Release for v0.3

.Rbuildignore

@@ -6,3 +6,5 @@
 ^docs$
 ^pkgdown$
 ^\.github$
+^doc$
+^Meta$

.gitignore

@@ -3,9 +3,15 @@
 .RData
 .Ruserdata
 *.Rproj
-
 .DS_Store
 /.quarto/
 /_site/
 docs
 inst/doc
+Report.sso
+petrale_convert_output.csv
+stock_assessment_reports
+/doc/
+/Meta/
+captions_alt_text.csv
+converted_file_1126.csv

DESCRIPTION

@@ -1,9 +1,35 @@
 Package: asar
 Title: Build NOAA Stock Assessment Report
 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"))
+Authors@R: c(
+      person(
+            "Samantha", "Schiano", 
+            email = "samantha.schiano@noaa.gov", 
+            role = c("aut", "cre"),
+            comment = c(ORCID = "0009-0003-3744-6428")
+            ),
+      person(
+            "Sophie", "Breitbart",
+             email = "sophie.breitbart@noaa.gov", 
+             role = c("aut", "ctb"),
+             comment = c(ORCID = "0000-0001-9641-9786")
+             ),
+      person(
+            "Steve", "Saul",
+             email = "steven.saul@noaa.gov",
+             role = c("aut", "ctb")
+             ),
+      person("Kelli", "Johnson",
+             email = "kelli.johnson@noaa.gov", 
+             role = c("ctb"),
+             comment = c(ORCID = "0000-0002-5149-451X")
+             ),
+      person(
+             "Bai", "Li",
+             email = "bai.li@noaa.gov", 
+             role = c("ctb"),
+             comment = c(ORCID = "0000-0002-8249-1442")
+             ))
 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.
@@ -15,13 +41,13 @@ Imports:
     forstringr,
     fs,
     ggplot2,
+    glue,
     gridExtra,
-    gt,
     naniar,
+    nmfspalette,
     officer,
     openxlsx,
     prodlim,
-    satf,
     stats,
     stringr,
     svDialogs,
@@ -30,19 +56,27 @@ Imports:
     tidyselect,
     utils
 Suggests: 
+    gt,
+    kableExtra,
     knitr,
     parallel,
     r4ss,
     rmarkdown,
+    satf,
     snowfall,
     testthat (>= 3.0.0)
 VignetteBuilder: 
     knitr
 Remotes:
     nmfs-ost/satf,
-    r4ss/r4ss
+    r4ss/r4ss,
+    nmfs-fish-tools/nmfspalette
 Config/testthat/edition: 3
 Config/testthat/parallel: true
 Encoding: UTF-8
+Language: en-US
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
+Depends: 
+    R (>= 2.10)
+LazyData: true

R/add_base_section.R

@@ -1,22 +1,22 @@
 #' Add selected sections to outline
 #'
-#' @param x inherited 'custom_sections' parameter from create_template
+#' @inheritParams create_template
 #'
 #' @return Call and copy the sections in the package templates to create an outline for a stock assessment
 #' @export
 #'
-#' @examples add_base_section(c("executive summary", "modeling approach", "results"))
-add_base_section <- function(x) {
-  sec_sel <- gsub(" ", "_", tolower(gsub("(.)([A-Z])", "\\1 \\2", x)))
+#' @examples add_base_section(c("executive summary", "assessment", "results"))
+add_base_section <- function(custom_sections) {
+  sec_sel <- gsub(" ", "_", tolower(gsub("(.)([A-Z])", "\\1 \\2", custom_sections)))
   section_list <- list()
   for (i in 1:length(sec_sel)) {
     sec_file <- grep(
-      x = list.files(system.file("templates", "skeleton", package = "asar")),
+      list.files(system.file("templates", "skeleton", package = "asar")),
       pattern = sec_sel[i],
       value = TRUE
     )
     if (identical(sec_file, character(0))) stop("One or more section name(s) does not exist. Please check the spelling or if you are tring to add a section that is not in the default template, please use parameter 'custom_sections' and refer to documentation. To check which sections are in the base template please run list.files(system.file('templates', 'skeleton', package = 'ASAR')) in your console")
-    sec_file -> section_list[i]
+    sec_file -> section_list[[i]]
   }
-  section_list
+  as.list(unlist(section_list))
 }

R/add_child.R

@@ -1,7 +1,7 @@
 #' Write R Chunk to Add Child Document
 #'
-#' @param x section .qmd file to add into the template, options for sections are in the 'skeleton' folder; only select XX_section.qmd files and not a, b, c... subfiles
-#' @param label description for the child document being added (short - one/two words max)
+#' @param x An additional section to add into the template. Options for additional sections are in the 'skeleton' folder. Appropriate files are .qmd files and are formatted as such: XX_section.qmd (i.e., not a, b, c... subfiles).
+#' @param label Description of the child document being added. It should be short- one or two words, maximum.
 #'
 #' @return Formatting R chunk for child document to add section into the template/skeleton.
 #'         Utilize the cat() function to implement into readable text.

