Some elements of good practices implemented

DESCRIPTION

@@ -28,7 +28,7 @@ Description: Creates exploratory and finished tables and figures for stock
     materials. The advantage of using this package over others is that it
     applies to a range of stock assessment model outputs and standardizes
     them.
-License: MIT + file LICENSE
+License: MIT
 URL: https://github.com/nmfs-ost/stockplotr,
     https://noaa-fisheries-integrated-toolbox.r-universe.dev/stockplotr
 BugReports: https://github.com/nmfs-ost/stockplotr/issues

R/convert_output.R

@@ -623,19 +623,6 @@ convert_output <- function(
                     df4 <- df4 |>
                       dplyr::filter(!(label %in% err_names[2:length(err_names)]))
                   }
-                  # Find overlapping error values if still present
-                  find_error_value <- function(column_names, to_match_vector) {
-                    vals <- vapply(column_names, function(col_name) {
-                      match <- vapply(to_match_vector, function(err) {
-                        pattern <- paste0("(^|[_.])", err, "($|[_.])")
-                        if (grepl(pattern, col_name)) err else NA_character_
-                      }, FUN.VALUE = character(1))
-                      stats::na.omit(match)[1]
-                    }, FUN.VALUE = character(1))
-                    # }
-                    # only unique values and those that intersect with values vector
-                    intersect(unique(vals), to_match_vector)
-                  }
                   # SS: I am not entirely sure what this step is doing, but is a good check
                   if (any(grepl(paste(err_names, collapse = "|"), colnames(df4)))) {
                     err_name <- find_error_value(names(df4), errors)

R/plot_biomass.R

@@ -1,9 +1,6 @@
 #' Plot Total Biomass
 #'
 #' @inheritParams plot_spawning_biomass
-#' @param unit_label String. Biomass units
-#'
-#' Default: "mt"
 #' @param ref_line String. Type of reference point to
 #'   compare biomass to. The default `"msy"` looks for
 #'   `"biomass_msy"` in the `"label"` column of `dat`. The actual

R/table_landings.R

@@ -1,15 +1,6 @@
 #' Landed catch by fleet and year table
 #'
 #' @inheritParams plot_recruitment
-#' @param unit_label String. Abbreviated landings units
-#'
-#' Default: "mt"
-#' @param group String. Single column that groups the data.
-#'
-#' Set group = "none" to summarize data over all indexing values.
-#'
-#' Default: NULL
-#' Options: Including, but not limited to: "year", "area", "fleet", "sex", "none", NULL
 #' @param method String. Method for summarizing data when group
 #' is set to "none".
 #'
@@ -29,8 +20,6 @@
 #' in this ordered list: "landings_weight",  "landings_numbers", "landings_expected",
 #' "landings_predicted", "landings".
 #'
-#' Default: NULL
-#'
 #' @returns A table ready of landed catch by fleet and year.
 #'
 #' @details The input is from an assessment model output file

R/utils_plot.R

@@ -257,6 +257,7 @@ plot_timeseries <- function(
 #' @details The user can create a line, point, or area plot, where the x-axis is
 #' year and y can vary for any time series quantity. Currently, grouping is
 #' restricted to one group where faceting can be any number of facets.
+#' @noRd
 #'
 plot_error <- function(
   dat,
@@ -545,6 +546,7 @@ cohort_line <- function(
 #' @param label_name String. Name of the quantity that users want to
 #' extract the reference point from
 #' @param ref_line String. Reference point(s)
+#' @param scale_amount The amount to scale the reference line value by.
 #' @param model_name String. Name of the model that will be present in the legend.
 #'
 #' Options: Including, but not limited to: "msy", "unfished", "target"
@@ -644,6 +646,14 @@ cap_first_letter <- function(s) {
 #' @inheritParams plot_spawning_biomass
 #' @param label_name String. Name of the label used to filter
 #' the data.
+#' @param module A character string specifying the module to filter by.
+#' @param era A character string specifying the era to filter by.
+#' @param geom The geometric object to use for the plot.
+#' @param group The grouping variable for the plot.
+#' @param facet The faceting variable for the plot.
+#' @param scale_amount The amount to scale the data by.
+#' @param interactive A logical value indicating whether to use interactive mode.
+#'
 #'
 #' @returns a data frame that is preformatted for plotting with ggplot2.
 #' @export

R/utils_rda.R

@@ -20,6 +20,7 @@
 #'   dat = dat
 #' )
 #' }
+#' @noRd
 calc_kqs <- function(returned_kq,
                      prepared_data = NULL,
                      dat = NULL,
@@ -351,6 +352,7 @@ calc_kqs <- function(returned_kq,
 #'   F.max
 #' )
 #' }
+#' @noRd
 fill_in_kqs <- function(df, ...) {
   arg_names <- sapply(substitute(list(...))[-1], deparse)
   arg_values <- list(...)
@@ -388,6 +390,7 @@ fill_in_kqs <- function(df, ...) {
 #'   F.max
 #' )
 #' }
+#' @noRd
 export_kqs <- function(...) {
   # Open new or existing key quantities csv
   if (file.exists(fs::path(getwd(), "key_quantities.csv"))) {
@@ -428,6 +431,7 @@ export_kqs <- function(...) {
 #'   F.max
 #' )
 #' }
+#' @noRd
 insert_kqs <- function(...) {
   if (file.exists(fs::path(getwd(), "captions_alt_text.csv"))) {
     cli::cli_alert_info("Captions/alternative text file (captions_alt_text.csv) exists. Newly calculated key quantities will be added to it.", wrap = TRUE)

R/utils_table.R

@@ -108,6 +108,8 @@ create_latex_table <- function(data,
 #' @param id_group String. The identifying index variable as a string
 #'
 #' Default: NULL
+#' @noRd
+#' 
 
 check_label_differences <- function(dat, index_variables, id_group = NULL) {
   # Loop over model to perform checks if the model columns are identical
@@ -192,6 +194,7 @@ check_label_differences <- function(dat, index_variables, id_group = NULL) {
 #' @returns List of formatted dataframes that contain column names formatted
 #' for a table along with a merge of values in the estimate and error columns
 #' to reduce redundancy in the table.
+#' @noRd
 #'
 merge_error <- function(
   table_data,