[feat] Add new template "type" for SEDAR reports

R/create_citation.R

@@ -19,10 +19,22 @@
 create_citation <- function(
   authors = NULL,
   title = "[TITLE]",
-  year = format(as.POSIXct(Sys.Date(), format = "%YYYY-%mm-%dd"), "%Y")
+  year = format(as.POSIXct(Sys.Date(), format = "%YYYY-%mm-%dd"), "%Y"),
+  type = NULL
 ) {
   # Check if authors is input - improved from previous fxn so did not fail
   if (is.null(authors) | any(authors == "")) {
+    if (tolower(type) == "sedar"){
+      citation <- paste0(
+        "{{< pagebreak >}} \n",
+        "\n",
+        "Please cite this publication as: \n",
+        "\n",
+        "SEDAR. ",
+        year, ". ",
+        title, ". SEDAR, North Charleston SC. \\pageref*{LastPage}{} pp."
+      )
+    } else {
     cli::cli_alert_warning("Authorship not defined.")
     cli::cli_alert_info("Did you forget to specify `authors`?")
     # Define default citation - needs authors editing
@@ -35,7 +47,7 @@ create_citation <- function(
       title, ". National Marine Fisheries Service, ",
       "[CITY], [STATE]. \\pageref*{LastPage}{} pp."
     )
-  } else {
+  } } else {
     # Authored by Kelli Johnson in previous PR
     author_data_frame <- data.frame(office = authors) |>
       tibble::rownames_to_column("input") |>
@@ -141,7 +153,7 @@ create_citation <- function(
       "\n",
       "Please cite this publication as: \n",
       "\n",
-      ifelse(primary_author_office[["office"]] == "SEFSC", "SEDAR.", author_list),
+      ifelse(primary_author_office[["office"]] == "SEFSC" | tolower(type) == "sedar", "SEDAR.", author_list),
       " ", year, ". ",
       glue::glue("{title}"), ". ",
       region_specific_part,

R/create_template.R

@@ -16,7 +16,9 @@
 #'
 #' Default: "sar" (a NOAA standard "Stock Assessment Report")
 #'
-#' Options: "sar" (Stock Assessment Report), "nemt" (Northeast Management Track), "pfmc" (Pacific Fishery Management Council), "safe" (Stock Assessment and Fishery Evaluation)
+#' Options: "sar" (Stock Assessment Report), "nemt" (Northeast Management Track),
+#' "pfmc" (Pacific Fishery Management Council), "safe" (Stock Assessment and 
+#' Fishery Evaluation), "sedar" (SouthEast Data, Assessment, and Review)
 #'
 #' @param office Regional Fisheries Science Center producing the report.
 #'
@@ -265,21 +267,26 @@ create_template <- function(
       "Pacific Fishery Management Council" = "pfmc",
       "Stock Assessment and Fishery Evaluation" = "safe",
       "Stock Assessment Report" = "skeleton",
+      "SouthEast Data, Assessment, and Review" = "sedar",
+      "SouthEast Data Assessment and Review" = "sedar",
       "sar" = "skeleton",
       "pfmc" = "pfmc",
       "nemt" = "nemt",
       "safe" = "safe",
+      "sedar" = "sedar",
+      "SEDAR" = "sedar",
       {
         type_fxn <- function() {
           selection <- utils::menu(
             title = "Unrecognized template type. Please select an option below: ",
-            choices = c("Default", "Pacific Fisheries Management Council", "Northeast Management Track", "SAFE")
+            choices = c("Default", "Pacific Fisheries Management Council", "Northeast Management Track", "SAFE", "SEDAR")
           )
           type <- switch(as.character(selection),
             "1" = "skeleton",
             "2" = "pfmc",
             "3" = "nemt",
             "4" = "safe",
+            "5" = "sedar",
             {
               "skeleton"
             }
@@ -462,7 +469,9 @@ create_template <- function(
 
     asar_folder <- system.file("templates", package = "asar")
     # copy files from specific type folder
-    current_folder <- ifelse(rerender_skeleton, subdir, file.path(asar_folder, type))
+    current_folder <- ifelse(rerender_skeleton,
+                             subdir,
+                             file.path(asar_folder, type))
     new_folder <- subdir
 
     ##### Identify files to copy ----
@@ -1115,7 +1124,10 @@ create_template <- function(
       citation <- create_citation(
         authors = authors,
         title = title,
-        year = year
+        year = year,
+        type = ifelse(tolower(office) == "sefsc",
+                      "sedar",
+                      type)
       )
       cli::cli_alert_success("Added report citation.")
     }

R/create_yaml.R

@@ -220,7 +220,12 @@ create_yaml <- function(
       toad <- paste(author_list[[i]], sep = ",")
       add_authors <- paste0(add_authors, toad) # -> add_authors
     }
-    yaml <- paste0(yaml, add_authors)
+
+    sedar_author <- "  - name: 'SEDAR'\n    affiliations: \n        address: '4055 Faber Place Drive, Suite 201' \n        city: 'North Charleston' \n        state: 'SC' \n        postal-code: '29405' \n"
+
+    yaml <- ifelse(tolower(type) == "sedar",
+                   paste0(yaml, sedar_author),
+                   paste0(yaml, add_authors))
 
