[refactor]: automate units in functions

R/plot_abundance_at_age.R

@@ -11,7 +11,7 @@
 #'
 #' @param unit_label String. Abundance units
 #'
-#' Default: "fish"
+#' Default: NULL
 #'
 #' @param scale_amount Number. A number describing how much to scale down the abundance at
 #' age. Please choose a value ranging from 1-1,000,000,000 (one billion) in orders
@@ -199,5 +199,10 @@ plot_abundance_at_age <- function(
       dat
     )
   }
+
+  if (exists("selected_module")) {
+    rm(selected_module, envir = .GlobalEnv)
+  }
+
   plot
 }

R/plot_biomass.R

@@ -3,7 +3,7 @@
 #' @inheritParams plot_spawning_biomass
 #' @param unit_label String. Biomass units
 #'
-#' Default: "mt"
+#' Default: NULL
 #' @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
@@ -337,10 +337,10 @@ plot_biomass <- function(
     )
   }
 
-  # remove global variable "selected_module"
-  if (exists("selected_module", envir = .GlobalEnv)) rm("selected_module", envir = .GlobalEnv)  
+  if (exists("selected_module")) {
+    rm(selected_module, envir = .GlobalEnv)
+  }
 
-  # Output final plot
   final
 
 }

R/plot_biomass_at_age.R

@@ -165,5 +165,10 @@ plot_biomass_at_age <- function(
       dat
     )
   }
+
+  if (exists("selected_module")) {
+    rm(selected_module, envir = .GlobalEnv)
+  }
+
   plot
 }

R/plot_catch_at_age.R

@@ -3,7 +3,7 @@
 #' @inheritParams plot_abundance_at_age
 #' @param unit_label String. Units of catch used to label the axis
 #'
-#' Default: "mt"
+#' Default: NULL
 #'
 #' @param scale_amount Number. A number describing how much to scale down the catch at
 #' age. Please choose a value ranging from 1-1,000,000,000 (one billion) in orders
@@ -183,9 +183,14 @@ plot_catch_at_age <- function(
       # get name of function and remove "plot_" from it
       topic_label = gsub("plot_", "", utils::tail(as.character(sys.call()[[1]]), n = 1)),
       fig_or_table = "figure",
-      dir=figures_dir,
+      dir = figures_dir,
       dat
     )
   }
+
+  if (exists("selected_module")) {
+    rm(selected_module, envir = .GlobalEnv)
+  }
+
   plot
 }

R/plot_discard.R

@@ -162,6 +162,10 @@ plot_discard <- function(
       scale_amount = scale_amount
     )
   }
-  # Output final plot
+
+  if (exists("selected_module")) {
+    rm(selected_module, envir = .GlobalEnv)
+  }
+
   final
 }

R/plot_fishing_mortality.R

@@ -203,10 +203,9 @@ plot_fishing_mortality <- function(
     )
   }
 
-  # remove global variable "selected_module"
-  if (exists("selected_module", envir = .GlobalEnv)) rm("selected_module", envir = .GlobalEnv) 
+  if (exists("selected_module")) {
+    rm(selected_module, envir = .GlobalEnv)
+  }
 
-  # Output final plot
-  final  
-
+  final
 }

R/plot_index.R

@@ -8,7 +8,7 @@
 #' Options: May include, but is not limited to: "fleet", "year", "area", NULL
 #' @param unit_label String. Index of abundance/CPUE units
 #'
-#' Default: ""
+#' Default: NULL
 #' @param focus Character vector. Column name or names used to filter data.
 #' (i.e. select names of fleets to zoom into the plot)
 #'
@@ -173,6 +173,10 @@ plot_index <- function(
       dir = figures_dir
     )
   }
-  # Output final plot
+
+  if (exists("selected_module")) {
+    rm(selected_module, envir = .GlobalEnv)
+  }
+
   plt
 }

R/plot_landings.R

@@ -60,10 +60,32 @@ plot_landings <- function(
   # filter NA from year
   # dplyr::filter(!is.na(year))
 
