[refactor]: automate units in functions

NAMESPACE

@@ -23,6 +23,7 @@ export(plot_recruitment)
 export(plot_recruitment_deviations)
 export(plot_selectivity)
 export(plot_spawning_biomass)
+export(plot_spawning_potential_ratio)
 export(plot_stock_recruitment)
 export(plot_timeseries)
 export(process_data)

R/plot_abundance_at_age.R

@@ -63,34 +63,28 @@
 #'
 #' @examples
 #' plot_abundance_at_age(
-#'   dat = stockplotr:::example_data,
+#'   dat = stockplotr::example_data,
 #'   facet = "growth_pattern",
 #'   unit_label = "fish",
 #'   scale_amount = 1000,
 #'   proportional = TRUE
 #' )
 #' plot_abundance_at_age(
-#'   dat = stockplotr:::example_data,
+#'   dat = stockplotr::example_data,
 #'   facet = "none",
 #'   proportional = FALSE
 #' )
 plot_abundance_at_age <- function(
   dat,
   facet = NULL,
-  unit_label = "fish",
-  scale_amount = 1000,
+  unit_label = NULL,
+  scale_amount = 1,
   proportional = TRUE,
   module = NULL,
   interactive = TRUE,
   make_rda = FALSE,
   figures_dir = getwd()
 ) {
-  # Create label for abundance units in legend
-  abundance_label <- label_magnitude(
-    label = "Abundance",
-    unit_label = unit_label,
-    scale_amount = scale_amount
-  )
   # Filter data
   b <- filter_data(
     dat = dat,
@@ -102,6 +96,21 @@ plot_abundance_at_age <- function(
     interactive = interactive
   )
 
+  # Create label for abundance units in legend
+  if (is.null(unit_label)) {
+    unit_label <- unique(b$unit)
+    if (grepl("number", unit_label)) unit_label <- "fish"
+    if (is.na(unit_label)) {
+      cli::cli_alert_warning("No unit label found in the data. Please provide a unit label using the 'unit_label' argument.")
+      unit_label <- ""
+    }
+  }
+  abundance_label <- label_magnitude(
+    label = "Abundance",
+    unit_label = unit_label,
+    scale_amount = scale_amount
+  )
+
   if (!is.null(facet) && facet == "none") {
     data <- b |>
       dplyr::group_by(year, age) |>

R/plot_biomass.R

@@ -28,15 +28,15 @@
 #'
 #' @examples
 #' plot_biomass(
-#'   dat = stockplotr:::example_data,
+#'   dat = stockplotr::example_data,
 #'   unit_label = "mt",
 #'   ref_line = c("target" = 20000),
 #'   scale_amount = 100,
 #'   module = "TIME_SERIES",
 #'   figures_dir = getwd()
 #' )
 #' plot_biomass(
-#'   dat = stockplotr:::example_data,
+#'   dat = stockplotr::example_data,
 #'   ref_line = NULL,
 #'   module = "TIME_SERIES",
 #'   figures_dir = getwd()
@@ -48,7 +48,7 @@ plot_biomass <- function(
   facet = NULL,
   ref_line = "msy",
   era = NULL,
-  unit_label = "mt",
+  unit_label = NULL,
   module = NULL,
   scale_amount = 1,
   relative = FALSE,
@@ -57,22 +57,6 @@ plot_biomass <- function(
   interactive = TRUE,
   ...
 ) {
-  # TODO: Fix the unit label if scaling. Maybe this is up to the user to do if
-  #       they want something scaled then they have to supply a better unit name
-  #       or we create a helper function to do this.
-  biomass_label <- ifelse(
-    relative,
-    yes = "Relative biomass",
-    no = {
-      label_magnitude(
-        label = "Biomass",
-        unit_label = unit_label,
-        scale_amount = scale_amount,
-        legend = FALSE
-      )
-    }
-  )
-
   # Pull first df if in a list to find reference point
   if (!is.data.frame(dat)) {
     rp_dat <- dat[[1]]
@@ -101,6 +85,28 @@ plot_biomass <- function(
     scale_amount = scale_amount,
     interactive = interactive
   )
+
+  if (is.null(unit_label)) {
+    unit_label <- unique(prepared_data$unit)
+    if (is.na(unit_label)) {
+      cli::cli_alert_warning("No unit label found in the data. Please provide a unit label using the 'unit_label' argument.")
+      unit_label <- ""
+    }
+  }
+
+  biomass_label <- ifelse(
+    relative,
+    yes = "Relative biomass",
+    no = {
+      label_magnitude(
+        label = "Biomass",
+        unit_label = unit_label,
+        scale_amount = scale_amount,
+        legend = FALSE
+      )
+    }
+  )
+
   if (relative) {
     if (nrow(prepared_data) == 0) {
       cli::cli_abort("No data found for relative biomass. Please check that your data contains a label for 'biomass_biomass_unfished'.")

