Create unit tests

.gitignore

@@ -4,3 +4,5 @@
 .Ruserdata
 petrale_convert_output.csv
 captions_alt_text.csv
+converted_file_1126.csv
+rda_files

DESCRIPTION

@@ -21,10 +21,13 @@ Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.3.2
 Imports: 
+    data.table,
     dplyr,
     flextable,
     ggplot2,
     glue,
+    gt,
+    kableExtra,
     naniar,
     nmfspalette,
     stringr,
@@ -34,3 +37,6 @@ Remotes:
     nmfs-fish-tools/nmfspalette
 Depends: 
     R (>= 2.10)
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3

NAMESPACE

@@ -1,10 +1,14 @@
 # Generated by roxygen2: do not edit by hand
 
 export(add_theme)
-export(exp_fig_accessible)
+export(exp_all_figs_tables)
+export(plot_biomass)
+export(plot_indices)
 export(plot_landings)
 export(plot_recruitment)
+export(plot_recruitment_deviations)
+export(plot_spawn_recruitment)
 export(plot_spawning_biomass)
-export(plot_total_biomass)
+export(table_bnc)
 export(table_indices)
 export(write_captions)

R/add_theme.R

@@ -12,12 +12,23 @@
 add_theme <- function(x) {
   # this is bad coding practice, but what I have for now
   if (class(x)[1] == "flextable") {
+    FitFlextableToPage <- function(ft, pgwidth = 6){
+
+      ft_out <- ft |> flextable::autofit()
+
+      ft_out <- flextable::width(ft_out, width = dim(ft_out)$widths*pgwidth /(flextable::flextable_dim(ft_out)$widths))
+      return(ft_out)
+    }
     theme_obj <- x |>
       flextable::merge_h(i = 1, part = "header") |>
       flextable::align(part = "header", align = "center") |>
-      # flextable::font(fontname = "cambria",
+      # flextable::font(fontname = "arial narrow",
       #                 part = "all") |>
-      flextable::add_header_lines(top = FALSE)
+      flextable::bold(part = "header") |>
+      flextable::add_header_lines(top = FALSE) |>
+      flextable::align(align = "center", part = "body") |>
+      flextable::autofit()
+      # FitFlextableToPage()
   } else if (class(x)[1] == "gt_tbl") {
     theme_obj <- x
     # gt object

