Style code and document

R/plot_biomass_at_age.R

@@ -98,7 +98,7 @@ plot_biomass_at_age <- function(
     create_rda(
       object = plot,
       # get name of function and remove "plot_" from it
-      topic_label = gsub("plot_", "", as.character(sys.call()[[1]])),     
+      topic_label = gsub("plot_", "", as.character(sys.call()[[1]])),
       fig_or_table = "figure",
       dat,
       unit_label = "mt"

R/plot_catch_comp.R

@@ -114,7 +114,7 @@ plot_catch_comp <- function(
     create_rda(
       object = plot,
       # get name of function and remove "plot_" from it
-      topic_label = gsub("plot_", "", as.character(sys.call()[[1]])),  
+      topic_label = gsub("plot_", "", as.character(sys.call()[[1]])),
       fig_or_table = "figure",
       dat,
       unit_label = "mt"

R/plot_indices.R

@@ -117,7 +117,7 @@ plot_indices <- function(
     create_rda(
       object = plt,
       # get name of function and remove "plot_" from it
-      topic_label = gsub("plot_", "", as.character(sys.call()[[1]])), 
+      topic_label = gsub("plot_", "", as.character(sys.call()[[1]])),
       fig_or_table = "figure",
       dat = dat,
       dir = figures_dir,

R/plot_landings.R

@@ -102,7 +102,7 @@ plot_landings <- function(
     create_rda(
       object = plt,
       # get name of function and remove "plot_" from it
-      topic_label = gsub("plot_", "", as.character(sys.call()[[1]])), 
+      topic_label = gsub("plot_", "", as.character(sys.call()[[1]])),
       fig_or_table = "figure",
       dat = dat,
       dir = figures_dir,

R/plot_natural_mortality.R

@@ -105,7 +105,7 @@ plot_natural_mortality <- function(
     create_rda(
       object = final,
       # get name of function and remove "plot_" from it
-      topic_label = gsub("plot_", "", as.character(sys.call()[[1]])),  
+      topic_label = gsub("plot_", "", as.character(sys.call()[[1]])),
       fig_or_table = "figure",
       dat = dat,
       dir = figures_dir

R/plot_recruitment.R

@@ -147,7 +147,7 @@ plot_recruitment <- function(
     create_rda(
       object = final,
       # get name of function and remove "plot_" from it
-      topic_label = gsub("plot_", "", as.character(sys.call()[[1]])),  
+      topic_label = gsub("plot_", "", as.character(sys.call()[[1]])),
       fig_or_table = "figure",
       dat = dat,
       dir = figures_dir # ,

R/plot_recruitment_deviations.R

@@ -103,7 +103,7 @@ plot_recruitment_deviations <- function(
     create_rda(
       object = final,
       # get name of function and remove "plot_" from it
-      topic_label = gsub("plot_", "", as.character(sys.call()[[1]])),  
+      topic_label = gsub("plot_", "", as.character(sys.call()[[1]])),
       fig_or_table = "figure",
       dat = selected_dat,
       dir = figures_dir,

R/plot_stock_recruitment.R

@@ -130,7 +130,7 @@ plot_stock_recruitment <- function(
     create_rda(
       object = final,
       # get name of function and remove "plot_" from it
-      topic_label = gsub("plot_", "", as.character(sys.call()[[1]])),  
+      topic_label = gsub("plot_", "", as.character(sys.call()[[1]])),
       fig_or_table = "figure",
       dat = dat,
       dir = figures_dir # ,

R/table_bnc.R

@@ -179,13 +179,13 @@
 #       fig_or_table = fig_or_table,
 #       dir = tables_dir
 #     )
-# 
+#
 #     export_rda(
 #       object = final,
 #       caps_alttext = caps_alttext,
 #       figures_tables_dir = tables_dir,
 #       # get name of function and remove "table_" from it
-#       topic_label = gsub("table_", "", as.character(sys.call()[[1]])), 
+#       topic_label = gsub("table_", "", as.character(sys.call()[[1]])),
 #       fig_or_table = fig_or_table
 #     )
 #   }

R/table_indices.R

@@ -155,14 +155,14 @@
 #     )
 