R/plot_biomass_at_age.R

@@ -27,35 +27,29 @@
 #'
 #' @examples
 #' plot_biomass_at_age(
-#'   dat = stockplotr:::example_data,
+#'   dat = stockplotr::example_data,
 #'   unit_label = "mt",
 #'   scale_amount = 100,
 #'   proportional = FALSE, # displays legend
 #'   make_rda = FALSE
 #' )
 #' plot_biomass_at_age(
-#'   dat = stockplotr:::example_data,
+#'   dat = stockplotr::example_data,
 #'   unit_label = "mt",
 #'   facet = "none",
 #'   proportional = FALSE
 #' )
 plot_biomass_at_age <- function(
   dat,
   facet = NULL,
-  unit_label = "mt",
-  scale_amount = 1000,
+  unit_label = NULL,
+  scale_amount = 1,
   proportional = TRUE,
   module = NULL,
   interactive = TRUE,
   make_rda = FALSE,
   figures_dir = getwd()
 ) {
-  # Create label for abundance units in legend
-  biomass_label <- label_magnitude(
-    label = "Biomass",
-    unit_label = unit_label,
-    scale_amount = scale_amount
-  )
   # Filter data
   b <- filter_data(
     dat = dat |>
@@ -68,6 +62,22 @@ plot_biomass_at_age <- function(
     scale_amount = scale_amount,
     interactive = interactive
   )
+
+  if (is.null(unit_label)) {
+    unit_label <- unique(b$unit)
+    if (is.na(unit_label)) {
+      cli::cli_alert_warning("No unit label found in the data. Please provide a unit label using the 'unit_label' argument.")
+      unit_label <- ""
+    }
+  }
+
+  # Create label for abundance units in legend
+  biomass_label <- label_magnitude(
+    label = "Biomass",
+    unit_label = unit_label,
+    scale_amount = scale_amount
+  )
+
   if (!is.null(facet) && facet == "none") {
     data <- b |>
       dplyr::group_by(year, age) |>

R/plot_catch_comp.R

@@ -47,17 +47,16 @@
 #' @export
 #' @examples
 #' plot_catch_comp(
-#'   dat = stockplotr:::example_data,
+#'   dat = stockplotr::example_data,
 #'   facet = "fleet",
-#'   unit_label = "mt",
 #'   scale_amount = 100,
 #'   interactive = FALSE,
 #'   make_rda = FALSE,
 #'   figures_dir = getwd()
 #' )
 #'
 #' plot_catch_comp(
-#'   dat = stockplotr:::example_data,
+#'   dat = stockplotr::example_data,
 #'   facet = "none",
 #'   unit_label = "mt",
 #'   scale_amount = 100,
@@ -69,21 +68,14 @@ plot_catch_comp <- function(
   dat,
   facet = NULL,
   era = "time",
-  unit_label = "mt",
+  unit_label = NULL,
   scale_amount = 1,
   proportional = TRUE,
   interactive = TRUE,
   module = NULL,
   make_rda = FALSE,
   figures_dir = getwd()
 ) {
-  # Create label for abundance units in legend
-  catch_label <- label_magnitude(
-    label = "catch",
-    unit_label = unit_label,
-    scale_amount = scale_amount,
-    legend = TRUE
-  )
   # Filter data
   catch <- filter_data(
     dat = dat |>
@@ -96,6 +88,21 @@ plot_catch_comp <- function(
     interactive = interactive,
     module = module
   )
+  if (is.null(unit_label)) {
+    unit_label <- unique(catch$unit)
+    if (is.na(unit_label)) {
+      cli::cli_alert_warning("No unit label found in the data. Please provide a unit label using the 'unit_label' argument.")
+      unit_label <- ""
+    }
+  }
+  # Create label for abundance units in legend
+  catch_label <- label_magnitude(
+    label = "catch",
+    unit_label = unit_label,
+    scale_amount = scale_amount,
+    legend = TRUE
+  )
+
   # Check for extracted data, if not return warning and empty plot
   if (nrow(catch) == 0) {
     cli::cli_alert_warning("No data found for catch at age. Please check the input data.")

