From 170a06c774e359af2d91ddad774487faccfaff52 Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Mon, 1 Jun 2026 16:55:18 -0400 Subject: [PATCH 01/24] add guidelines to website as living document; make adjustments to guidelines based on feedback from workshops and improve clarity --- pkgdown/_pkgdown.yml | 8 ++- vignettes/articles/std_guidelines.qmd | 87 +++++++++++++++++++++++++++ 2 files changed, 94 insertions(+), 1 deletion(-) create mode 100644 vignettes/articles/std_guidelines.qmd diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml index dfa9129d..cc6b586f 100644 --- a/pkgdown/_pkgdown.yml +++ b/pkgdown/_pkgdown.yml @@ -50,6 +50,13 @@ navbar: # Make the link open in a new tab target: "_blank" + guidelines: + text: NMFS Report Guidlines + icon: fas fa-book fa-lg + href: articles/std_guidelines.html + # Make the link open in a new tab + target: "_blank" + cheatsheet: text: Cheatsheet href: asar_cheatsheet.pdf @@ -66,4 +73,3 @@ navbar: structure: left: [home, overview, reference, cheatsheet, tutorial, articles, examples] - right: [search, issue, github] diff --git a/vignettes/articles/std_guidelines.qmd b/vignettes/articles/std_guidelines.qmd new file mode 100644 index 00000000..5c8ca759 --- /dev/null +++ b/vignettes/articles/std_guidelines.qmd @@ -0,0 +1,87 @@ +--- +title: "NMFS Stock Assessment Guidelines" +format: + html: + toc: true + toc-depth: 3 + anchor-sections: true + other-links: + - text: stockplotr + href: https://nmfs-ost.github.io/stockplotr/ +knitr: + opts_chunk: + collapse: true + comment: '#>' +--- + +## General guidance + +The following sections are a recommended outline for a U.S. fisheries stock assessment report. The goal is to effectively present information to managers to provide the best scientific advice available within a reasonable framework. This effort shifts the focus of assessment documents from being SSC and statistical review focus to more succinct review of information to aid in quicker decision making. {asar} is a tool that can generate a template that will meet the following guidelines. It contains standardized sections, figures, and tables for the user as well as formatting so the title page and authorship sections are not included here. Authors not using the template generated from {asar} should place tables and figures at the end of the document. + +Note: terms of reference are intended to remain as a stand alone document or can be included in an appendix at the end of the report. Direct answers to the terms of reference should not be included in the body of the stock assessment report. + +## Outline for Stock Assessment Reports + +### Executive Summary: + +Where possible the executive summary should paraphrase the shared content of the body of the report to minimize redundancy. + +The executive summary should include the following: + +* Short statement describing assessment model used for the current management cycle and any data updates. +* Short summary of reference points, stock status, and projections. In the future, when using the {asar} R package, tables of reference points and projections will be automatically generated. + +### Introduction: + +The intent is to keep this section to two to three pages and provide a high level summary of the stock. The intention is to provide enough information in this section so the audience does not need to reference previous documents. Please include the species scientific name at the first mention of its common name. + +* Stock ID (detailed description if appropriate and quantitative studies or data are behind the decision-making) +* Management history: Briefly describe the management history of the stock and status. Please only touch on historical policies that would have impacted modeling decisions or would be critical knowledge about the species that might affect its population dynamics. +* Assessment history +* Fishery Description: Short summary of fleet composition (i.e., boat types), gear types, species targeted, and fishing grounds (one paragraph) +* Ecosystem Considerations: If this section is not relevant, please ignore; however the default will state “Ecosystem considerations and/or climate indicators were not included in this assessment.” + +### Data: + +Please provide relevant data that entered the assessment model including temporal and spatial resolutions, sample size, and units where appropriate for each of the following: + +* Life History (growth, maturity, fecundity, natural mortality, meristics, etc.) +* Catch (retained and discarded) +* Indices and standardization (Fishery dependent and independent) +* Composition data - age, length (Description, aging error, reweighting) +* Absolute abundance (if applicable) +* Environmental/ecosystem indicator data. Please include a blanket statement if none are considered. + +### Assessment + +Current modeling approach: short general overview of modeling platform including the reference to model paper or online reference. Please include a short description of changes between the approach from the last assessment cycle to the current. Please also note the version of the modelling platform used for this assessment. + +* Configuration of the base model: please describe the setup of the stock assessment model. Please also include any environmental relationships/hypotheses that informed the configuration of the base model. +* Bridging: Briefly describe the bridging analysis performed to the previous assessment. +* Modeling Results: for each of the following please describe the results for the base model. +* Parameter Estimates +* Time Series +* Model Fits +* Model Diagnostics +* Sensitivity Analyses +* Management Benchmarks: decisions on management metrics/benchmarks (i.e. provide a rationale for why a specific F-proxy was recommended for management) +* Projections: Description of stock status, biological reference points (BRPs), and trends for each scenario; rebuilding times + +### Discussion: + +Dependent on analyst/assessment/region; please include sub sections discussing ecosystem considerations (if applicable) and research recommendations/improvements to the assessment + +* Research Recommendations + +### References + +### Tables: + +At minimum, please include the following tables into the report (when applicable to the stock). Pre-made figures can be found in the {stockplotr} package downloaded from GitHub. + +### Figures: + +At minimum, please include the following figures into the report (when applicable to the stock). Pre-made figures can be found in the {stockplotr} package downloaded from GitHub. + +### Appendices: 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. It is not intended for the appendices to be a catch-all. We highly encourage authors to review the need and irreplaceable value of the report's content when it comes to addressing the audience. + From d4e0937713b6c97462a689261e83e45ff05708fb Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Tue, 2 Jun 2026 15:29:49 -0400 Subject: [PATCH 02/24] remove guidelines from header bar --- pkgdown/_pkgdown.yml | 7 ------- 1 file changed, 7 deletions(-) diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml index cc6b586f..e0d8b0c3 100644 --- a/pkgdown/_pkgdown.yml +++ b/pkgdown/_pkgdown.yml @@ -50,13 +50,6 @@ navbar: # Make the link open in a new tab target: "_blank" - guidelines: - text: NMFS Report Guidlines - icon: fas fa-book fa-lg - href: articles/std_guidelines.html - # Make the link open in a new tab - target: "_blank" - cheatsheet: text: Cheatsheet href: asar_cheatsheet.pdf From 20d1ff80c0f86b7e6e071bd4e1d3537677c6befa Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Tue, 2 Jun 2026 16:28:57 -0400 Subject: [PATCH 03/24] fix error in suggests --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index ba1bdf06..d434d475 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -44,7 +44,7 @@ Suggests: kableExtra, knitr, parallel, - quarto, + quarto (>= 1.6.0), r4ss, rmarkdown, snowfall, From b20384b91dd7d2cf4a9480ed10b7a3b33b6eb9c5 Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Tue, 2 Jun 2026 16:30:39 -0400 Subject: [PATCH 04/24] revert description --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index d434d475..ba1bdf06 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -44,7 +44,7 @@ Suggests: kableExtra, knitr, parallel, - quarto (>= 1.6.0), + quarto, r4ss, rmarkdown, snowfall, From 610a0b4148bfa831b3db6f12d40f9fb91b218029 Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Tue, 2 Jun 2026 17:01:13 -0400 Subject: [PATCH 05/24] add guidelines to articles --- pkgdown/_pkgdown.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml index e0d8b0c3..cd1f752f 100644 --- a/pkgdown/_pkgdown.yml +++ b/pkgdown/_pkgdown.yml @@ -32,6 +32,8 @@ navbar: text: Articles icon: fas fa-file-contract fa-lg menu: + - text: NMFS SAR Guidelines + href: articles/std_guidelines.html - text: Markdown Notation href: articles/markdown_notation.html - text: Increasing Report Accessibility From ea7b69c7e006a0595ad92d5b0781237ada7f20d0 Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Tue, 2 Jun 2026 17:03:24 -0400 Subject: [PATCH 06/24] add back in right side of site strucutre --- pkgdown/_pkgdown.