(" ", "_", sec_names[i]), ".qmd")
     local_section <- forstringr::str_extract_part(location[i], "-", before = FALSE)
-    local_section_prev <- forstringr::str_extract_part(location[i-1], "-", before = FALSE)
+    local_section_prev <- forstringr::str_extract_part(location[i - 1], "-", before = FALSE)
 
     if (any("TRUE" %in% grepl("-", location))) {
       locality <- forstringr::str_extract_part(location[i], "-", before = TRUE)
-      locality_prev <- forstringr::str_extract_part(location[i-1], "-", before = TRUE)
+      locality_prev <- forstringr::str_extract_part(location[i - 1], "-", before = TRUE)
     } else if (any("TRUE" %in% grepl(" ", location))) {
       locality <- forstringr::str_extract_part(location[i], " ", before = TRUE)
-      locality_prev <- forstringr::str_extract_part(location[i-1], "-", before = TRUE)
+      locality_prev <- forstringr::str_extract_part(location[i - 1], "-", before = TRUE)
     }
 
     section_i <- paste0(
@@ -60,8 +60,8 @@ add_section <- function(
     if (locality == "before") {
       other_sections <- append(other_sections, section_i_name, after = (which(grepl(local_section, other_sections)) - 1))
     } else if (locality == "after") {
-      if(locality %in% locality_prev & local_section %in% local_section_prev){
-        other_sections <- append(other_sections, section_i_name, after = which(grepl(gsub(" ", "_", sec_names[i-1]), other_sections)))
+      if (locality %in% locality_prev & local_section %in% local_section_prev) {
+        other_sections <- append(other_sections, section_i_name, after = which(grepl(gsub(" ", "_", sec_names[i - 1]), other_sections)))
       } else {
         other_sections <- append(other_sections, section_i_name, after = which(grepl(local_section, other_sections)))
       }

diff --git a/R/afsc_tier_table.R b/R/afsc_tier_table.R
@@ -1,5 +1,5 @@
 # AFSC Tier Table
-afsc_tier_table <- function(){
+afsc_tier_table <- function() {
   level <- c(
     "Level 1: Normal",
     "Level 2: Substantially Increased Concerns",
@@ -32,11 +32,13 @@ afsc_tier_table <- function(){
   )
   tier_df <- data.frame(level, ass_considerations, popdy_considerations, eco_considerations, fish_performance)
   flextable::flextable(tier_df) |>
-    flextable::set_header_labels(level = "",
-                                 ass_considerations = "Assessment-related considerations",
-                                 popdy_considerations = "Population dynamics considerations",
-                                 eco_considerations = "Environmental/ecosystems considerations",
-                                 fish_performance = "Fishery Performance") |>
+    flextable::set_header_labels(
+      level = "",
+      ass_considerations = "Assessment-related considerations",
+      popdy_considerations = "Population dynamics considerations",
+      eco_considerations = "Environmental/ecosystems considerations",
+      fish_performance = "Fishery Performance"
+    ) |>
     flextable::italic(part = "header") |>
     flextable::bold(part = "header") |>
     flextable::hline(i = c(1, 2, 3))

diff --git a/R/create_template.R b/R/create_template.R
@@ -309,7 +309,7 @@ create_template <- function(
     # Add chunk to load in assessment data
     ass_output <- chunkr(
       paste0(
-        "convert_output(output.file = ", "c('", paste(model_results, collapse="', '"), "')",
+        "convert_output(output.file = ", "c('", paste(model_results, collapse = "', '"), "')",
         ", model = ", "'", model, "'",
         ", outdir = ", "'", resdir, "'", ")"
       ),

diff --git a/R/generate_citation.R b/R/generate_citation.R
@@ -25,7 +25,7 @@ generate_citation <- function(
   }
 
   # Pull affiliation of first author
-  if(length(unlist(strsplit(author[1], " ")))==3){
+  if (length(unlist(strsplit(author[1], " "))) == 3) {
     primauth_loc <- utils::read.csv(system.file("resources", "authorship.csv", package = "ASAR", mustWork = TRUE)) |>
       dplyr::filter(last == unlist(strsplit(author[1], " "))[3])
   } else {
@@ -34,7 +34,7 @@ generate_citation <- function(
   }
 
   # Check and fix if there is more than one author with the same last name
-  if(nrow(primauth_loc)>1){
+  if (nrow(primauth_loc) > 1) {
     primauth_loc <- utils::read.csv(system.file("resources", "authorship.csv", package = "ASAR", mustWork = TRUE)) |>
       dplyr::filter(last == unlist(strsplit(author[1], " "))[1])
   }

diff --git a/R/update_text.R b/R/update_text.R
@@ -2,25 +2,30 @@ update_text <- function(
     office = NULL,
     region = NULL,
     species = NULL,
-    year = NULL
-    ){
+    year = NULL) {
   # Kind of wrapper function for trackdown::download_file so all sections in assessment document are updated
 