R/add_chunk.R

@@ -1,12 +1,16 @@
 #' Write R chunk to template
 #'
-#' @param x content within the R chunk to be written contained inside quotation marks
-#' @param label What to name the chunk in the 'label:' section of the r code chunk; should be in snakecase
-#' @param echo repeat code into the document; default is false
-#' @param warnings Report warnings into console during render? Default is false
-#' @param eval Evaluate the chunk? default is true
-#' @param add_option TRUE/FALSE add additional chunk options? default is FALSE
-#' @param chunk_op list of chunk options to add; example: c("output: true", "error: false)
+#' @param x Content to be written within the R chunk. Wrap in quotation marks ("").
+#' @param label The name of the chunk in the 'label:' section of the R code chunk.
+#'  This should be in snakecase (i.e., in which words are written in lowercase and
+#'   connected by underscores).
+#' @param echo TRUE/FALSE; Option to repeat code in the document. Default is false.
+#' @param warnings TRUE/FALSE; Option to report warnings in the console during render.
+#'  Default is false.
+#' @param eval TRUE/FALSE; Option to evaluate the chunk. Default is true.
+#' @param add_option TRUE/FALSE; Option to add additional chunk options. Default is false.
+#' @param chunk_op List of chunk options to add. For example: c("output: true", "error: false)
+#' @param rmark_op List of chunk options to add after indicating the language of the chunk as used in Rmarkdown.
 #'
 #' @return Write an additional R chunk into the template using this function.
 #'         The code can be written as usual, just remember to put it entirely
@@ -21,9 +25,10 @@ add_chunk <- function(
     eval = "true",
     label = NULL,
     add_option = FALSE,
-    chunk_op = NULL) {
+    chunk_op = NULL,
+    rmark_op = NULL) {
   chunk <- paste0(
-    "```{r} \n"
+    "```{r", ifelse(add_option, paste0(c("",rmark_op), collapse = ", "), ""), "} \n"
   )
   if (!is.null(label)) {
     chunk <- paste0(
@@ -36,12 +41,13 @@ add_chunk <- function(
     chunk,
     "#| echo: ", echo, " \n",
     "#| warning: ", warnings, " \n",
-    "#| eval: ", eval, " \n"
+    "#| eval: ", eval, " \n",
+    ifelse(add_option & !is.null(chunk_op), paste0(paste0("#| ", chunk_op, collapse = " \n"), "\n"), "")
   )
-  if (add_option == TRUE) {
-    for (i in 1:length(chunk_op)) {
-      chunk <- paste0(chunk, "#| ", chunk_op[i], " \n")
-    }
-  }
+  # if (add_option == TRUE) {
+  #   for (i in 1:length(chunk_op)) {
+  #     chunk <- paste0(chunk, "#| ", chunk_op[i], " \n")
+  #   }
+  # }
   paste0(chunk, x, "\n", "``` \n")
 }