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml index cd1f752f..688f0f03 100644 --- a/pkgdown/_pkgdown.yml +++ b/pkgdown/_pkgdown.yml @@ -68,3 +68,4 @@ navbar: structure: left: [home, overview, reference, cheatsheet, tutorial, articles, examples] + right: [search, issue, github] From 81c01fd113485b5e71a22a7495f6a2646febe736 Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Tue, 2 Jun 2026 17:04:42 -0400 Subject: [PATCH 07/24] update wordlist --- inst/WORDLIST | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/inst/WORDLIST b/inst/WORDLIST index 275b9d57..ae6f0734 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -1,6 +1,7 @@ AFSC Arial BAM +BRPs Blackspotted Blockquote Bolded @@ -12,8 +13,8 @@ Canelón Coates DocumentMetadata Drs -EcoMon ECOMON +EcoMon Fabio Flextable Gertseva @@ -36,6 +37,7 @@ PFMC's PIFSC Pandoc Pomatomus +Pre Quillback README RStudio @@ -45,7 +47,6 @@ Rockfish Rockfishes Rosemond Rougheye -RTF SBPR SEFSC SSC @@ -74,8 +75,8 @@ findability flextable flextables frac -goa gls +goa hardcoding is’ jpg @@ -83,6 +84,8 @@ knitr kobe labelled le +meristics +modelling modularized multispecies nefsc @@ -105,6 +108,7 @@ rdas rdat rda’s readLines +reweighting roboto saltatrix sar From 5b7cc2b8356a8fd31a526a383a359fcffa3cdaad Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Thu, 4 Jun 2026 08:54:34 -0400 Subject: [PATCH 08/24] Update vignettes/articles/std_guidelines.qmd Co-authored-by: Sophie Breitbart --- vignettes/articles/std_guidelines.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/articles/std_guidelines.qmd b/vignettes/articles/std_guidelines.qmd index 5c8ca759..6b255b11 100644 --- a/vignettes/articles/std_guidelines.qmd +++ b/vignettes/articles/std_guidelines.qmd @@ -79,7 +79,7 @@ Dependent on analyst/assessment/region; please include sub sections discussing e At minimum, please include the following tables into the report (when applicable to the stock). Pre-made figures can be found in the {stockplotr} package downloaded from GitHub. -### Figures: +### Figures At minimum, please include the following figures into the report (when applicable to the stock). Pre-made figures can be found in the {stockplotr} package downloaded from GitHub. From c3b6674f12a48e58fe2c60180549b2439a164ffc Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Thu, 4 Jun 2026 08:54:53 -0400 Subject: [PATCH 09/24] Update vignettes/articles/std_guidelines.qmd Co-authored-by: Sophie Breitbart --- vignettes/articles/std_guidelines.qmd | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/vignettes/articles/std_guidelines.qmd b/vignettes/articles/std_guidelines.qmd index 6b255b11..89e926b0 100644 --- a/vignettes/articles/std_guidelines.qmd +++ b/vignettes/articles/std_guidelines.qmd @@ -83,5 +83,6 @@ At minimum, please include the following tables into the report (when applicable At minimum, please include the following figures into the report (when applicable to the stock). Pre-made figures can be found in the {stockplotr} package downloaded from GitHub. -### Appendices: 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. It is not intended for the appendices to be a catch-all. We highly encourage authors to review the need and irreplaceable value of the report's content when it comes to addressing the audience. +### Appendices +Any information relevant for evaluation of the stock either during SSC or statistical 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. It is not intended for the appendices to be a catch-all. We highly encourage authors to review the need and irreplaceable value of the report's content when it comes to addressing the audience. From 83170598719037c85fad7bb29632662eacd2f008 Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Thu, 4 Jun 2026 08:55:05 -0400 Subject: [PATCH 10/24] Update vignettes/articles/std_guidelines.qmd Co-authored-by: Sophie Breitbart --- vignettes/articles/std_guidelines.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/articles/std_guidelines.qmd b/vignettes/articles/std_guidelines.qmd index 89e926b0..288a467c 100644 --- a/vignettes/articles/std_guidelines.qmd +++ b/vignettes/articles/std_guidelines.qmd @@ -75,7 +75,7 @@ Dependent on analyst/assessment/region; please include sub sections discussing e ### References -### Tables: +### Tables At minimum, please include the following tables into the report (when applicable to the stock). Pre-made figures can be found in the {stockplotr} package downloaded from GitHub. From ec4b47594ccc53bcb8d38ef2522d264a7551af3b Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Thu, 4 Jun 2026 08:55:21 -0400 Subject: [PATCH 11/24] Update vignettes/articles/std_guidelines.qmd Co-authored-by: Sophie Breitbart --- vignettes/articles/std_guidelines.