Style code and document

R/convert_output.R

@@ -2,21 +2,21 @@
 #'
 #' Format stock assessment output file to a standardized tibble.
 #'
-#' @param file Path. Assessment model output file path. Currently accepts SS3 
+#' @param file Path. Assessment model output file path. Currently accepts SS3
 #' Report.sso file, BAM .rda file, Rceattle model object, and FIMS model object.
 #' @param model String. Assessment model used in evaluation
 #'
 #' Default: NULL
 #'
 #' Options: "ss3", "bam", "fims", "rceattle"
 #' @param fleet_names Character vector. Names of fleets in the assessment model as
-#'  shortened in the output file or names of fleets to replace the native fleet 
-#'  names in the output. For example, if fleet names in the model are 1, 2, 3 
+#'  shortened in the output file or names of fleets to replace the native fleet
+#'  names in the output. For example, if fleet names in the model are 1, 2, 3
 #'  then fleet_names = c("fleet1" = 1, "fleet2" = 2, "fleet3" = 3).
 #'
 #'  Default: NULL
-#' @param save_dir Path. Full file path to save the converted output file. If 
-#' saved file name is not indicated, the file will be saved as "std_output.rda" 
+#' @param save_dir Path. Full file path to save the converted output file. If
+#' saved file name is not indicated, the file will be saved as "std_output.rda"
 #' in the file path provided.
 #'
 #' Default: NULL
@@ -297,7 +297,7 @@ convert_output <- function(
       # Extract start year and end year
       start_year <- file$startyr
       end_year <- file$endyr
-      
+
       param_names <- names(dat)
 
       std <- c(
@@ -667,10 +667,10 @@ convert_output <- function(
                   TRUE ~ label
                 ),
                 estimate = suppressWarnings(as.numeric(estimate))
-                  # dplyr::if_else(
-                  # grepl("-|_", as.numeric(estimate)),
-                  # NA,
-                  # estimate
+                # dplyr::if_else(
+                # grepl("-|_", as.numeric(estimate)),
+                # NA,
+                # estimate
                 # )
               )
 
@@ -1168,8 +1168,8 @@ convert_output <- function(
             #   df2[setdiff(tolower(names(out_new)), tolower(names(df2)))] <- NA
             #   # Add to out list
             #   out_list[[parm_sel]] <- df2
-            # } else 
-           if (parm_sel == "DEFINITIONS") {
+            # } else
+            if (parm_sel == "DEFINITIONS") {
               # Extract start year and end year for iding era
               start_year <- as.numeric(extract[which(apply(extract, 1, function(row) any(row == "Start_year:"))), 2])
               end_year <- as.numeric(extract[which(apply(extract, 1, function(row) any(row == "End_year:"))), 2])
@@ -1430,7 +1430,7 @@ convert_output <- function(
           year < start_year ~ "init",
           year >= start_year & year <= end_year ~ "time",
           year > end_year ~ "fore",
-        TRUE ~ NA_character_
+          TRUE ~ NA_character_
         )
       )
   } else if (model %in% c("bam", "BAM")) {

