Merge branch 'master' into reformat-fxns

.gitignore

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

DESCRIPTION

@@ -21,6 +21,7 @@ Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.3.2
 Imports: 
+    data.table,
     dplyr,
     flextable,
     ggplot2,
@@ -34,3 +35,6 @@ Remotes:
     nmfs-fish-tools/nmfspalette
 Depends: 
     R (>= 2.10)
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3

NAMESPACE

@@ -1,7 +1,7 @@
 # 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_landings)
 export(plot_recruitment)

R/exp_all_figs_tables.R

@@ -0,0 +1,133 @@
+#' Export all figures and tables
+#'
+#' Export all figures and tables to Rda files within one function.
+#'
+#' @inheritParams plot_recruitment
+#' @param ref_line @inheritParams plot_biomass
+#' @param spawning_biomass_label @inheritParams plot_spawn_recruitment
+#' @param recruitment_label @inheritParams plot_spawn_recruitment
+#' @param ref_line_sb Identical definition as `ref_line`, but this argument is
+#' applied to plot_spawning_biomass.
+#'
+#' @return
+#'
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' exp_all_figs_tables(dat, ref_line = "unfished",
+#' ref_line_sb = "target", make_rda = TRUE)
+#' }
+
+exp_all_figs_tables <- function(
+
+  # imported from plot_recruitment
+  dat,
+  unit_label = "metric tons",
+  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"),
+
+  # imported from plot_landings- zero unique arguments
+
+  # imported from plot_recruitment_deviations- zero unique arguments
+
+  # imported from plot_spawn_recruitment
+  spawning_biomass_label = "metric tons",
+  recruitment_label = "metric tons",
+
+  # imported from plot_spawning_biomass
+  # changed ref_line to ref_line_sb to differentiate from plot_biomass arg
+  ref_line_sb = c("target", "MSY", "msy", "unfished")
+
+  # imported from table_afsc_tier- add potential unique arguments after dev
+  # imported from table_bnc- add potential unique arguments after dev
+  # imported from table_harvest_projection- add potential unique arguments after dev
+  # imported from table_indices- zero unique arguments
+
+) {
+
+  make_rda = TRUE
+
+  # figures
+
+  satf::plot_recruitment(dat,
+                         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,
+                     scale_amount,
+                     ref_line,
+                     end_year,
+                     relative,
+                     make_rda,
+                     rda_dir) |> suppressWarnings() |> invisible()
+
+  message("Exported plot_biomass")
+
+  satf::plot_landings(dat,
+                      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,
+                         end_year,
+                         make_rda,
+                         rda_dir) |> suppressWarnings() |> invisible()
+
+  message("Exported plot_spawn_recruitment")
+
+  satf::plot_spawning_biomass(dat,
+                              unit_label,
+                              scale_amount,
+                              ref_line_sb,
+                              end_year,
+                              relative,
+                              n_projected_years,
+                              make_rda,
+                              rda_dir) |>
+ #   suppressWarnings() |>
+    invisible()
+
+  message("Exported plot_spawning_biomass")
+
+  # tables
+
+  # uncomment when this is working properly
+  # table_indices(dat,
+  #               make_rda,
+  #               rda_dir) |> suppressWarnings() |> invisible()
+  #
+  # message("Exported table_indices")
+  #
+  # undeveloped tables - add arguments after more development
+  # table_afsc_tier() |> suppressWarnings() |> invisible()
+  # table_bnc() |> suppressWarnings() |> invisible()
+  # table_harvest_projection() |> suppressWarnings() |> invisible()
+
+}

R/plot_biomass.R

@@ -8,6 +8,10 @@
 #'   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).
 #' @return Plot total biomass from a stock assessment model as found in a NOAA
 #' stock assessment report. Units of total biomass can either be manually added
 #' or will be extracted from the provided file if possible. In later releases, model will not
@@ -18,12 +22,17 @@ plot_biomass <- function(
     unit_label = "metric tons",
     scale_amount = 1,
     ref_line = c("target", "MSY", "msy", "unfished"),
+    ref_point = NULL,
     end_year = NULL,
-    relative = FALSE
+    relative = FALSE,
+    make_rda = FALSE,
+    rda_dir = getwd()
 ){
 