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/articles/std_guidelines.qmd b/vignettes/articles/std_guidelines.qmd index 288a467c..5ab8caaf 100644 --- a/vignettes/articles/std_guidelines.qmd +++ b/vignettes/articles/std_guidelines.qmd @@ -67,7 +67,7 @@ Current modeling approach: short general overview of modeling platform including * Management Benchmarks: decisions on management metrics/benchmarks (i.e. provide a rationale for why a specific F-proxy was recommended for management) * Projections: Description of stock status, biological reference points (BRPs), and trends for each scenario; rebuilding times -### Discussion: +### Discussion Dependent on analyst/assessment/region; please include sub sections discussing ecosystem considerations (if applicable) and research recommendations/improvements to the assessment From 4513ec976ca97bdeb509369da8066a2e6536d2b5 Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Thu, 4 Jun 2026 08:55:34 -0400 Subject: [PATCH 12/24] Update vignettes/articles/std_guidelines.qmd Co-authored-by: Sophie Breitbart --- vignettes/articles/std_guidelines.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/articles/std_guidelines.qmd b/vignettes/articles/std_guidelines.qmd index 5ab8caaf..3c524d67 100644 --- a/vignettes/articles/std_guidelines.qmd +++ b/vignettes/articles/std_guidelines.qmd @@ -41,7 +41,7 @@ The intent is to keep this section to two to three pages and provide a high leve * Fishery Description: Short summary of fleet composition (i.e., boat types), gear types, species targeted, and fishing grounds (one paragraph) * Ecosystem Considerations: If this section is not relevant, please ignore; however the default will state “Ecosystem considerations and/or climate indicators were not included in this assessment.” -### Data: +### Data Please provide relevant data that entered the assessment model including temporal and spatial resolutions, sample size, and units where appropriate for each of the following: From 62e330959e564ce4a5c2be090795c3402ae58495 Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Thu, 4 Jun 2026 08:55:46 -0400 Subject: [PATCH 13/24] Update vignettes/articles/std_guidelines.qmd Co-authored-by: Sophie Breitbart --- vignettes/articles/std_guidelines.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/articles/std_guidelines.qmd b/vignettes/articles/std_guidelines.qmd index 3c524d67..ce4d02d3 100644 --- a/vignettes/articles/std_guidelines.qmd +++ b/vignettes/articles/std_guidelines.qmd @@ -31,7 +31,7 @@ The executive summary should include the following: * Short statement describing assessment model used for the current management cycle and any data updates. * Short summary of reference points, stock status, and projections. In the future, when using the {asar} R package, tables of reference points and projections will be automatically generated. -### Introduction: +### Introduction The intent is to keep this section to two to three pages and provide a high level summary of the stock. The intention is to provide enough information in this section so the audience does not need to reference previous documents. Please include the species scientific name at the first mention of its common name. From f6ac7f8f30dab78e7147f7366544c91b6617bdfc Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Thu, 4 Jun 2026 08:56:09 -0400 Subject: [PATCH 14/24] Update vignettes/articles/std_guidelines.qmd Co-authored-by: Sophie Breitbart --- vignettes/articles/std_guidelines.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/articles/std_guidelines.qmd b/vignettes/articles/std_guidelines.qmd index ce4d02d3..5b4fbc79 100644 --- a/vignettes/articles/std_guidelines.qmd +++ b/vignettes/articles/std_guidelines.qmd @@ -22,7 +22,7 @@ Note: terms of reference are intended to remain as a stand alone document or can ## Outline for Stock Assessment Reports -### Executive Summary: +### Executive Summary Where possible the executive summary should paraphrase the shared content of the body of the report to minimize redundancy. From 7b09c893d2bf5f81077517c53add460c0accffb9 Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Thu, 4 Jun 2026 08:56:50 -0400 Subject: [PATCH 15/24] Update vignettes/articles/std_guidelines.qmd Co-authored-by: Sophie Breitbart --- vignettes/articles/std_guidelines.qmd | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/vignettes/articles/std_guidelines.qmd b/vignettes/articles/std_guidelines.qmd index 5b4fbc79..35c71005 100644 --- a/vignettes/articles/std_guidelines.qmd +++ b/vignettes/articles/std_guidelines.qmd @@ -16,7 +16,9 @@ knitr: ## General guidance -The following sections are a