R/html_all_figs_tables.R

@@ -28,14 +28,14 @@
 #'     cli::cli_alert_info("Did you enter the correct argument for figures_tables_dir?")
 #'     cli::cli_alert_info("figures_tables_dir entered as {figures_tables_dir}")
 #'   }
-#' 
+#'
 #'   if (!dir.exists(fs::path(figures_tables_dir, "tables"))) {
 #'     cli::cli_alert_danger("'tables' folder not found.")
 #'     cli::cli_alert_warning("Tables will not be included in the html.")
 #'     cli::cli_alert_info("Did you enter the correct argument for figures_tables_dir?")
 #'     cli::cli_alert_info("figures_tables_dir entered as {figures_tables_dir}")
 #'   }
-#' 
+#'
 #'   # check if dir exists and present warning message/option message
 #'   if (dir.exists(fs::path(figures_tables_dir, "all_tables_figures"))) {
 #'     question1 <- readline(
@@ -45,33 +45,33 @@
 #'     # indicate to proceed with function
 #'     question1 <- "y"
 #'   }
-#' 
+#'
 #'   if (regexpr(question1, "y", ignore.case = TRUE) == 1) {
 #'     # create new folder for the html and qmd files
 #'     doc_path <- fs::path(figures_tables_dir, "all_tables_figures")
 #'     dir.create(doc_path)
-#' 
+#'
 #'     asar::create_tables_doc(
 #'       subdir = figures_tables_dir,
 #'       tables_dir = figures_tables_dir
 #'     )
-#' 
+#'
 #'     asar::create_figures_doc(
 #'       subdir = figures_tables_dir,
 #'       figures_dir = figures_tables_dir
 #'     )
-#' 
+#'
 #'     tab_doc_name <- list.files(figures_tables_dir)[grepl("_tables.qmd", list.files(figures_tables_dir))]
 #'     tab_doc <- readLines(fs::path(figures_tables_dir, tab_doc_name))
-#' 
+#'
 #'     fig_doc_name <- list.files(figures_tables_dir)[grepl("_figures.qmd", list.files(figures_tables_dir))]
 #'     fig_doc <- readLines(fs::path(figures_tables_dir, fig_doc_name))
-#' 
+#'
 #'     tabs_figs_text <- c(
 #'       tab_doc,
 #'       fig_doc
 #'     )
-#' 
+#'
 #'     yaml_text <-
 #'       "---
 #' title: 'All Tables & Figures'
@@ -81,38 +81,38 @@
 #'     embed-resources: true
 #' ---
 #' "
-#' 
+#'
 #'     new_html_qmd <- c(yaml_text, tabs_figs_text)
-#' 
+#'
 #'     writeLines(
 #'       new_html_qmd,
 #'       fs::path(figures_tables_dir, "all_tables_figures.qmd")
 #'     )
-#' 
+#'
 #'     withr::with_dir(
 #'       figures_tables_dir,
 #'       quarto::quarto_render(
 #'         input = fs::path(figures_tables_dir, "all_tables_figures.qmd"),
 #'         output_file = fs::path("all_tables_figures.html")
 #'       )
 #'     )
-#' 
+#'
 #'     file.rename(
 #'       from = fs::path(figures_tables_dir, "all_tables_figures.html"),
 #'       to = fs::path(
 #'         doc_path,
 #'         "all_tables_figures.html"
 #'       )
 #'     )
-#' 
+#'
 #'     file.rename(
 #'       from = fs::path(figures_tables_dir, "all_tables_figures.qmd"),
 #'       to = fs::path(
 #'         doc_path,
 #'         "all_tables_figures.qmd"
 #'       )
 #'     )
-#' 
+#'
 #'     cli::cli_alert_success("Generated html and qmd with all tables and figures", wrap = TRUE)
 #'     cli::cli_alert_info("Overwrote previous html and qmd")
 #'   } else {

R/plot_biomass.R

@@ -203,26 +203,38 @@ plot_biomass <- function(
     B.ref.pt <- as.character(ref_line)
     B.units <- as.character(unit_label)
 
-    B.start.year <- calc_kqs(returned_kq = "B.start.year",
-                             prepared_data = prepared_data)
-    B.end.year <- calc_kqs(returned_kq = "B.end.year", 
-                           prepared_data = prepared_data)
-    B.terminal.year <- calc_kqs(returned_kq = "B.terminal.year",
-                                dat = dat,
-                                relative = relative,
-                                module = selected_module)
-    B.terminal.est <- calc_kqs(returned_kq = "B.terminal.est",
-                               dat = dat,
-                               relative = relative,
-                               module = selected_module)
-    B.terminal.min <- calc_kqs(returned_kq = "B.terminal.min",
-                               dat = dat,
-                               relative = relative,
-                               module = selected_module)
-    B.terminal.max <- calc_kqs(returned_kq = "B.terminal.max",
-                               dat = dat,
-                               relative = relative,
-                               module = selected_module)
+    B.start.year <- calc_kqs(
+      returned_kq = "B.start.year",
+      prepared_data = prepared_data
+    )
+    B.end.year <- calc_kqs(
+      returned_kq = "B.end.year",
+      prepared_data = prepared_data
+    )
+    B.terminal.year <- calc_kqs(
+      returned_kq = "B.terminal.year",
+      dat = dat,
+      relative = relative,
+      module = selected_module
+    )
+    B.terminal.est <- calc_kqs(
+      returned_kq = "B.terminal.est",
+      dat = dat,
+      relative = relative,
+      module = selected_module
+    )
+    B.terminal.min <- calc_kqs(
+      returned_kq = "B.terminal.min",
+      dat = dat,
+      relative = relative,
+      module = selected_module
+    )
+    B.terminal.max <- calc_kqs(
+      returned_kq = "B.terminal.max",
+      dat = dat,
+      relative = relative,
+      module = selected_module
+    )
 