-  if(length(ref_line)>1){
-    ref_line = "target"
+  if (!is.null(ref_point)) {
+    ref_line <- names(ref_point)
+  } else if(length(ref_line)>1){
+    ref_line <- "target"
   } else {
     ref_line <- match.arg(ref_line, several.ok = FALSE)
   }
@@ -37,22 +46,45 @@ plot_biomass <- function(
   # Select value for reference line and label
   # update the target option later
   # TODO: add option to indicate the reference pt
-  ref_line_val <- as.numeric(dat[
-    grep(
-      pattern = glue::glue("^biomass.*{tolower(ref_line)}$"),
-      x = dat[["label"]]
-    ),
-    "estimate"
-  ])
+  if (!is.null(ref_point)) {
+    ref_line_val <- as.numeric(ref_point)
+  } else {
+    if ( inherits( try( solve(as.numeric(dat[
+      grep(
+        pattern = glue::glue("^biomass.*{tolower(ref_line)}$"),
+        x = dat[["label"]]
+      ),
+      "estimate"
+    ])), silent = TRUE), "try-error")) {
+      ref_line_val <- NULL
+    } else {
+      ref_line_val <- as.numeric(dat[
+        grep(
+          pattern = glue::glue("^biomass.*{tolower(ref_line)}$"),
+          x = dat[["label"]]
+        ),
+        "estimate"
+      ])
+    }
+    # ref_line_val <- as.numeric(dat[
+    #   grep(
+    #     pattern = glue::glue("^biomass.*{tolower(ref_line)}$"),
+    #     x = dat[["label"]]
+    #   ),
+    #   "estimate"
+    # ])
+  }
+
   if (length(ref_line_val) == 0) {
-    stop(glue::glue(
+    warning(glue::glue(
       "The resulting reference value of `biomass_{ref_line}` was
       not found in `dat[[\"label\"]]`."
     ))
+    warning("Reference line will not be plotted on the figure.")
   } else if (length(ref_line_val) > 1) {
     warning(glue::glue(
       "More than one of the resulting reference value of 'biomass_{ref_line}` was
-      not in `dat[[\"label\"]]`."
+      not in `dat[[\"label\"]]`. \n Both reference points will be plotted on the figure."
     ))
   }
 
@@ -97,47 +129,49 @@ plot_biomass <- function(
         ymax = estimate_upper),
       colour = "grey",
       alpha = 0.3) +
-    ggplot2::geom_hline(
-      yintercept = ref_line_val / ifelse(relative, ref_line_val, scale_amount),
-      linetype = 2) +
+    {if(!is.null(ref_line_val)) ggplot2::geom_hline(yintercept = ref_line_val / ifelse(relative, ref_line_val, scale_amount),linetype = 2)} +
     ggplot2::labs(
       x = "Year",
       y = biomass_label) +
     ggplot2::scale_x_continuous(
       n.breaks = x_n_breaks,
-      guide = ggplot2::guide_axis(minor.ticks = TRUE))
+      guide = ggplot2::guide_axis(minor.ticks = TRUE)) +
+    ggplot2::annotate(
+      geom = "text",
+      x = end_year + 0.05,
+      y = ref_line_val / ifelse(relative, ref_line_val, scale_amount),
+      label = list(bquote(B[.(ref_line)])),
+      parse = TRUE
+    )
 
   plt_fin <- add_theme(plt)
 
-  # create plot-specific variables to use throughout fxn for naming and IDing
-  topic_label <- "biomass"
-
-  # identify output
-  fig_or_table <- "figure"
+  # export figure to rda if argument = T
+  if (make_rda == TRUE){
+    # create plot-specific variables to use throughout fxn for naming and IDing
+    topic_label <- "biomass"
 
-  # run write_captions.R if its output doesn't exist
-  if (!file.exists(
-    fs::path(getwd(), "captions_alt_text.csv"))
-  ) {
-    satf::write_captions(dat = dat,
-                         dir = getwd(),
-                         year = end_year)
-  }
+    # identify output
+    fig_or_table <- "figure"
 
-  # extract this plot's caption and alt text
-  caps_alttext <- extract_caps_alttext(topic_label = topic_label,
-                                       fig_or_table = fig_or_table)
+    # run write_captions.R if its output doesn't exist
+    if (!file.exists(
+      fs::path(getwd(), "captions_alt_text.csv"))
+    ) {
+      satf::write_captions(dat = dat,
+                           dir = rda_dir,
+                           year = end_year)
+    }
 
-  # export figure to rda if argument = T
-  if (make_rda == TRUE){
+    # extract this plot's caption and alt text
+    caps_alttext <- extract_caps_alttext(topic_label = topic_label,
+                                         fig_or_table = fig_or_table)
 
     export_rda(plt_fin = plt_fin,
                caps_alttext = caps_alttext,
                rda_dir = rda_dir,
                topic_label = topic_label,
                fig_or_table = fig_or_table)
-
   }
-
   return(plt_fin)
 }