     # Add other parts
     yaml <- paste0(

inst/README.md

@@ -16,4 +16,5 @@ This folder contains various files which support the creation of materials for r
   * `preamble` R file used to extract key quantities from model results file used in asar report (`preamble.R`)
   * Images of species used for asar report cover pages (`spp_img` folder)
   * US Dept of Commerce logo placed on report title page (`us_doc_logo.png`)
-* The `templates` sub-folder contains the child documents used for each report "type": Northeast management track (nemt); Pacific Fisheries Marine Council (pfmc); Stock Assessment and Fishery Evaluation (safe); standard report format (skeleton)
+* The `templates` sub-folder contains the child documents used for each report "type": Northeast management track (nemt); Pacific Fisheries Marine Council (pfmc); Stock Assessment and Fishery Evaluation (safe); SouthEast Data, Assessment, and Review (sedar),
+standard report format (skeleton)

inst/WORDLIST

@@ -53,6 +53,7 @@ SEFSC
 SSC
 SWA
 SWFSC
+SouthEast
 Strikethrough
 TOC
 TinyTeX
@@ -119,6 +120,7 @@ roboto
 saltatrix
 sar
 se
+sedar
 snakecase
 socio
 sso

inst/templates/sedar/01_introduction.qmd

@@ -0,0 +1,15 @@
+# Introduction {#sec-intro}
+
+
+## Workshop Time and Place
+
+
+## Terms of Reference
+
+
+## List of Participants
+
+
+## List of Working Papers and Reference Documents
+
+

inst/templates/sedar/02_data_review.qmd

@@ -0,0 +1,68 @@
+# Data Review and Update {#sec-data}
+
+
+## Stock Structure and Management Unit
+
+
+## Life History Parameters
+
+
+### Morphometric and Conversion Factors
+
+
+### Age and Growth
+
+
+### Natural Mortality
+
+
+### Maturity
+
+
+### Sexual Transition
+
+
+### Fecundity
+
+
+### Discard Mortality
+
+
+## Fishery-Dependent Data
+
+
+### Commercial Landings
+
+
+### Recreational Landings
+
+
+### Commercial Discards
+
+
+### Recreational Discards
+
+
+### Commercial Size Composition
+
+
+### Recreational Size Composition
+
+
+### Commercial Age Composition
+
+
+### Recreational Age Composition
+
+
+### Commercial Catch Per Unit of Effort Indices of Abundance
+
+
+### Recreational Catch Per Unit of Effort Indices of Abundance
+
+
+## Fishery-Independent Surveys
+
+
+## Environmental Considerations and Contributions from Stakeholders
+

inst/templates/sedar/03_model-configuration.qmd

@@ -0,0 +1,70 @@
+# Stock Assessment Model Configuration {#sec-mod-config}
+
+## Model Configuration
+
+
+### Initial Conditions
+
+
+### Temporal Structure
+
+
+### Spatial Structure
+
+
+### Life History
+
+
+### Recruitment Dynamics
+
+
+### Fleet Structure and Surveys
+
+
+### Selectivity
+
+
+### Retention
+
+
+### Landings and Associated Length and Age Compositions
+
+
+### Discards and Associated Length Compositions
+
+
+### Indices
+
+
+## Goodness of Fit and Assumed Error Structure
+
+
+## Estimated Parameters
+
+
+## Model Diagnostics
+
+
+### Residual Analysis
+
+
+### Correlation Analysis
+
+
+### Profile Likelihoods
+
+
+### Jitter Analysis
+
+
+### Retrospective Analysis
+
+
+### Jack-knife Analysis on Indices of Abundance
+
+
+### Additional Diagnostics
+
+
+## Sensitivity Runs
+

inst/templates/sedar/04_model-results.qmd

@@ -0,0 +1,55 @@
+# Stock Assessment Model Results {#sec-model-results}
+
+## Estimated Parameters
+
+
+## Fishing Mortality
+
+
+## Selectivity
+
+
+## Recruitment
+
+
+## Biomass and Abundance Trajectories
+
+
+## Model Fit and Residual Analysis
+
+
+### Landings
+
+
+### Discards
+
+
+### Indices
+
+
+### Length Compositions
+
+
+### Age Compositions
+
+## Model Diagnostics
+
+### Correlation Analysis
+
+
+### Profile Likelihoods
+
+
+### Jitter Analysis
+
+
+### Retrospective Analysis
+
+
+### Bridging Analysis
+
+
+### Sensitivity Model Runs
+
+
+

inst/templates/sedar/05_discussion.qmd

@@ -0,0 +1,3 @@
+# Discussion {#sec-discussion}
+
+<!--- The discussion is dependent on analyst/assessment/region. Include subsections discussing ecosystem considerations (if applicable) and research recommendations/improvements to the assessment. --->

inst/templates/sedar/06_projections.qmd

@@ -0,0 +1,19 @@
+# Projections {#sec-projections}
+
+## Introduction
+
+
+## Projection Methods
+
+
+## Projection Results
+
+
+### Biological Reference Points
+
+
+### Stock Status
+
+
+### Overfishing Limit and Acceptable Biological Catch Projections
+

inst/templates/sedar/07_acknowledgments.qmd

@@ -0,0 +1,7 @@
+# Acknowledgements {#sec-acknowledgements}
+
+
+
+<!--- Please leave in the following: --->
+
+This document was produced using the R package asar [@asar_2026], which is free to use and publicly available on [GitHub](https://github.com/nmfs-ost/asar).

inst/templates/sedar/08_references.qmd

@@ -0,0 +1,4 @@
+# References {#sec-refs}
+
+::: {#refs} 
+:::

inst/templates/sedar/11_appendix.qmd

@@ -0,0 +1,9 @@
+\appendix
+\setcounter{figure}{0}
+\setcounter{table}{0}
+
+# Appendices {#sec-appendix}
+
+<!--- 
+Any information relevant for evaluation of the stock either during SSC or management review should be included in the appendix. The main assessment document should contain the minimum necessary information to inform and provide management advice for the stock while additional materials can be found in the appendix.
+--->