R/plot_discard.R

@@ -21,14 +21,15 @@
 #'
 #' @examples
 #' plot_discard(
-#'   dat = stockplotr:::example_data,
+#'   dat = stockplotr::example_data,
+#'   unit_label = "fish",
 #'   module = "DISCARD_OUTPUT"
 #' )
 plot_discard <- function(
   dat,
   group = NULL,
   facet = NULL,
-  unit_label = "mt",
+  unit_label = NULL,
   era = NULL,
   lbs = FALSE,
   scale_amount = 1,
@@ -43,17 +44,6 @@ plot_discard <- function(
     unit_label <- "lbs"
   }
 
-  discard_label <- label_magnitude(
-    label = "Discard",
-    unit_label = unit_label,
-    scale_amount = dplyr::if_else(
-      lbs,
-      ifelse(unit_label %in% c("mt", "mts", "metric tons", "metric ton"), 1000, 1) * scale_amount,
-      scale_amount
-    ),
-    legend = TRUE
-  )
-
   # Filter data for discards
   prepared_data <- filter_data(
     dat = dat,
@@ -66,6 +56,24 @@ plot_discard <- function(
     scale_amount = scale_amount,
     interactive = interactive
   )
+
+  # extract unit if unit_label is null and set lbs to F by default
+  lbs <- FALSE
+  if (is.null(unit_label)) {
+    unit_label <- unique(prepared_data$unit)
+    if (is.na(unit_label)) {
+      cli::cli_alert_warning("No unit label found in the data. Please provide a unit label using the 'unit_label' argument.")
+      unit_label <- ""
+    }
+  } else {
+    if (grepl("lbs|pounds|lb", unit_label, ignore.case = TRUE)) lbs <- TRUE
+  }
+  discard_label <- label_magnitude(
+    label = "Discard",
+    unit_label = unit_label,
+    scale_amount = scale_amount,
+    legend = TRUE
+  )
 
   if (any(grepl("observed|predicted", unique(prepared_data$label)))) {
     # select only the observed and predicted discards for plotting

R/plot_index.R

@@ -33,7 +33,7 @@
 #'
 plot_index <- function(
   dat,
-  unit_label = "",
+  unit_label = NULL,
   group = NULL,
   # facet always assigned to fleet since that is how indices are calc'd -- unless replaced with NULL
   facet = NULL,
@@ -44,13 +44,6 @@ plot_index <- function(
   figures_dir = getwd(),
   ...
 ) {
-  # Set cpue unit label for plot
-  u_units <- ifelse(
-    is.null(unit_label) | unit_label == "",
-    glue::glue("Estimated Index"),
-    glue::glue("Estimated Index ({unit_label})")
-  )
-
   if (is.null(facet) || "fleet" %notin% facet) {
     facet <- c(facet, "fleet")
   }
@@ -68,6 +61,17 @@ plot_index <- function(
     interactive = interactive,
     module = module
   )
+  if (unit_label != "" && !is.na(unique(prepared_data$unit))) unit_label <- unique(prepared_data$unit)
+  if (is.na(unit_label)) {
+    cli::cli_alert_warning("No unit label found in the data. Please provide a unit label using the 'unit_label' argument.")
+    unit_label <- ""
+  }
+  # Set cpue unit label for plot
+  u_units <- ifelse(
+    is.null(unit_label) | unit_label == "",
+    glue::glue("Estimated Index"),
+    glue::glue("Estimated Index ({unit_label})")
+  )
 
   # Subset data if focus
   if (!is.null(focus)) {
@@ -102,7 +106,7 @@ plot_index <- function(
     predicted_label = "index_predicted",
     geom = "line",
     xlab = "Year",
-    ylab = "Estimated Index",
+    ylab = u_units,
     group = group,
     facet = facet
   ) +