From 527537396d2d64057d21c7769ef6396ef56f84ca Mon Sep 17 00:00:00 2001 From: sbreitbart-NOAA Date: Fri, 10 Jul 2026 10:31:46 -0400 Subject: [PATCH 1/5] Add new template "type" for SEDAR reports, with reports identical to skeleton except author = SEDAR only (no scientists' names added) --- R/create_template.R | 21 ++++++++++++++++++--- R/create_yaml.R | 7 ++++++- inst/README.md | 3 ++- inst/WORDLIST | 2 ++ man/create_template.Rd | 4 +++- man/create_title.Rd | 4 +++- man/create_yaml.Rd | 4 +++- man/format_quarto.Rd | 4 +++- 8 files changed, 40 insertions(+), 9 deletions(-) diff --git a/R/create_template.R b/R/create_template.R index a9a4b8e9..8ed0263f 100644 --- a/R/create_template.R +++ b/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 +469,15 @@ 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)) + if (rerender_skeleton){ + current_folder <- subdir + } else { + current_folder <- file.path(asar_folder, + # sedar report files identical to skeleton + ifelse(type == tolower("sedar"), + "skeleton", + type)) + } new_folder <- subdir ##### Identify files to copy ---- diff --git a/R/create_yaml.R b/R/create_yaml.R index cccc42d8..b5bf9095 100644 --- a/R/create_yaml.R +++ b/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(type == "sedar", + paste0(yaml, sedar_author), + paste0(yaml, add_authors)) # Add other parts yaml <- paste0( diff --git a/inst/README.md b/inst/README.md index 6c75715c..ed91df39 100644 --- a/inst/README.md +++ b/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) diff --git a/inst/WORDLIST b/inst/WORDLIST index 822ed5e1..42bc66c1 100644 --- a/inst/WORDLIST +++ b/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 diff --git a/man/create_template.Rd b/man/create_template.Rd index 5ca8274f..42d4521a 100644 --- a/man/create_template.Rd +++ b/man/create_template.Rd @@ -41,7 +41,9 @@ Options: "pdf", "html"} 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)} \item{office}{Regional Fisheries Science Center producing the report. diff --git a/man/create_title.Rd b/man/create_title.Rd index 620c4b30..53064a5e 100644 --- a/man/create_title.Rd +++ b/man/create_title.Rd @@ -19,7 +19,9 @@ create_title( 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)} \item{office}{Regional Fisheries Science Center producing the report. diff --git a/man/create_yaml.Rd b/man/create_yaml.Rd index 7e335d77..96825216 100644 --- a/man/create_yaml.Rd +++ b/man/create_yaml.Rd @@ -107,7 +107,9 @@ Default: NULL} 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)} } \value{ Create a string indicating the important formatting pieces for a diff --git a/man/format_quarto.Rd b/man/format_quarto.Rd index 7ad4f580..780cbd9f 100644 --- a/man/format_quarto.Rd +++ b/man/format_quarto.Rd @@ -18,7 +18,9 @@ Options: "pdf", "html"} 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)} } \value{ This function returns part of a quarto YAML header From d89d711eea5935ec2470be5f2c1248867de7efac Mon Sep 17 00:00:00 2001 From: sbreitbart-NOAA Date: Wed, 22 Jul 2026 11:47:38 -0400 Subject: [PATCH 2/5] create SEDAR template based off of https://sedarweb.org/documents/sedar-85-gulf-of-mexico-yellowedge-grouper-final-stock-assessment-report/ , https://sedarweb.org/documents/sedar-72-gulf-of-mexico-gag-grouper-final-stock-assessment-report_october2021/ , and https://www.fisheries.noaa.gov/inport/item/71013 --- R/create_yaml.R | 2 +- inst/templates/sedar/01_introduction.qmd | 15 ++++ inst/templates/sedar/02_data_review.qmd | 68 ++++++++++++++++++ .../sedar/03_model-configuration.qmd | 70 +++++++++++++++++++ inst/templates/sedar/04_model-results.qmd | 55 +++++++++++++++ inst/templates/sedar/05_discussion.qmd | 3 + inst/templates/sedar/06_projections.qmd | 21 ++++++ inst/templates/sedar/07_acknowledgments.qmd | 7 ++ inst/templates/sedar/08_references.qmd | 4 ++ inst/templates/sedar/11_appendix.qmd | 9 +++ man/create_template.Rd | 2 +- man/create_title.Rd | 2 +- man/create_yaml.Rd | 2 +- man/format_quarto.Rd | 2 +- 14 files changed, 257 insertions(+), 5 deletions(-) create mode 100644 inst/templates/sedar/01_introduction.qmd create mode 100644 inst/templates/sedar/02_data_review.qmd create mode 100644 inst/templates/sedar/03_model-configuration.qmd create mode 100644 inst/templates/sedar/04_model-results.qmd create mode 100644 inst/templates/sedar/05_discussion.qmd create mode 100644 inst/templates/sedar/06_projections.qmd create mode 100644 inst/templates/sedar/07_acknowledgments.qmd create mode 100644 inst/templates/sedar/08_references.qmd create mode 100644 inst/templates/sedar/11_appendix.qmd diff --git a/R/create_yaml.R b/R/create_yaml.R index b5bf9095..9684dadc 100644 --- a/R/create_yaml.R +++ b/R/create_yaml.R @@ -223,7 +223,7 @@ create_yaml <- function( 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(type == "sedar", + yaml <- ifelse(office == "SEFSC", paste0(yaml, sedar_author), paste0(yaml, add_authors)) diff --git a/inst/templates/sedar/01_introduction.qmd b/inst/templates/sedar/01_introduction.qmd new file mode 100644 index 00000000..1e64b329 --- /dev/null +++ b/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 + + diff --git a/inst/templates/sedar/02_data_review.qmd b/inst/templates/sedar/02_data_review.qmd new file mode 100644 index 00000000..df8e418d --- /dev/null +++ b/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 + diff --git a/inst/templates/sedar/03_model-configuration.qmd b/inst/templates/sedar/03_model-configuration.qmd new file mode 100644 index 00000000..26dc7a1a --- /dev/null +++ b/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 + diff --git a/inst/templates/sedar/04_model-results.qmd b/inst/templates/sedar/04_model-results.qmd new file mode 100644 index 00000000..4be3e908 --- /dev/null +++ b/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 + + + diff --git a/inst/templates/sedar/05_discussion.qmd b/inst/templates/sedar/05_discussion.qmd new file mode 100644 index 00000000..4097bf8a --- /dev/null +++ b/inst/templates/sedar/05_discussion.qmd @@ -0,0 +1,3 @@ +# Discussion {#sec-discussion} + + diff --git a/inst/templates/sedar/06_projections.qmd b/inst/templates/sedar/06_projections.qmd new file mode 100644 index 00000000..be722696 --- /dev/null +++ b/inst/templates/sedar/06_projections.qmd @@ -0,0 +1,21 @@ +# Projections {#sec-projections} + +## Introduction + + +## Projection Methods + + +## Projection Results + + +### Biological Reference Points + + +### Stock Status + + +### Overfishing Limit and Acceptable Biological Catch Projections + + +### Constant Catch diff --git a/inst/templates/sedar/07_acknowledgments.qmd b/inst/templates/sedar/07_acknowledgments.qmd new file mode 100644 index 00000000..5ca54c37 --- /dev/null +++ b/inst/templates/sedar/07_acknowledgments.qmd @@ -0,0 +1,7 @@ +# Acknowledgements {#sec-acknowledgements} + + + + + +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). diff --git a/inst/templates/sedar/08_references.qmd b/inst/templates/sedar/08_references.qmd new file mode 100644 index 00000000..2ce18b27 --- /dev/null +++ b/inst/templates/sedar/08_references.qmd @@ -0,0 +1,4 @@ +# References {#sec-refs} + +::: {#refs} +::: diff --git a/inst/templates/sedar/11_appendix.qmd b/inst/templates/sedar/11_appendix.qmd new file mode 100644 index 00000000..e78e6aaf --- /dev/null +++ b/inst/templates/sedar/11_appendix.qmd @@ -0,0 +1,9 @@ +\appendix +\setcounter{figure}{0} +\setcounter{table}{0} + +# Appendices {#sec-appendix} + + diff --git a/man/create_template.Rd b/man/create_template.Rd index 42d4521a..c54ae655 100644 --- a/man/create_template.Rd +++ b/man/create_template.Rd @@ -43,7 +43,7 @@ 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), "sedar" (SouthEast Data, Assessment, and Review)} +Fishery Evaluation)} \item{office}{Regional Fisheries Science Center producing the report. diff --git a/man/create_title.Rd b/man/create_title.Rd index 53064a5e..fb30d258 100644 --- a/man/create_title.Rd +++ b/man/create_title.Rd @@ -21,7 +21,7 @@ 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), "sedar" (SouthEast Data, Assessment, and Review)} +Fishery Evaluation)} \item{office}{Regional Fisheries Science Center producing the report. diff --git a/man/create_yaml.Rd b/man/create_yaml.Rd index 96825216..a93f94e9 100644 --- a/man/create_yaml.Rd +++ b/man/create_yaml.Rd @@ -109,7 +109,7 @@ 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), "sedar" (SouthEast Data, Assessment, and Review)} +Fishery Evaluation)} } \value{ Create a string indicating the important formatting pieces for a diff --git a/man/format_quarto.Rd b/man/format_quarto.Rd index 780cbd9f..0e168181 100644 --- a/man/format_quarto.Rd +++ b/man/format_quarto.Rd @@ -20,7 +20,7 @@ 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), "sedar" (SouthEast Data, Assessment, and Review)} +Fishery Evaluation)} } \value{ This function returns part of a quarto YAML header From 95f9fe5d8d13f5b86bc4999cc95c2a519264aee9 Mon Sep 17 00:00:00 2001 From: sbreitbart-NOAA Date: Wed, 22 Jul 2026 13:00:19 -0400 Subject: [PATCH 3/5] Update citation formula if type = SEDAR or office = SEFSC; update documentation --- R/create_citation.R | 18 +++++++++++++++--- R/create_template.R | 17 +++++++---------- R/create_yaml.R | 2 +- man/create_citation.Rd | 11 ++++++++++- man/create_template.Rd | 2 +- man/create_title.Rd | 2 +- man/create_yaml.Rd | 2 +- man/format_quarto.Rd | 2 +- 8 files changed, 37 insertions(+), 19 deletions(-) diff --git a/R/create_citation.R b/R/create_citation.R index b2a8de60..b1fc2e44 100644 --- a/R/create_citation.R +++ b/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, diff --git a/R/create_template.R b/R/create_template.R index 8ed0263f..5d20f21d 100644 --- a/R/create_template.R +++ b/R/create_template.R @@ -469,15 +469,9 @@ create_template <- function( asar_folder <- system.file("templates", package = "asar") # copy files from specific type folder - if (rerender_skeleton){ - current_folder <- subdir - } else { - current_folder <- file.path(asar_folder, - # sedar report files identical to skeleton - ifelse(type == tolower("sedar"), - "skeleton", - type)) - } + current_folder <- ifelse(rerender_skeleton, + subdir, + file.path(asar_folder, type)) new_folder <- subdir ##### Identify files to copy ---- @@ -1130,7 +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.") } diff --git a/R/create_yaml.R b/R/create_yaml.R index 9684dadc..a959047a 100644 --- a/R/create_yaml.R +++ b/R/create_yaml.R @@ -223,7 +223,7 @@ create_yaml <- function( 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(office == "SEFSC", + yaml <- ifelse(tolower(type) == "sedar", paste0(yaml, sedar_author), paste0(yaml, add_authors)) diff --git a/man/create_citation.Rd b/man/create_citation.Rd index 2120ef09..95923723 100644 --- a/man/create_citation.Rd +++ b/man/create_citation.Rd @@ -7,7 +7,8 @@ create_citation( 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 ) } \arguments{ @@ -34,6 +35,14 @@ Default: \verb{[TITLE]}. If species and region are provided, a title will be gen \item{year}{Year the assessment is conducted. Default: the year in which the report is rendered.