Dev (#456)

* Small change to make new dev branch

* Remove Regional Workflows vignette

* Replace bib entries from sa4ss with updated entries from https://github.com/pfmc-assessments/yellowtail_2025/blob/main/report/yellowtail.bib, while keeping the asar and NEFSC references

* Revert "Replace bib entries from sa4ss with updated entries from https://github.com/pfmc-assessments/yellowtail_2025/blob/main/report/yellowtail.bib, while keeping the asar and NEFSC references"

This reverts commit 2952d6f.

* Shorten glossary labels by subbing FSC acronyms in for full names (#448)

* Shorten glossary labels by subbing FSC acronyms in for full names

* Add guidance to glossary about how to search for survey names

* Add nefsc glossary entries (#454)

* Update FAQs vignette with questions about making reports without model results converted with stockplotr

* Add entries from CRDabbreviatedlocales.tex

* Add terms from NEFSC's glossary as per #438

* Vignettes to articles (#453)

* Replace old bib file entries with those in https://github.com/pfmc-assessments/yellowtail_2025/blob/main/report/yellowtail.bib, except for asar citation and NEFSC's citations (as per this comment: pfmc-assessments/yellowtail_2025#12 (comment)) (#449)

* Replace bib entries from sa4ss with updated entries from https://github.com/pfmc-assessments/yellowtail_2025/blob/main/report/yellowtail.bib, while keeping the asar and NEFSC references

* Create quarto-based articles for FAQ and custom figures/tables vignettes, and erase those vignettes, to allow for better navigability on website, as per #316

* Create quarto-based articles for example reports and alt workflows vignettes, and erase those vignettes

* Remove unnecessary article-related files made by rendering locally

* update WORDLIST

* adjust create_yaml example to remove warning

* Update skeleton labels (#459)

* Update FAQs vignette with questions about making reports without model results converted with stockplotr

* remove faqs.Rmd

* Change skeleton chunk labels for clarity: doc_parameters → R_parameters and output_and_quantities → preamble

* Update readme with project/milestone status (#458)

* Update FAQs vignette with questions about making reports without model results converted with stockplotr

* remove faqs.Rmd

* Update readme with project/milestone status

* remove r4ss as dependency

* add bootstrap 5 per error rec

---------

Co-authored-by: sbreitbart-NOAA <sophie.breitbart@noaa.gov>

Author: Schiano-NOAA

.Rbuildignore

@@ -14,3 +14,6 @@
 ^\.octocov\.yml$
 ^\.devcontainer$
 ^CODE_OF_CONDUCT\.md$
+^vignettes/articles/\.quarto$
+^vignettes/articles/*_files$
+^vignettes/articles$

.gitignore

@@ -20,3 +20,4 @@ Meta
 report
 spp_conout.csv
 ASAR.Rproj
+**/.quarto/

DESCRIPTION

@@ -54,12 +54,12 @@ Suggests:
 VignetteBuilder: 
     knitr
 Remotes:
-    nmfs-ost/stockplotr,
-    r4ss/r4ss
+    nmfs-ost/stockplotr
 Config/testthat/edition: 3
 Config/testthat/parallel: false
 Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.3
+Config/Needs/website: quarto

R/create_template.R

@@ -721,8 +721,8 @@ create_template <- function(
 
     ##### Params chunk ----
     if (rerender_skeleton) {
-      params_chunk_start <- grep("doc_parameters", prev_skeleton) - 1
-      if (!any(grepl("doc_parameters", prev_skeleton)) & parameters) {
+      params_chunk_start <- grep("R_parameters", prev_skeleton) - 1
+      if (!any(grepl("R_parameters", prev_skeleton)) & parameters) {
         params_chunk <- add_chunk(
           paste0(
             "# Parameters \n",
@@ -744,7 +744,7 @@ create_template <- function(
               )
             }
           ),
-          label = "doc_parameters"
+          label = "R_parameters"
         )
       } else if (parameters) {
         params_chunk_end <- grep("```", prev_skeleton)[which(grep("```", prev_skeleton) > params_chunk_start)][1]
@@ -790,7 +790,7 @@ create_template <- function(
             )
           }
         ),
-        label = "doc_parameters"
+        label = "R_parameters"
       )
     }
     params_chunk <- add_chunk(
@@ -814,7 +814,7 @@ create_template <- function(
           )
         }
       ),
-      label = "doc_parameters"
+      label = "R_parameters"
     )
 