R/add_section.R

@@ -1,55 +1,45 @@
-#' Add New Section to Template
+#' Add New Section or Subsection to Template
 #'
-#' @param sec_names section_names of the subsection. Please keep this short as the template
-#'                  will be created as a quarto document into your skeleton and saved
-#'                  later for reference. More than one section can be added. Please
-#'                  make a list if this is desired.
-#' @param location Where the section will be added in the generic template using
-#'                 the notation of 'placement-section'. Example would be 'in-introduction'
-#'                 where the new content would be created as a child document
-#'                 and added into the 02_introduction.qmd. There is an option to
-#'                 add more than one section. Add the location as a list
-#'                 corresponding to the order of section names listed in the
-#'                 'title' parameter
-#' @param other_sections List of other sections that the added sections will be combined with (if not NULL)
-#' @param subdir directory where the new sections will be saved - in the create_template
-#'               fxn this defaults to the location where the template is saved
+#' @inheritParams create_template
+#' @param subdir Directory where the new sections will be saved. In the
+#' create_template function, this defaults to the location where the
+#' template is saved.
 #'
-#' @return Add an additional section to the report template if it is not already
-#'         in the default template. This provides the option to adding it as a
-#'         subsection either before or after it or within the subsection itself
-#'         as a child document.
+#' @return Add an additional section or subsection to the report template
+#' if it is not already present in the default template. This provides
+#' the option to add it as a section before or after an existing section,
+#' or within a section as a child document.
 #' @export
 #'
 #' @examples add_section(
-#'   sec_names = "Ecosystem Considerations", location = "after-discussion",
-#'   other_sections = c("introduction.qmd", "model.qmd", "results.qmd", "discussion.qmd"),
+#'   new_section = "Ecosystem Considerations", section_location = "after-discussion",
+#'   custom_sections = c("introduction.qmd", "model.qmd", "results.qmd", "discussion.qmd"),
 #'   subdir = tempdir()
 #' )
 add_section <- function(
-    sec_names = NULL,
-    location = NULL,
-    other_sections = NULL,
+    new_section = NULL,
+    section_location = NULL,
+    custom_sections = NULL,
     subdir = NULL) {
   # Location options
   # before-section
   # after-section
   # in-section (will always append to the end of the section)
-  for (i in 1:length(sec_names)) {
-    section_i_name <- paste0(gsub(" ", "_", sec_names[i]), ".qmd")
-    local_section <- forstringr::str_extract_part(location[i], "-", before = FALSE)
-    local_section_prev <- forstringr::str_extract_part(location[i - 1], "-", before = FALSE)
+  for (i in 1:length(new_section)) {
+    section_i_name <- paste0(gsub(" ", "_", tolower(new_section[i])), ".qmd")
+    local_section <- forstringr::str_extract_part(section_location[i], "-", before = FALSE)
+    local_section_prev <- forstringr::str_extract_part(section_location[i - 1], "-", before = FALSE)
 
-    if (any("TRUE" %in% grepl("-", location))) {
-      locality <- forstringr::str_extract_part(location[i], "-", before = TRUE)
-      locality_prev <- forstringr::str_extract_part(location[i - 1], "-", before = TRUE)
-    } else if (any("TRUE" %in% grepl(" ", location))) {
-      locality <- forstringr::str_extract_part(location[i], " ", before = TRUE)
-      locality_prev <- forstringr::str_extract_part(location[i - 1], "-", before = TRUE)
+    if (any("TRUE" %in% grepl("-", section_location))) {
+      locality <- forstringr::str_extract_part(section_location[i], "-", before = TRUE)
+      locality_prev <- forstringr::str_extract_part(section_location[i - 1], "-", before = TRUE)
+    } else if (any("TRUE" %in% grepl(" ", section_location))) {
+      locality <- forstringr::str_extract_part(section_location[i], " ", before = TRUE)
+      locality_prev <- forstringr::str_extract_part(section_location[i - 1], "-", before = TRUE)
     }
 
     section_i <- paste0(
-      "## ", stringr::str_to_title(sub("_", " ", sec_names[i])), "\n",
+      "## ", stringr::str_to_title(sub("_", " ", tolower(new_section[i]))), "\n",
       "\n",
       "[Insert text here]", "\n",
       "\n",
@@ -58,18 +48,18 @@ add_section <- function(
     utils::capture.output(cat(section_i), file = paste0(subdir, "/", section_i_name), append = FALSE)
 
     if (locality == "before") {
-      other_sections <- append(other_sections, section_i_name, after = (which(grepl(local_section, other_sections)) - 1))
+      custom_sections <- append(custom_sections, section_i_name, after = (which(grepl(local_section, custom_sections)) - 1))
     } else if (locality == "after") {
       if (locality %in% locality_prev & local_section %in% local_section_prev) {
-        other_sections <- append(other_sections, section_i_name, after = which(grepl(gsub(" ", "_", sec_names[i - 1]), other_sections)))
+        custom_sections <- append(custom_sections, section_i_name, after = which(grepl(gsub(" ", "_", tolower(new_section[i - 1])), custom_sections)))
       } else {
-        other_sections <- append(other_sections, section_i_name, after = which(grepl(local_section, other_sections)))
+        custom_sections <- append(custom_sections, section_i_name, after = max(which(grepl(local_section, custom_sections))))
       }
     } else if (locality == "in") {
       stop("No available option for adding a new section 'in' another quarto document.", call. = FALSE)
     } else {
       stop("Invalid selection for placement of section. Please name the follow the format 'placement-section_name' for adding a new section.")
     }
   }
-  other_sections
+  custom_sections
 }