[fix]: Fix all existing build warnings with the pkg

.Rbuildignore

@@ -9,4 +9,8 @@
 ^\.positai$
 ^\.claude$
 ^\.octocov\.yml$
-^\.devcontainer$
+^\.devcontainer$
+^CITATION\.cff$
+^CODE_OF_CONDUCT\.md$
+^CONTRIBUTING\.md$
+^(R|data|inst|tests|vignettes)/README\.md$

.github/workflows/update-ss3-example-data.yml

@@ -27,7 +27,9 @@ jobs:
           extra-packages: any::pak, any::usethis, local::.
 
       - name: Update example data
-        run: Rscript data-raw/DATASET_SS3.R
+        run: Rscript data-raw/DATASET_SS3-r4ss.R
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Commit and push updated example data
         if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository

NAMESPACE

@@ -39,3 +39,4 @@ export(table_total_catch)
 export(theme_noaa)
 export(theme_table)
 importFrom(lifecycle,deprecated)
+importFrom(rlang,.data)

R/conout_bam.R

@@ -3,6 +3,8 @@
 #' Does not change naming conventions.
 #'
 #' @inheritParams convert_output
+#' @param out_new The empty standard output data frame from
+#' [convert_output()], which sets the columns of the output.
 #'
 #' @returns Reshaped data frame.
 conout_bam <- function(

R/conout_rceattle.R

@@ -3,6 +3,8 @@
 #' Does not change naming conventions.
 #'
 #' @inheritParams convert_output
+#' @param out_new The empty standard output data frame from
+#' [convert_output()], which sets the columns of the output.
 #'
 #' @returns Reshaped data frame.
 conout_rceattle <- function(

R/conout_ss3.R

@@ -4,6 +4,8 @@
 #' file or returned object from `r4ss::ss_output()`.
 #'
 #' @inheritParams convert_output
+#' @param out_new The empty standard output data frame from
+#' [convert_output()], which sets the columns of the output.
 #'
 #' @returns Reshaped data frame.
 conout_ss3 <- function(

R/data.R

@@ -44,10 +44,8 @@
 
 #' 2018 Gulf of Alaska Pollock stock assessment output
 #'
-#' Standardized output of the 2018 Gulf of Alaska Pollock stock assessment 
-#' produced from Rceattle including all of the values needed to create 
-#' plots and tables in {stockplotr}. The example can be found and run from the 
-#' Rceattle repository.
+#' Output of the 2018 Gulf of Alaska Pollock stock assessment produced from Rceattle, standardized 
+#' using stockplotr::convert_output(). The example can be found and run from the Rceattle repository.
 #'
 #' @docType data
 #'
@@ -93,7 +91,7 @@
 #' @keywords datasets
 #'
 #' @references Adams, G. D., Holsman, K. K., Barbeaux, S. J., Dorn, M. W., Ianelli, J. N., Spies, I., … Punt, A. E. (2022)
-#' (\href{https://doi.org/10.1016/j.fishres.2022.106303})
+#' (\doi{10.1016/j.fishres.2022.106303})
 #'
 #' @source \href{https://github.com/afsc-assessments/Rceattle/blob/main/examples/Fit_2018_GOA_single-species_models.R}{Rceattle Example}
 #'
@@ -152,7 +150,7 @@
 #' @keywords datasets
 #' 
 #' @references SEDAR (2018)
-#' (\href{https://sedarweb.org/documents/sedar-55-stock-assessment-report-south-atlantic-vermilion-snapper/})
+#' (\url{https://sedarweb.org/documents/sedar-55-stock-assessment-report-south-atlantic-vermilion-snapper/})
 #'
 #' @examples
 #' data(vermilion_snapper)
@@ -215,4 +213,4 @@
 #' data(ss3_simple)
 #' head(ss3_simple)
 #' unique(ss3_simple$label)
-"ss3_simple"
+"ss3_simple"

