style and docs: run devtools::document() and styler::style_pkg() (#98)

Co-authored-by: Schiano-NOAA <Schiano-NOAA@users.noreply.github.com>

DESCRIPTION

@@ -52,14 +52,14 @@ Suggests:
 VignetteBuilder: 
     knitr
 Remotes:
+    nmfs-fish-tools/nmfspalette,
     nmfs-fish-tools/nmfspalette,
     nmfs-ost/satf,
-    r4ss/r4ss,
-    nmfs-fish-tools/nmfspalette
+    r4ss/r4ss
 Config/testthat/edition: 3
 Config/testthat/parallel: true
 Encoding: UTF-8
 Language: en-US
+LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
-LazyData: true

R/add_chunk.R

@@ -28,7 +28,7 @@ add_chunk <- function(
     chunk_op = NULL,
     rmark_op = NULL) {
   chunk <- paste0(
-    "```{r", ifelse(add_option, paste0(c("",rmark_op), collapse = ", "), ""), "} \n"
+    "```{r", ifelse(add_option, paste0(c("", rmark_op), collapse = ", "), ""), "} \n"
   )
   if (!is.null(label)) {
     chunk <- paste0(

R/asar-package.R

@@ -6,8 +6,10 @@
 NULL
 
 ## quiets concerns of R CMD check re: the .'s that appear in pipelines
-globvar <- c("yr","value","estimate","seas","subseas","age_bins","morph",
-             "age","year","nsim","fleet","uncertainty","initial","alt_label",
-             "last","affiliation","label","type","caption","alt_text","caption",
-             "name",".")
-if(getRversion() >= "2.15.1")  utils::globalVariables(globvar)
+globvar <- c(
+  "yr", "value", "estimate", "seas", "subseas", "age_bins", "morph",
+  "age", "year", "nsim", "fleet", "uncertainty", "initial", "alt_label",
+  "last", "affiliation", "label", "type", "caption", "alt_text", "caption",
+  "name", "."
+)
+if (getRversion() >= "2.15.1") utils::globalVariables(globvar)

R/convert_output.R

@@ -720,13 +720,13 @@ convert_output <- function(
       # Extract names from landings
       landings <- dat$t.series |>
         dplyr::select(dplyr::contains("L.") & dplyr::contains(".ob") |
-                      dplyr::contains("D.") & dplyr::contains(".ob"))
+          dplyr::contains("D.") & dplyr::contains(".ob"))
       fleets_land <- stringr::str_extract(as.vector(colnames(landings)), "(?<=L\\.)\\w+(?=\\.ob)")
       fleets_disc <- stringr::str_extract(as.vector(colnames(landings)), "(?<=D\\.)\\w+(?=\\.ob)")
       # Extract names from lof F dev
       parm <- dat$parm.tvec |>
-        dplyr::select(dplyr::contains("log.F.dev.")|
-                        dplyr::contains("log.F.dev.") & dplyr::contains(".D"))
+        dplyr::select(dplyr::contains("log.F.dev.") |
+          dplyr::contains("log.F.dev.") & dplyr::contains(".D"))
       # fleets_parm_D <- stringr::str_extract(as.vector(colnames(parm)), "(?<=log\\.F\\.dev\\.)\\w+(?=\\.D)")
       fleets_parm <- stringr::str_extract(as.vector(colnames(parm)), "(?<=log\\.F\\.dev\\.)\\w+")
       fleets <- unique(c(fleets_ind, fleets_land, fleets_disc, fleets_parm))
@@ -1183,7 +1183,7 @@ convert_output <- function(
     var_names_sheet <- openxlsx::read.xlsx(con_file)
   }
   if (file.exists(con_file)) {
-    out_new <- dplyr::inner_join(out_new, var_names_sheet, by = c("module_name","label")) |>
+    out_new <- dplyr::inner_join(out_new, var_names_sheet, by = c("module_name", "label")) |>
       dplyr::mutate(label = dplyr::case_when(
         !is.na(alt_label) ~ alt_label,
         TRUE ~ label

R/create_figures_doc.R

@@ -18,22 +18,20 @@ create_figures_doc <- function(resdir = NULL,
                                subdir = NULL,
                                include_all = TRUE,
                                rda_dir = NULL) {
-
   model <- match.arg(model, several.ok = FALSE)
 
   if (include_all) {
-
     # add header
     figures_doc <- paste0("## Figures \n \n")
 
     # add chunk that creates object as the directory of all rdas
-figures_doc <- paste0(
+    figures_doc <- paste0(
       figures_doc,
       add_chunk(
         paste0("rda_dir <- '", rda_dir, "/rda_files'"),
         label = "set-rda-dir-figs",
         eval = "true"
-        ),
+      ),
       "\n"
     )
 
@@ -283,7 +281,6 @@ spawning_recruitment_alt_text <- spawning_recruitment_plot_rda$alt_text"),
       ),
       "\n"
     )
-
   } else {
     # add option for only adding specified figures
   }

R/create_tables_doc.R

@@ -17,11 +17,9 @@ create_tables_doc <- function(resdir = NULL,
                               subdir = NULL,
                               include_all = TRUE,
                               rda_dir = NULL) {
-
   model <- match.arg(model, several.ok = FALSE)
 
   if (include_all) {
-
     # add header
     tables_doc <- paste0("## Tables \n \n")
 
@@ -32,7 +30,7 @@ create_tables_doc <- function(resdir = NULL,
         paste0("rda_dir <- '", rda_dir, "/rda_files'"),
         label = "set-rda-dir-tbls",
         eval = "false"
-        ),
+      ),
       "\n"
     )
 
@@ -74,7 +72,6 @@ indices_cap <- indices_table_rda$cap"),
     )
 
     # Add other tables follow the same above format
-
   } else {
     # add option for only adding specified tables
   }