Merge branch 'main' of https://github.com/Schiano-NOAA/ASAR

DESCRIPTION

@@ -4,13 +4,10 @@ Version: 0.0.0.9000
 Authors@R: 
     person("Samantha", "Schiano", , "samantha.schiano@noaa.gov", role = c("aut", "cre"),
            comment = c(ORCID = "0009-0003-3744-6428"))
-Description: Build a full or update stock assessment report for any stock 
-             assessment model. Parameterization allows the user to call a 
-             template based on their regional science center, species, area, ect.
+Description: Build a full or update stock assessment report for any stock
+    assessment model. Parameterization allows the user to call a template
+    based on their regional science center, species, area, ect.
 License: MIT + file LICENSE
-Encoding: UTF-8
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
 Imports: 
     dplyr,
     flextable,
@@ -22,3 +19,6 @@ Imports:
     openxlsx,
     purrr,
     readr
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.1

R/add_section.R

@@ -20,28 +20,25 @@
 #' @export
 #'
 #' @examples add_section(title = "Ecosystem Considerations", location = "after-discussion")
-
 add_section <- function(
     title = NULL,
     location = NULL,
-    multi = FALSE
-){
+    multi = FALSE) {
   # Location options
-    # before-section
-    # after-section
-    # in-section (will always apend to the end of the section)
+  # before-section
+  # after-section
+  # in-section (will always apend to the end of the section)
   section_name <- forstringr::str_extract_part(location, "-", before = FALSE)
 
-  if(grepl("before-", location)){
+  if (grepl("before-", location)) {
 
   }
 
-  if(grepl("in-", location)){
+  if (grepl("in-", location)) {
 
   }
 
-  if(grepl("after-", location)){
+  if (grepl("after-", location)) {
 
   }
-
 }

R/chunkr.R

@@ -19,18 +19,19 @@ chunkr <- function(
     warnings = "false",
     eval = "true",
     add_option = FALSE,
-    chunk_op = NULL){
+    chunk_op = NULL) {
   chunk <- paste0(
     "```{r} \n",
     # Add output options
     "#| echo: ", echo, " \n",
     "#| warning: ", warnings, " \n",
-    "#| eval: ", eval, " \n")
-    if(add_option==TRUE){
-      for (i in 1:length(chunk_op)) {
-        chunk <- paste0(chunk, "#| ", chunk_op[i], " \n")
-      }
+    "#| eval: ", eval, " \n"
+  )
+  if (add_option == TRUE) {
+    for (i in 1:length(chunk_op)) {
+      chunk <- paste0(chunk, "#| ", chunk_op[i], " \n")
     }
-    chunk <- paste0(chunk, x, "\n", "``` \n")
-    return(chunk)
+  }
+  chunk <- paste0(chunk, x, "\n", "``` \n")
+  return(chunk)
 }

R/convert_output.R

@@ -14,32 +14,27 @@
 #'         adapt results among regional assessments.
 #'
 #' @examples
-#' convert_output(output.file = "CumReport.sso", outdir = "~", model = 'ss', file.format = 'multi', multi.file = FALSE)
+#' convert_output(output.file = "CumReport.sso", outdir = "~", model = "ss", file.format = "multi", multi.file = FALSE)
 #'
 #' @export
 #'
 convert_output <- function(
     output.file = NULL,
     outdir = NULL,
-    model = NULL){
-
-  if(model=="ss"){
+    model = NULL) {
+  if (model == "ss") {
     # Fxn adapted from r4ss::SS_output
-
   }
 
-  if(model=='bam'){
-      dat <- dget(output.file)
+  if (model == "bam") {
+    dat <- dget(output.file)
   }
 
-  if(model=='asap'){
-
+  if (model == "asap") {
     # This is how Bai read the ASAP output
     # asap_output conversion written by Bai Li
-    asap_output <- dget(file.path(casedir, "output", subdir, paste("s", keep_sim_id[om_sim], sep=""), "asap3.rdat"))
-    setwd(file.path(casedir, "output", subdir, paste("s", keep_sim_id[om_sim], sep="")))
+    asap_output <- dget(file.path(casedir, "output", subdir, paste("s", keep_sim_id[om_sim], sep = ""), "asap3.rdat"))
+    setwd(file.path(casedir, "output", subdir, paste("s", keep_sim_id[om_sim], sep = "")))
     asap_std <- readRep("asap3", suffix = ".std")
-
   }
-
 }

R/create_style_css.R

@@ -1,18 +1,17 @@
 create_styles_css <- function(
     species = NULL,
-    savedir = NULL
-){
-  #Add species image to title
+    savedir = NULL) {
+  # Add species image to title
   spp_name <- sub(" ", "_", species)
-  spp_image <- list.files(path = here::here('inst', 'resources', 'spp_img'), pattern = spp_name)
+  spp_image <- list.files(path = here::here("inst", "resources", "spp_img"), pattern = spp_name)
   styles_css <- paste(
     ".quarto-title-block .quarto-title-banner {", "\n",
-      "  ", "background-image: ", spp_image, ";", "\n",
-      "  ", "background-size: 300px;", "\n",
-      "  ", "background-position: left;", "\n",
-      "  ", "background-repeat: no-repeat;", "\n",
-      "  ", "padding-left: 10px;", "\n",
-      "  ", "background-origin: content-box;", "\n",
+    "  ", "background-image: ", spp_image, ";", "\n",
+    "  ", "background-size: 300px;", "\n",
+    "  ", "background-position: left;", "\n",
+    "  ", "background-repeat: no-repeat;", "\n",
+    "  ", "padding-left: 10px;", "\n",
+    "  ", "background-origin: content-box;", "\n",
     "}", "\n"
   )