R/extract_sis_data.R

@@ -383,15 +383,15 @@ extract_sis_data <- function(sis_data_dir = getwd(),
     cli::cli_alert_info("Existing sis_assmt_template.csv or sis_ts_template.csv found in {sis_data_dir}.")
     overwrite <- readline("Do you want to overwrite the existing files? (y/n): ")
     if (tolower(overwrite) == "y") {
-      write.csv(assmt_dat, assmt_dat_path, row.names = FALSE)
-      write.csv(ts_dat_filled, ts_dat_path, row.names = FALSE)
+      utils::write.csv(assmt_dat, assmt_dat_path, row.names = FALSE)
+      utils::write.csv(ts_dat_filled, ts_dat_path, row.names = FALSE)
       cli::cli_alert_success("Files overwritten successfully.")
     } else {
       cli::cli_alert_info("Files not overwritten. Please rename the files, then rerun this function to save the data extracted in this function.")
     }
   } else {
-    write.csv(assmt_dat, assmt_dat_path, row.names = FALSE)
-    write.csv(ts_dat_filled, ts_dat_path, row.names = FALSE)
+    utils::write.csv(assmt_dat, assmt_dat_path, row.names = FALSE)
+    utils::write.csv(ts_dat_filled, ts_dat_path, row.names = FALSE)
     cli::cli_alert_success("Files saved successfully in {sis_data_dir}.")
   }
 

R/plot_spawning_biomass.R

@@ -130,7 +130,7 @@ plot_spawning_biomass <- function(
   ref_line = "msy",
   unit_label = NULL,
   era = NULL,
-  lbs = lifecycle::deprecate(),
+  lbs = lifecycle::deprecated(),
   module = NULL,
   scale_amount = 1,
   relative = FALSE,

R/save_all_plots.R

@@ -6,6 +6,10 @@
 #' plotting functions for greater customization of figures and tables.
 #'
 #' @inheritParams plot_spawning_biomass
+#' @param figures_tables_dir Path. Directory where the rda files are saved,
+#' in "figures" and "tables" folders that are created if needed.
+#'
+#' Default: the working directory (`getwd()`)
 #'
 #' @param plot_recruitment_options List. List object of parameter values to pass 
 #' directly to the `plot_recruitment` function. All default parameters for the

R/stockplotr-package.R

@@ -3,6 +3,7 @@
 
 ## usethis namespace: start
 #' @importFrom lifecycle deprecated
+#' @importFrom rlang .data
 ## usethis namespace: end
 NULL
 

R/table_biomass_abundance_catch.R

@@ -115,7 +115,7 @@ table_biomass_abundance_catch <- function(
             estimate_lower = mean(as.numeric(estimate_lower), na.rm = TRUE),
             uncertainty_label = unique(uncertainty_label),
             uncertainty = mean(uncertainty, na.rm = TRUE),
-            unit = unique(unit),
+            unit = unique(.data$unit),
             .by = c(year, model, label)
           ) # |>
         # dplyr::ungroup()
@@ -129,7 +129,7 @@ table_biomass_abundance_catch <- function(
             estimate_lower = mean(as.numeric(estimate_lower), na.rm = TRUE),
             uncertainty_label = unique(uncertainty_label),
             uncertainty = mean(uncertainty, na.rm = TRUE),
-            unit = unique(unit),
+            unit = unique(.data$unit),
             .by = c(year, model, label)
           ) # |>
         # dplyr::ungroup()
@@ -163,8 +163,8 @@ table_biomass_abundance_catch <- function(
       if (is.null(get(paste0(unit_name, "_label")))) {
         unit_label <- filtered_data |>
           dplyr::filter(grepl(x, unit_name),
-                        !is.na(unit)) |>
-          dplyr::pull(unit) |>
+                        !is.na(.data$unit)) |>
+          dplyr::pull("unit") |>
           unique()
         if (is.na(unit_label) || length(unit_label) == 0) {
           cli::cli_alert_warning("No unit label found in the data for {unit_name}. Please provide a unit label using the '{unit_name}_label' argument.")

R/utils_rda.R

@@ -549,10 +549,6 @@ insert_kqs <- function(..., dir=getwd()) {
 #'
 #' Default: the working directory (`getwd()`)
 #'
-#' @param year Number. Assessment year
-#'
-#' Default: the current year
-#'
 #' @param ref_line String. Reference line value
 #'
 #' Default: "msy"