     ##### Preamble ----
@@ -884,7 +884,7 @@ create_template <- function(
         "h # steepness\n",
         "R0 # recruitment\n"
       ),
-      label = "output_and_quantities",
+      label = "preamble",
       chunk_option = c("warning: false", ifelse(is.null(model_results), "eval: false", "eval: true"), "include: false")
     )
 
@@ -897,7 +897,7 @@ create_template <- function(
         question1 <- "n"
       }
       if (regexpr(question1, "n", ignore.case = TRUE) == 1) {
-        start_line <- grep("output_and_quantities", prev_skeleton) - 1
+        start_line <- grep("preamble", prev_skeleton) - 1
         # find next trailing "```"` in case it was edited at the end
         end_line <- grep("```", prev_skeleton)[grep("```", prev_skeleton) > start_line][1]
         # preamble <- paste(prev_skeleton[start_line:end_line], collapse = "\n")

R/create_yaml.R

@@ -23,11 +23,21 @@
 #'
 #' @examples
 #' \dontrun{
+#' my_author_list <- paste(
+#' "  - name: 'Patrick Star'",
+#' "    affiliations:",
+#' "      - name: 'NOAA Fisheries Southeast Fisheries Science Center'",
+#' "        address: '75 Virginia Beach Drive'",
+#' "        city: 'Miami'",
+#' "        state: 'FL'",
+#' "        postal-code: '33149'"
+#' sep = "\n"
+#' )
 #' create_yaml(
 #'   rerender_skeleton = FALSE,
 #'   prev_skeleton = NULL,
 #'   title = "My title",
-#'   author_list = "  - name: 'Patrick Star'\n    affiliations:\n      - name: 'NOAA Fisheries Southeast Fisheries Science Center'\n        address: '75 Virginia Beach Drive'\n        city: 'Miami'\n        state: 'FL'\n        postal-code: '33149'\n",
+#'   author_list = my_author_list,
 #'   author = c("Patrick Star" = "SEFSC"),
 #'   office = "SEFSC",
 #'   add_author = NULL,

R/export_glossary.R

@@ -52,9 +52,6 @@ export_glossary <- function() {
       Shared_mean = duplicated(meaning_lower)
     )
 