     # SS3, FIMS
     if ("spawning_biomass_msy" %in% dat$label) {
@@ -242,13 +254,19 @@ plot_biomass <- function(
       B.msy.max <- NA
       # BAM
     } else if ("bmsy" %in% dat$label) {
-      B.msy <- calc_kqs(returned_kq = "B.msy", 
-                        dat = dat)
-      B.msy.min <- calc_kqs(returned_kq = "B.msy.min", 
-                            dat = dat)
-      B.msy.max <- calc_kqs(returned_kq = "B.msy.max",
-                            dat = dat)
-    # Rceattle
+      B.msy <- calc_kqs(
+        returned_kq = "B.msy",
+        dat = dat
+      )
+      B.msy.min <- calc_kqs(
+        returned_kq = "B.msy.min",
+        dat = dat
+      )
+      B.msy.max <- calc_kqs(
+        returned_kq = "B.msy.max",
+        dat = dat
+      )
+      # Rceattle
     } else {
       B.msy <- NA
       B.msy.min <- NA

R/plot_fishing_mortality.R

@@ -116,31 +116,48 @@ plot_fishing_mortality <- function(
     F.start.year <- min(prepared_data$year)
     F.end.year <- max(prepared_data$year)
 
-    F.terminal.year <- calc_kqs(returned_kq = "F.terminal.year",
+    F.terminal.year <- calc_kqs(
+      returned_kq = "F.terminal.year",
       dat = dat,
       module = selected_module
     )
-
-    F.target <- calc_kqs(returned_kq = "F.target",
-                         dat = dat)
-    F.limit <- calc_kqs(returned_kq = "F.limit",
-                        dat = dat)
-    F.terminal.est <- calc_kqs(returned_kq = "F.terminal.est",
-                        dat = dat,
-                        module = selected_module)
-    F.terminal.min <- calc_kqs(returned_kq = "F.terminal.min",
-                               dat = dat,
-                               module = selected_module)
-    F.terminal.max <- calc_kqs(returned_kq = "F.terminal.max",
-                               dat = dat,
-                               module = selected_module)
-    F.MSY.terminal <- calc_kqs(returned_kq = "F.MSY.terminal",
-                               dat = dat)
-    F.MSY.terminal.max <- calc_kqs(returned_kq = "F.MSY.terminal.max",
-                               dat = dat)
-    F.MSY.terminal.min <- calc_kqs(returned_kq = "F.MSY.terminal.min",
-                               dat = dat)
-
+
+    F.target <- calc_kqs(
+      returned_kq = "F.target",
+      dat = dat
+    )
+    F.limit <- calc_kqs(
+      returned_kq = "F.limit",
+      dat = dat
+    )
+    F.terminal.est <- calc_kqs(
+      returned_kq = "F.terminal.est",
+      dat = dat,
+      module = selected_module
+    )
+    F.terminal.min <- calc_kqs(
+      returned_kq = "F.terminal.min",
+      dat = dat,
+      module = selected_module
+    )
+    F.terminal.max <- calc_kqs(
+      returned_kq = "F.terminal.max",
+      dat = dat,
+      module = selected_module
+    )
+    F.MSY.terminal <- calc_kqs(
+      returned_kq = "F.MSY.terminal",
+      dat = dat
+    )
+    F.MSY.terminal.max <- calc_kqs(
+      returned_kq = "F.MSY.terminal.max",
+      dat = dat
+    )
+    F.MSY.terminal.min <- calc_kqs(
+      returned_kq = "F.MSY.terminal.min",
+      dat = dat
+    )
+
     export_kqs(
       F.ref.pt,
       F.start.year,