Style code and document

DESCRIPTION

@@ -61,10 +61,10 @@ Suggests:
     r4ss,
     rmarkdown,
     testthat (>= 3.0.0)
-Remotes:
-    r4ss/r4ss
 VignetteBuilder: 
     knitr
+Remotes:
+    r4ss/r4ss
 Config/roxygen2/version: 8.1.1
 Config/testthat/edition: 3
 Config/testthat/parallel: true

R/add_caption_alt_text.R

@@ -4,25 +4,25 @@
 #' caption, and alt_text for a figure or table not present in stockplotr.
 #'
 #' @inheritParams create_rda
-#' 
-#' @param topic_label String. Figure/table label. For automated matching in 
+#'
+#' @param topic_label String. Figure/table label. For automated matching in
 #' asar-based report, it must match the label in your plot's chunk options, MINUS
-#' the "fig-" or "tab-". For example, the label "custom_table1" would match up 
+#' the "fig-" or "tab-". For example, the label "custom_table1" would match up
 #' properly with the "tbl-custom_table1" code chunk label.
-#' 
+#'
 #' @param caption String. Figure/table caption.
-#' 
+#'
 #' @param alt_text String. Figure alternative text. Unnecessary for text-based tables.
-#' 
+#'
 #' Default: ""
-#' 
+#'
 #' @param dir Path. Path to the existing captions_alt_text.csv file that will be
 #' updated with the new caption and alt text.
 #'
 #' Default: file.path(getwd(), "captions_alt_text.csv")
 #'
 #' @export
-#' 
+#'
 #' @examples \dontrun{
 #' add_caption_alt_text(
 #'   topic_label = "my_topic",
@@ -38,22 +38,22 @@ add_caption_alt_text <- function(topic_label,
                                  alt_text = "",
                                  dir = file.path(getwd(), "captions_alt_text.csv")) {
   captions_alt_text <- utils::read.csv(dir)
-  
+
   if (fig_or_table == tolower("figure") & alt_text == "") {
     cli::cli_alert_warning("No alt text provided for figure {topic_label}.")
     cli::cli_alert_warning("Figure alt text is necessary to pass asar report accessibility checks.")
     cli::cli_alert_info("Learn how to write descriptive alt text with the asar 'Increasing Report Accessibility' vignette: {.url https://nmfs-ost.github.io/asar/articles/accessibility_guide.html#alternative-text}.")
   }
-  
+
   new_row <- data.frame(
     label = topic_label,
     type = fig_or_table,
     caption = caption,
     alt_text = alt_text
   )
-  
+
   captions_alt_text <- rbind(captions_alt_text, new_row)
-  
+
   utils::write.csv(
     captions_alt_text,
     file = dir,

R/conout_bam.R

@@ -1,5 +1,5 @@
 #' Code to convert BAM output to standard framework.
-#' 
+#'
 #' Does not change naming conventions.
 #'
 #' @inheritParams convert_output
@@ -8,13 +8,13 @@
 #'
 #' @returns Reshaped data frame.
 conout_bam <- function(
-    file,
-    out_new,
-    fleet_names = NULL
+  file,
+  out_new,
+  fleet_names = NULL
 ) {
   # Extract values from BAM output - model file after following ADMB2R
   dat <- dget(file)
-  
+
   # Find fleet names
   if (is.null(fleet_names)) {
     # Extract names from indices
@@ -24,13 +24,13 @@ conout_bam <- function(
     # Extract names from landings
     landings <- dat$t.series |>
       dplyr::select(dplyr::contains("L.") & dplyr::contains(".ob") |
-                      dplyr::contains("D.") & dplyr::contains(".ob"))
+        dplyr::contains("D.") & dplyr::contains(".ob"))
     fleets_land <- stringr::str_extract(as.vector(colnames(landings)), "(?<=L\\.)\\w+(?=\\.ob)")
     fleets_disc <- stringr::str_extract(as.vector(colnames(landings)), "(?<=D\\.)\\w+(?=\\.ob)")
     # Extract names from lof F dev
     parm <- dat$parm.tvec |>
       dplyr::select(dplyr::contains("log.F.dev.") |
-                      dplyr::contains("log.F.dev.") & dplyr::contains(".D"))
+        dplyr::contains("log.F.dev.") & dplyr::contains(".D"))
     # fleets_parm_D <- stringr::str_extract(as.vector(colnames(parm)), "(?<=log\\.F\\.dev\\.)\\w+(?=\\.D)")
     fleets_parm <- stringr::str_extract(as.vector(colnames(parm)), "(?<=log\\.F\\.dev\\.)\\w+")
     fleets <- unique(tolower(c(fleets_ind, fleets_land, fleets_disc, fleets_parm)))
@@ -48,13 +48,13 @@ conout_bam <- function(
   cli::cli_alert_info("{fleet_names}")
   # Create list for morphed dfs to go into (for rbind later)
   out_list <- list()
-  
+
   factors <- c("year", "fleet", "fleet_name", "age", "sex", "area", "seas", "season", "time", "era", "subseas", "subseason", "platoon", "platoo", "growth_pattern", "gp", "nsim", "age_a")
   errors <- c("StdDev", "sd", "se", "SE", "cv", "CV", "stddev")
   units <- c("mt", "lbs", "eggs")
   # argument for function when model == BAM
   # fleet_names <- c("cl", "cL","cp","mrip","ct", "hb", "HB", "comm","Mbft","CVID")
-  
+
   ##### BAM loop ----
   # Extract data from list fit to output df
   # Loop over all items to output each object/transform
@@ -97,7 +97,7 @@ conout_bam <- function(
               df <- df |>
                 dplyr::rename_with(
                   ~ ifelse(max(as.numeric(df$year)) < 50,
-                           c("age_a"), c("year")
+                    c("age_a"), c("year")
                   ),
                   year
                 )
@@ -127,7 +127,7 @@ conout_bam <- function(
                     TRUE ~ names(extract[[1]][i])
                   )
                   # label_init = names(extract[[1]][i]),
-                  
+
                   # label = dplyr::case_when(
                   #   is.na(fleet) ~ names(extract[[1]][i]),
                   #   TRUE ~ stringr::str_replace(tolower(label), paste(".", fleet_names, sep = "", collapse = "|"), "")
@@ -505,7 +505,7 @@ conout_bam <- function(
       cli::cli_alert_warning(paste(names(extract), " not compatible.", sep = ""))
     } # close if statement
   } # close loop over objects listed in dat file
-  
+
   # Place out_list into a single data frame
   # VIRG, INIT, TIME, FORE
   out_new <- Reduce(rbind, out_list) |>
@@ -515,15 +515,15 @@ conout_bam <- function(
       label = tolower(label)
     )
   # if (model == "bam") {
-    out_new <- dplyr::mutate(
-      out_new,
-      era = dplyr::case_when(
-        year < dat$parms$styr ~ "init",
-        year >= dat$parms$styr & year <= dat$parms$endyr ~ "time",
-        year > dat$parms$endyr ~ "fore",
-        TRUE ~ NA
-      )
+  out_new <- dplyr::mutate(
+    out_new,
+    era = dplyr::case_when(
+      year < dat$parms$styr ~ "init",
+      year >= dat$parms$styr & year <= dat$parms$endyr ~ "time",
+      year > dat$parms$endyr ~ "fore",
+      TRUE ~ NA
     )
+  )
   # }
   return(out_new)
 }