R/exp_all_figs_tables.R

@@ -0,0 +1,183 @@
+#' Export all figures and tables
+#'
+#' Export all figures and tables to Rda files within one function.
+#'
+#' @inheritParams plot_recruitment
+#' @param recruitment_unit_label Units for recruitment
+#' @param ref_line A string specifying the type of reference you want to
+#' compare biomass to. The default is `"target"`, which looks for
+#' `"biomass_target"` in the `"label"` column of `dat`. The actual
+#' searching in `dat` is case agnostic and will work with either upper- or
+#' lower-case letters but you must use one of the options specified in the
+#' default list to ensure that the label on the figure looks correct
+#' regardless of how it is specified in `dat`.
+#' @param ref_point A known value of the reference point along with the label
+#' for the reference point as specified in the output file. Please use this
+#' option if the ref_line cannot find your desired point. Indicate the
+#' reference point in the form c("label" = value).
+#' @param landings_unit_label Units for landings
+#' @param biomass_unit_label Units for biomass
+#' @param spawning_biomass_label Units for spawning biomass
+#' @param ref_line_sb Identical definition as `ref_line`, but this argument is
+#' applied to plot_spawning_biomass.
+#' @param ref_point_sb Identical definition as `ref_point`, but this argument is
+#' applied to plot_spawning_biomass.
+#' @param indices_unit_label Units for index of abundance/CPUE
+#' @param biomass_unit_label Abbreviated units for biomass
+#' @param catch_unit_label Abbreviated units for catch
+#'
+#' @return Rda files for each figure/table.
+#'
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' exp_all_figs_tables(dat, end_year = 2022, ref_line = "unfished", ref_point = 13000,
+#' ref_point_sb = 13000, ref_line_sb = "target", indices_unit_label = "CPUE")
+#' }
+
+exp_all_figs_tables <- function(
+
+  # imported from plot_recruitment
+  dat,
+  recruitment_unit_label = "mt", # changed from unit_label to recruitment_unit_label for specificity
+  scale_amount = 1,
+  end_year = NULL,
+  n_projected_years = 10,
+  relative = FALSE,
+  rda_dir = getwd(),
+
+  # imported from plot_biomass
+  ref_line = c("target", "MSY", "msy", "unfished"),
+  ref_point = NULL,
+
+  # imported from plot_landings
+  landings_unit_label = "mt",
+
+  # imported from plot_recruitment_deviations- zero unique arguments
+
+  # imported from plot_spawn_recruitment
+  spawning_biomass_label = "mt",
+
+  # imported from plot_spawning_biomass
+  ref_line_sb = c("target", "MSY", "msy", "unfished"),
+  ref_point_sb = NULL,
+
+  # imported from plot_indices
+  indices_unit_label = NULL,
+
+  # imported from table_afsc_tier- add potential unique arguments after dev
+
+  # imported from table_bnc
+  biomass_unit_label = "mt",
+  catch_unit_label = "mt"
+
+  # imported from table_harvest_projection- add potential unique arguments after dev
+
+  # imported from table_indices- zero unique arguments
+
+) {
+
+  make_rda <- TRUE
+
+  message("Starting export of figures and tables:")
+
+  # figures
+
+  satf::plot_recruitment(dat,
+                         unit_label = recruitment_unit_label,
+                         scale_amount,
+                         end_year,
+                         n_projected_years,
+                         relative,
+                         make_rda,
+                         rda_dir) |> suppressWarnings() |> invisible()
+
+  message("Exported plot_recruitment")
+
+  satf::plot_biomass(dat,
+                     unit_label = biomass_unit_label,
+                     scale_amount,
+                     ref_line,
+                     ref_point,
+                     end_year,
+                     relative,
+                     make_rda,
+                     rda_dir) |> suppressWarnings() |> invisible()
+
+  message("Exported plot_biomass")
+
+  satf::plot_landings(dat,
+                      unit_label = landings_unit_label,
+                      make_rda,
+                      rda_dir) |> suppressWarnings() |> invisible()
+
+  message("Exported plot_landings")
+
+  satf::plot_recruitment_deviations(dat,
+                                    end_year,
+                                    n_projected_years,
+                                    make_rda,
+                                    rda_dir) |> suppressWarnings() |> invisible()
+
+  message("Exported plot_recruitment_deviations")
+
+  # satf::plot_spawn_recruitment(dat,
+  #                        spawning_biomass_label,
+  #                        recruitment_label = recruitment_unit_label,
+  #                        end_year,
+  #                        make_rda,
+  #                        rda_dir) |> suppressWarnings() |> invisible()
+  #
+  # message("Exported plot_spawn_recruitment")
+
+  satf::plot_spawning_biomass(dat,
+                              unit_label = spawning_biomass_label,
+                              scale_amount,
+                              ref_line = ref_line_sb,
+                              ref_point = ref_point_sb,
+                              end_year,
+                              relative,
+                              n_projected_years,
+                              make_rda,
+                              rda_dir) |>
+ #   suppressWarnings() |>
+    invisible()
+
+  message("Exported plot_spawning_biomass")
+
+  # uncomment when this is working properly
+  # satf::plot_indices(dat,
+  #                    unit_label = indices_unit_label,
+  #                    make_rda,
+  #                    rda_dir) |> suppressWarnings() |> invisible()
+  #
+  # message("Exported plot_indices")
+
+  # tables
+  satf::table_bnc(dat,
+            end_year,
+            biomass_unit_label,
+            catch_unit_label,
+            make_rda,
+            rda_dir) |> suppressWarnings() |> invisible()
+
+  message("Exported table_bnc")
+
+  satf::table_indices(dat,
+                make_rda,
+                rda_dir) |> suppressWarnings() |> invisible()
+
+  message("Exported table_indices")
+
+  # uncomment when finished
+  # satf::table_landings(dat) |> suppressWarnings() |> invisible()
+  #
+  # message("Exported table_landings")
+  #
+  # undeveloped tables - add arguments after more development
+  # table_afsc_tier() |> suppressWarnings() |> invisible()
+  # table_harvest_projection() |> suppressWarnings() |> invisible()
+  message("Finished export of figures and tables.")
+
+}