   # Downloading version of google doc content onto local drive
   # Will overwrite current content - add warning box
 
   # Check if want to proceed bc this overwrites the local file(s)
-  if(interactive() && isFALSE(force)){
+  if (interactive() && isFALSE(force)) {
     response <- utils::menu(
       c("Yes", "No"),
-      title = paste("Downloading the file from Google Drive will overwrite local file.",
-                    "Do you want to proceed?"))
+      title = paste(
+        "Downloading the file from Google Drive will overwrite local file.",
+        "Do you want to proceed?"
+      )
+    )
 
     if (response == 1L) {
       select_change <- utils::menu(
         c("Yes", "No"),
-        title = paste("Downloading the file from Google Drive will overwrite local file.",
-                      "Do you want to proceed?"))
+        title = paste(
+          "Downloading the file from Google Drive will overwrite local file.",
+          "Do you want to proceed?"
+        )
+      )
     }
 
     if (response == 2L) {
@@ -29,28 +34,32 @@ update_text <- function(
     }
   }
 
-  if (select_change == 1L)
+  if (select_change == 1L) {
 
-  # directory where templates were created
-  if (!is.null(region)) {
-    subdir <- paste0("~/stock_assessment_templates", "/", office, "/", species, "/", region, "/", year)
-  } else {
-    subdir <- paste0("~/stock_assessment_templates", "/", office, "/", species, "/", year)
+    # directory where templates were created
+    if (!is.null(region)) {
+      subdir <- paste0("~/stock_assessment_templates", "/", office, "/", species, "/", region, "/", year)
+    } else {
+      subdir <- paste0("~/stock_assessment_templates", "/", office, "/", species, "/", year)
+    }
   }
 
   all_sections <- list.files(subdir, pattern = ".qmd")
   sections <- all_sections[!grepl("skeleton.qmd", all_sections)]
 
-  for(i in sections){
-    if(!is.null(region)){
-      trackdown::download_file(file = i,
-                               gfile = i,
-                               shared_drive = paste("National Stock Assessment Archives", office, region, species, year, sep = "/"))
+  for (i in sections) {
+    if (!is.null(region)) {
+      trackdown::download_file(
+        file = i,
+        gfile = i,
+        shared_drive = paste("National Stock Assessment Archives", office, region, species, year, sep = "/")
+      )
     } else {
-      trackdown::download_file(file = i,
-                               gfile = i,
-                               shared_drive = paste("National Stock Assessment Archives", office, species, year, sep = "/"))
+      trackdown::download_file(
+        file = i,
+        gfile = i,
+        shared_drive = paste("National Stock Assessment Archives", office, species, year, sep = "/")
+      )
     }
   }
-
 }
diff --git a/man/create_template.Rd b/man/create_template.Rd
diff --git a/tests/testthat/test-add_section.R b/tests/testthat/test-add_section.R
@@ -19,16 +19,18 @@ test_that("Adding new sections works.", {
 })
 
 test_that("Adding new sections works.", {
-  sec_list <- add_base_section(c("introduction","data","model","acknowledgements","tables","figures","appendix","references"))
+  sec_list <- add_base_section(c("introduction", "data", "model", "acknowledgements", "tables", "figures", "appendix", "references"))
   sections <- add_section(
-    sec_names = c("Harvest Control Rules", "Regional Management Considerations","Research and Data Needs"),
+    sec_names = c("Harvest Control Rules", "Regional Management Considerations", "Research and Data Needs"),
     location = c("after-model", "after-model", "after-model"),
     other_sections = sec_list,
     subdir = tempdir()
   )
-  exp_list <- list("02_introduction.qmd","03_data.qmd","04_model.qmd","Harvest_Control_Rules.qmd",
-                "Regional_Management_Considerations.qmd","Research_and_Data_Needs.qmd",
-                "07_acknowledgements.qmd","09_tables.qmd","10_figures.qmd","11_appendix.qmd","08_references.qmd")
+  exp_list <- list(
+    "02_introduction.qmd", "03_data.qmd", "04_model.qmd", "Harvest_Control_Rules.qmd",
+    "Regional_Management_Considerations.qmd", "Research_and_Data_Needs.qmd",
+    "07_acknowledgements.qmd", "09_tables.qmd", "10_figures.qmd", "11_appendix.qmd", "08_references.qmd"
+  )
   expect_equal(sections, exp_list)
 })
 

diff --git a/tests/testthat/test-generate_citation.R b/tests/testthat/test-generate_citation.R
@@ -1,12 +1,15 @@
 test_that("citaiton generated properly for SWFSC", {
   fxn_test <- generate_citation(
-      author = c("Peter T. Kuriyama",
-                 "Caitlin Allen Akselrud",
-                 "Juan P. Zwolinski",
-                 "Kevin T. Hill"),
-      title = "Check",
-      year = 2024,
-      office = "SWFSC")
+    author = c(
+      "Peter T. Kuriyama",
+      "Caitlin Allen Akselrud",
+      "Juan P. Zwolinski",
+      "Kevin T. Hill"
+    ),
+    title = "Check",
+    year = 2024,
+    office = "SWFSC"
+  )
   expected_output <- "{{< pagebreak >}} \n\nPlease cite this publication as \n\nKuriyama, P.T., C.Allen Akselrud, J.P. Zwolinski, K.T. Hill. 2024. Check. NOAA Fisheries Science Center, La Jolla, CA. "
   expect_equal(fxn_test, expected_output)
 })