} + +\item{type}{Report template type. + +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), "sedar" (SouthEast Data, Assessment, and Review)} } \value{ Generate a citation for use in publications and other diff --git a/man/create_template.Rd b/man/create_template.Rd index c54ae655..42d4521a 100644 --- a/man/create_template.Rd +++ b/man/create_template.Rd @@ -43,7 +43,7 @@ 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)} +Fishery Evaluation), "sedar" (SouthEast Data, Assessment, and Review)} \item{office}{Regional Fisheries Science Center producing the report. diff --git a/man/create_title.Rd b/man/create_title.Rd index fb30d258..53064a5e 100644 --- a/man/create_title.Rd +++ b/man/create_title.Rd @@ -21,7 +21,7 @@ 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)} +Fishery Evaluation), "sedar" (SouthEast Data, Assessment, and Review)} \item{office}{Regional Fisheries Science Center producing the report. diff --git a/man/create_yaml.Rd b/man/create_yaml.Rd index a93f94e9..96825216 100644 --- a/man/create_yaml.Rd +++ b/man/create_yaml.Rd @@ -109,7 +109,7 @@ 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)} +Fishery Evaluation), "sedar" (SouthEast Data, Assessment, and Review)} } \value{ Create a string indicating the important formatting pieces for a diff --git a/man/format_quarto.Rd b/man/format_quarto.Rd index 0e168181..780cbd9f 100644 --- a/man/format_quarto.Rd +++ b/man/format_quarto.Rd @@ -20,7 +20,7 @@ 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)} +Fishery Evaluation), "sedar" (SouthEast Data, Assessment, and Review)} } \value{ This function returns part of a quarto YAML header From aed1d7670d575fde38455de4d1584d9d7d56bd9e Mon Sep 17 00:00:00 2001 From: sbreitbart-NOAA Date: Wed, 22 Jul 2026 13:13:54 -0400 Subject: [PATCH 4/5] Update and add new create_citation() test for SEFSC --- tests/testthat/test-create_citation.R | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/tests/testthat/test-create_citation.R b/tests/testthat/test-create_citation.R index 9db78405..94249cb6 100644 --- a/tests/testthat/test-create_citation.R +++ b/tests/testthat/test-create_citation.R @@ -7,8 +7,20 @@ test_that("citation generated properly for SWFSC", { "Kevin T. Hill" = "SWFSC" ), title = "Check", - year = 2024 + year = 2024, + type = "SAR" ) expected_output <- "{{< pagebreak >}} \n\nPlease cite this publication as: \n\nKuriyama, P. T., Allen Akselrud, C., Zwolinski, J. P., and Hill, K. T. 2024. Check. Pacific Fishery Management Council, Portland, OR. Available from https://www.pcouncil.org/stock-assessments-and-fishery-evaluation-safe-documents/. \\pageref*{LastPage}{} pp." expect_equal(fxn_test, expected_output) }) + +test_that("citation generated properly for SEFSC", { + fxn_test <- create_citation( + type = "sedar", + title = "Check", + year = 2024 + ) + expected_output <- "{{< pagebreak >}} \n\nPlease cite this publication as: \n\nSEDAR. 2024. Check. SEDAR, North Charleston SC. \\pageref*{LastPage}{} pp." + expect_equal(fxn_test, expected_output) +}) + From b699b84e0db0653908dee5847f5344496f59abf9 Mon Sep 17 00:00:00 2001 From: sbreitbart-NOAA Date: Mon, 27 Jul 2026 15:43:39 -0400 Subject: [PATCH 5/5] Remove "constant catch" subheader from SEDAR Projections doc --- inst/templates/sedar/06_projections.qmd | 2 -- 1 file changed, 2 deletions(-) diff --git a/inst/templates/sedar/06_projections.qmd b/inst/templates/sedar/06_projections.qmd index be722696..beaba563 100644 --- a/inst/templates/sedar/06_projections.qmd +++ b/inst/templates/sedar/06_projections.qmd @@ -17,5 +17,3 @@ ### Overfishing Limit and Acceptable Biological Catch Projections - -### Constant Catch