-  # min length of consolidated acronyms: ~818
-  # length(unique(acronyms$Acronym))
-
   # for a given acronym: if there is a row with an identical acronym,
   # and there is a row with an identical meaning_lower, and at least one
   # row has a definition, then keep the row with the definition
@@ -117,7 +114,8 @@ export_glossary <- function() {
       !Meaning %in% c(
         "Biomass (in either weight or other appropriate unit)",
         "Biomass at maximum sustainable yield",
-        "Biomass at MSY"
+        "Biomass at MSY",
+        "Northwest Atlantic Fisheries Organization viii"
       ),
       !Acronym %in% "BMSY (B sub MSY)"
     ) |>
@@ -142,6 +140,7 @@ export_glossary <- function() {
         "Ecosystem-based fishery management",
         "East Pacific Ocean",
         "Division of Fish and Wildlife, Northern Mariana Islands",
+        "Groundfish Assessment Review Committee",
         "A measure of the instantaneous rate of fishing mortality",
         "instantaneous rate of fishing mortality",
         "Mortality due to fishing",
@@ -220,7 +219,8 @@ export_glossary <- function() {
         "BO",
         "DAR",
         "ITA",
-        "NS#"
+        "NS#",
+        "CTLISTS"
       ),
       !(is.na(Definition) & Meaning == "Marine Recreational Fishing Statistical Survey"),
       !(is.na(Definition) & Acronym == "P*"),
@@ -243,6 +243,13 @@ export_glossary <- function() {
         "Ecological and Socioeconomic Profile",
         "Ecosystem and Socioeconomic Profile"
       )
+    ) |> # correct acronym
+    dplyr::mutate(
+      Acronym = dplyr::if_else(
+        Acronym == "CC" & Meaning == "Connecticut", 
+        "CT", 
+        Acronym
+      )
     ) |>
     dplyr::filter(!Definition %in% "An advisory committee of the PFMC made up of scientists and economists. The Magnuson-Stevens Act requires that each council maintain an SSC to assist in gathering and analyzing statistical, biological, ecological, economic, social, and other scientific information that is relevant to the management of Council fisheries.") |>
     # recreate meaning_lower after updates
@@ -326,7 +333,31 @@ export_glossary <- function() {
         "SBA",
         "Secretary",
         "SSB",
-        "STT"
+        "STT",
+        "BLSPR",
+        "BSB",
+        "EXL",
+        "Fbar5:7",
+        "Fbar7:8",
+        "FLSPR",
+        "FLXSPR",
+        "FXL",
+        "FXLMSP",
+        "FXLSPR",
+        "FXX",
+        "MNKN",
+        "MNKS",
+        "OPTUNIT",
+        "OQUNIT",
+        "PLA",
+        "Q",
+        "REDUNIT",
+        "SBpr",
+        "SBXL",
+        "SCUNIT",
+        "SPRLX",
+        "SSBpr",
+        "ssbratio"
       ),
       !(source == "PFMC" & Acronym == "ABC"),
       !(source == "SAFMC" & Acronym == "ALS"),
@@ -510,7 +541,8 @@ export_glossary <- function() {
       Meaning = ifelse(Meaning == "Optimum sustainable production, Oregon State Police", "optimum sustainable production", Meaning),
       Meaning = ifelse(Meaning == "Spawning Abundance at MSY", "spawning abundance at MSY", Meaning),
       Meaning = ifelse(Meaning == "Spawning Stock Biomass at MSY", "spawning stock biomass at MSY", Meaning),
-      Meaning = ifelse(Acronym == "R", "Programming environment for statistical processing and presentation", Meaning)
+      Meaning = ifelse(Acronym == "R", "Programming environment for statistical processing and presentation", Meaning),
+      Meaning = ifelse(Acronym == "GARM", "Groundfish Assessment Review Meeting", Meaning)
     ) |>
     # add periods to end of Definition
     dplyr::mutate(
@@ -644,7 +676,26 @@ export_glossary <- function() {
       !(Meaning == "CalCOFI_Spring" & Acronym == "CS"),
       !(Meaning == "Northern CalCOFI" & Acronym == "NC"),
       !(is.na(Definition) & Acronym == "SEAMAP"),
-      !(Meaning == "Connecticut Long Island Sound Trawl Survey" & Label == "ct lists")
+      !(Meaning == "Connecticut Long Island Sound Trawl Survey" & Label == "ct lists"),
+      !(Meaning == "autoregressive model" & Label == "ar"),
+      !(Meaning == "biomass" & Label == "bm"),
+      !(Meaning == "centimeters, fish length" & Label == "cm"),
+      !(Meaning == "fishing mortality at 50% of msy" & Label == "fl"),
+      !(Meaning == "operational assessment, biennial" & Label == "oa"),
+      !(Meaning == "Portable Document Format" & Label == "pdf"),
+      !(Meaning == "Quantitative Ecology and Socioeconomics Training" & Label == "qus"),
+      !(Meaning == "subarea (nafo)" & Label == "sa"),
+      !(Meaning == "School for Marine Science and Technology" & Label == "smast"),
+      !(Meaning == "Transboundary Resources Assessment Committee" & is.na(Definition)),
+      !(Meaning == "Univ. of Rhode Island, GSO" & Label == "uri"),
+      !(Meaning == "young of the year or age 0" & Label == "yoy"),
+      !(Label == "msyxl"),
+      !(Label == "msypr"),
+      !(Label == "msyxl"),
+      !(Label == "sbmsypr"),
+      !(Label == "ssbmsypr"),
+      !(Label == "ssbxl"),
+      !(Label == "sbxl")
     ) |>
     # add backslash to escape special characters
     # (underscores, ampersands) when rendering tex file
@@ -672,7 +723,15 @@ export_glossary <- function() {
       Label,
       "[\\(\\)]",
       "-"
-    ))
+    )) |>
+    # make labels shorter by subbing FSCs acronyms
+    dplyr::mutate(
+      Label = gsub("alaska fisheries science center", "afsc", Label, ignore.case = TRUE),
+      Label = gsub("northeast fisheries science center", "nefsc", Label, ignore.case = TRUE),
+      Label = gsub("northwest fisheries science center", "nwfsc", Label, ignore.case = TRUE),
+      Label = gsub("pacific islands fisheries science center", "pifsc", Label, ignore.case = TRUE),
+      Label = gsub("southeast fisheries science center", "sefsc", Label, ignore.case = TRUE),
+      Label = gsub("southwest fisheries science center", "swfsc", Label, ignore.case = TRUE))
 
   duplicate_acronyms <- unique_all_cleaning3 |>
     dplyr::add_count(Acronym) |>
@@ -784,6 +843,15 @@ export_glossary <- function() {
     ) |>
     dplyr::arrange(tolower(Label))
 