+  # Process data
+  processed_data <- process_data(
+    dat = prepared_data,
+    group = group,
+    facet = facet,
+    lbs = lbs
+  )
+  landings_data <- processed_data[[1]]
+  group <- processed_data[[2]]
+  facet <- processed_data[[3]]
+
+  # Check if there is >1 label
+  if (length(landings_data$label) > 1) {
+    landings_data <- landings_data |>
+      # always select the first label if TRUE
+      dplyr::filter(label == unique(label)[1])
+  }
+
   # extract unit if unit_label is null and set lbs to F by default
   lbs <- FALSE
   if (is.null(unit_label)) {
-    unit_label <- unique(prepared_data$unit)
+    labels <- unique(landings_data$label)
+    unit_label <- prepared_data |>
+      dplyr::filter(label %in% labels) |>
+      dplyr::pull(unit) |>
+      unique()
     if (is.na(unit_label)) {
       cli::cli_alert_warning("No unit label found in the data. Please provide a unit label using the 'unit_label' argument.")
       unit_label <- ""
@@ -79,33 +101,15 @@ plot_landings <- function(
     scale_amount = dplyr::if_else(lbs, 1000 * scale_amount, scale_amount),
     legend = FALSE
   )
-
-  # Process data
-  processed_data <- process_data(
-    dat = prepared_data,
-    group = group,
-    facet = facet,
-    lbs = lbs
-  )
-  prepared_data <- processed_data[[1]]
-  group <- processed_data[[2]]
-  facet <- processed_data[[3]]
-
-  # Check if there is >1 label
-  if (length(prepared_data$label) > 1) {
-    prepared_data <- prepared_data |>
-      # always select the first label if TRUE
-      dplyr::filter(label == unique(label)[1])
-  }
 
   # Override grouping variable when there is only NA's
   if (!is.null(group)) {
-    if (group %notin% colnames(prepared_data)) group <- NULL
+    if (group %notin% colnames(landings_data)) group <- NULL
   }
 
   # inital base plot
   plt <- plot_timeseries(
-    dat = prepared_data,
+    dat = landings_data,
     y = "estimate",
     geom = geom,
     ylab = landings_label,
@@ -114,17 +118,17 @@ plot_landings <- function(
     ...
   ) + theme_noaa()
 
-  if (length(unique(prepared_data$group_var)) == 1) {
+  if (length(unique(landings_data$group_var)) == 1) {
     plt <- plt + ggplot2::theme(legend.position = "none")
   }
 
   ### Make RDA ----
   if (make_rda) {
     # Obtain relevant key quantities for captions/alt text
-    landings.start.year <- min(prepared_data$year)
-    landings.end.year <- max(prepared_data$year)
-    landings.min <- min(prepared_data$estimate) |> round(digits = 3)
-    landings.max <- max(prepared_data$estimate) |> round(digits = 3)
+    landings.start.year <- min(landings_data$year)
+    landings.end.year <- max(landings_data$year)
+    landings.min <- min(landings_data$estimate) |> round(digits = 3)
+    landings.max <- max(landings_data$estimate) |> round(digits = 3)
     landings.units <- unit_label
 
     # calculate & export key quantities
@@ -157,6 +161,10 @@ plot_landings <- function(
       scale_amount = scale_amount
     )
   }
-  # Output final plot
+
+  if (exists("selected_module")) {
+    rm(selected_module, envir = .GlobalEnv)
+  }
+
   plt
 }

R/plot_natural_mortality.R

@@ -142,6 +142,10 @@ plot_natural_mortality <- function(
       dir = figures_dir
     )
   }
-  # Output final plot
+
+  if (exists("selected_module")) {
+    rm(selected_module, envir = .GlobalEnv)
+  }
+
   final
 }

R/plot_spawning_biomass.R

@@ -141,7 +141,6 @@ plot_spawning_biomass <- function(
 ) {
   check_data(dat)
 
-  # TODO: start deprecation procedure for argument lbs
   if (relative & scale_amount > 1) {
     cli::cli_alert_warning("Scale amount is not applicable when relative = TRUE. Resetting scale_amount to 1.")
     scale_amount <- 1