 
-    # export_rda(
-    #   object = final,
-    #   caps_alttext = caps_alttext,
-    #   figures_tables_dir = tables_dir,
-    #   # get name of function and remove "table_" from it
-    #   topic_label = gsub("table_", "", as.character(sys.call()[[1]])),
-    #   fig_or_table = fig_or_table
-    # )
+# export_rda(
+#   object = final,
+#   caps_alttext = caps_alttext,
+#   figures_tables_dir = tables_dir,
+#   # get name of function and remove "table_" from it
+#   topic_label = gsub("table_", "", as.character(sys.call()[[1]])),
+#   fig_or_table = fig_or_table
+# )
 #   }
 #   final
 # }

R/theme_noaa.R

@@ -17,20 +17,19 @@
 #' ) +
 #'   ggplot2::geom_point() +
 #'   theme_noaa()
-#'\dontrun{
-#'  ggplot2::theme_set(stockplotr::theme_noaa())
-#'}
+#' \dontrun{
+#' ggplot2::theme_set(stockplotr::theme_noaa())
+#' }
 theme_noaa <- function(discrete = TRUE,
                        ...) {
-
   if (utils::packageVersion("ggplot2") < "4.0.0") {
     rlang::warn(
       message = paste0("Your `ggplot2` version is ", utils::packageVersion("ggplot2"), ", which is older than the version required to use `theme_noaa()` (4.0.0). Please update your `ggplot2` package."),
       .frequency = "once",
       .frequency_id = "ggplot2_version_warning"
     )
   }
-  
+
   theme <- ggplot2::theme_bw() +
     ggplot2::theme(
       plot.background = ggplot2::element_rect(fill = "transparent"),
@@ -40,24 +39,24 @@ theme_noaa <- function(discrete = TRUE,
       text = ggplot2::element_text(size = 14),
       plot.margin = ggplot2::margin(0.5, 1, 0.5, 0.5, "cm"),
       ...
-  )
+    )
 
   # create main palette
   pal <- function(n) viridisLite::mako(n, begin = 0.1, end = 0.85)
-  
+
   if (discrete) {
     theme <- theme +
       ggplot2::theme(
-       palette.colour.discrete = pal,
-       palette.fill.discrete = pal
-       )
-    } else {
-      theme <- theme +
-        ggplot2::theme(
-          palette.colour.continuous = pal,
-          palette.fill.continuous = pal
-        )
-    }
-  
+        palette.colour.discrete = pal,
+        palette.fill.discrete = pal
+      )
+  } else {
+    theme <- theme +
+      ggplot2::theme(
+        palette.colour.continuous = pal,
+        palette.fill.continuous = pal
+      )
+  }
+
   theme
 }

R/utils_rda.R

@@ -195,10 +195,10 @@ add_more_key_quants <- function(
   # write analogous code for each in this section, and remove placeholders from
   # the end of write_captions (once we get clarity about how to extract Btarg,
   # ssbtarg, and R0)
-  # 
-  
-  #TODO: When adding code extracting values for landings and/or indices figures/tables, be aware that both figure/table share the same label ("landings" and "indices"). If there's reason, add in extra conditional to check if value is from a figure or table
-  
+  #
+
+  # TODO: When adding code extracting values for landings and/or indices figures/tables, be aware that both figure/table share the same label ("landings" and "indices"). If there's reason, add in extra conditional to check if value is from a figure or table
+
   ## biomass
   if (topic_cap_alt$label == "biomass") {
     if (is.null(dat)) {

tests/testthat/test-save_all_plots.R

@@ -40,16 +40,16 @@ test_that("save_all_plots works when all figures/tables are plotted", {
     sort(fig_base_temp_files)
   )
 
- # # expect that the tables are all created with expected names
- #  tab_base_temp_files <- c(
- #   # "bnc_table.rda",
- #  #  "indices.abundance_table.rda",
- #    "landings_table.rda"
- #  )
- #  expect_equal(
- #    list.files(fs::path(getwd(), "tables")),
- #    tab_base_temp_files
- #  )
+  # # expect that the tables are all created with expected names
+  #  tab_base_temp_files <- c(
+  #   # "bnc_table.rda",
+  #  #  "indices.abundance_table.rda",
+  #    "landings_table.rda"
+  #  )
+  #  expect_equal(
+  #    list.files(fs::path(getwd(), "tables")),
+  #    tab_base_temp_files
+  #  )
 
   # erase temporary testing files
   file.remove(fs::path(getwd(), "captions_alt_text.csv"))