+  cat(paste0(
+    "% NOTE ON SURVEYS:\n",
+    "% To increase findability, surveys may have multiple entries to link informal with formal names.\n",
+    "% Specifically, there may be more than one 'label' (first curly braces entry) or 'acronym' (second curly braces entry) with the same 'long form' (third curly braces entry).\n",
+    "% If the first 'label' you find for a given survey seems too long, look for an alternative entry with the same 'long form' but a different 'label' and/or 'acronym'.\n",
+    "% For example, there are three entries for the 'long form' 'Northeast Ecosystem Monitoring (EcoMon)\\_Fall':\n\n",
+    "%     \\newacronym{ecomon fall}{ECOMON Fall}{Northeast Ecosystem Monitoring (EcoMon)\\_Fall}\n",
+    "%     \\newacronym{fall nefsc ecosystem monitoring survey}{Fall Northeast Fisheries Science Center Ecosystem Monitoring Survey}{Northeast Ecosystem Monitoring (EcoMon)\\_Fall}\n",
+    "%     \\newacronym{nemef}{NEMEF}{Northeast Ecosystem Monitoring (EcoMon)\\_Fall}\n\n"))
 
   for (i in 1:dim(tex_acs)[1]) {
     cat(
@@ -801,3 +869,4 @@ export_glossary <- function() {
   }
   sink()
 }
+

README.md

@@ -9,7 +9,7 @@ Download using the directions below and fill in `create_template.R` function wit
 the desired parameters (follow example below) to create a template Quarto document 
 to be rendered to create a stock assessment report.
 
-The goal of ASAR is to automate stock assessment reports for NOAA science centers
+The goal of `asar` is to automate stock assessment reports for NOAA science centers
 so they are reproducible and cohesive across the agency. This project intends 
 to create a streamlined workflow that allows the analyst to create a customized 
 report tailored to their needs and requirements by the SSC, council, or other 
@@ -135,6 +135,10 @@ Have you identified any suggestions for improvement, bugs, or questions? Please
 
 Thank you for helping us improve this package!
 
+## Progress, Goals, & Timeline
+
+What are we working on? When do we aim to complete it? What have we accomplished? Check out our [GitHub Project Board](https://github.com/orgs/nmfs-ost/projects/44/) and [Milestones](https://github.com/nmfs-ost/asar/milestones) to see the package development status and our goals for the next few months.
+
 ## Tips
 
 If you have additional questions, there is a helpful Q&A guide available in the 

inst/WORDLIST

@@ -1,5 +1,4 @@
 AFSC
-APA
 Arial
 BAM
 Blackspotted
@@ -10,12 +9,9 @@ CTAN
 Calibri
 Caltabellotta
 Canelón
-cjfas
 Coates
-csl
 DocumentMetadata
 Drs
-ewide
 Fabio
 Flextable
 Gertseva
@@ -40,31 +36,32 @@ Pomatomus
 Quillback
 README
 RStudio
+RTF
 Rmarkdown
 Rockfish
 Rockfishes
 Rosemond
 Rougheye
-RTF
 SBPR
 SEFSC
 SSC
 SWA
 SWFSC
 Strikethrough
-tabset
-TLDR
 TOC
 TinyTeX
 Vladlena
 asis
 bcurrent
 blockquote
+cjfas
 conf
+csl
 csv
 documentclass
 docx
 ect
+ewide
 flextable
 flextables
 frac
@@ -77,12 +74,12 @@ kobe
 labelled
 le
 modularized
-msy
 multispecies
 nmfs
 noaa
 ost
 overline
+pagebreak
 params
 petrale
 png
@@ -103,6 +100,7 @@ socio
 sso
 stockplotr
 subfiles
+tabset
 taggable
 tagpdf
 tbl