recommended outline for a U.S. fisheries stock assessment report. The goal is to effectively present information to managers to provide the best scientific advice available within a reasonable framework. This effort shifts the focus of assessment documents from being SSC and statistical review focus to more succinct review of information to aid in quicker decision making. {asar} is a tool that can generate a template that will meet the following guidelines. It contains standardized sections, figures, and tables for the user as well as formatting so the title page and authorship sections are not included here. Authors not using the template generated from {asar} should place tables and figures at the end of the document. +The following sections are components of a recommended outline for a U.S. fisheries stock assessment report. **The goal of reports created with these guidelines is to effectively present information to managers so as to provide the best scientific advice available within a reasonable framework.** This effort represents a shift in assessment document formatting from a focus on SSC/statistical review towards a more succinct presentation of information to aid in quicker decision-making. Therefore, **the main body of the report should contain the minimum necessary information to inform and provide management advice for the stock; additional materials, including information relevant for evaluation of the stock either during SSC or statistical review, should be placed in the appendix.** + +{asar} is a tool that can generate a report template aligning with the following guidelines. As the template contains standardized sections and formatting, some components-- such as the title page and authorship sections-- are not included here as each are generated automatically. Authors not using the template generated from {asar} should place tables and figures at the end of the document. Note: terms of reference are intended to remain as a stand alone document or can be included in an appendix at the end of the report. Direct answers to the terms of reference should not be included in the body of the stock assessment report. From 7fc7a987ca0b6a419db188b5aa8bf110d0dd043e Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Thu, 4 Jun 2026 08:59:27 -0400 Subject: [PATCH 16/24] Update vignettes/articles/std_guidelines.qmd Co-authored-by: Sophie Breitbart --- vignettes/articles/std_guidelines.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/articles/std_guidelines.qmd b/vignettes/articles/std_guidelines.qmd index 35c71005..572be16f 100644 --- a/vignettes/articles/std_guidelines.qmd +++ b/vignettes/articles/std_guidelines.qmd @@ -35,7 +35,7 @@ The executive summary should include the following: ### Introduction -The intent is to keep this section to two to three pages and provide a high level summary of the stock. The intention is to provide enough information in this section so the audience does not need to reference previous documents. Please include the species scientific name at the first mention of its common name. +The intent is to keep this section to **2-3 pages** and **provide a high level summary of the stock**. The intention is to provide enough information in this section so the audience does not need to reference previous documents. Please include the species' scientific name at the first mention of its common name. * Stock ID (detailed description if appropriate and quantitative studies or data are behind the decision-making) * Management history: Briefly describe the management history of the stock and status. Please only touch on historical policies that would have impacted modeling decisions or would be critical knowledge about the species that might affect its population dynamics. From 61e82114bf2b367b351c01f5e50ea0e020e2863a Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Thu, 4 Jun 2026 08:59:42 -0400 Subject: [PATCH 17/24] Update vignettes/articles/std_guidelines.qmd Co-authored-by: Sophie Breitbart --- vignettes/articles/std_guidelines.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/articles/std_guidelines.qmd b/vignettes/articles/std_guidelines.qmd index 572be16f..545c0641 100644 --- a/vignettes/articles/std_guidelines.qmd +++ b/vignettes/articles/std_guidelines.qmd @@ -38,7 +38,7 @@ The executive summary should include the following: The intent is to keep this section to **2-3 pages** and **provide a high level summary of the stock**. The intention is to provide enough information in this section so the audience does not need to reference previous documents. Please include the species' scientific name at the first mention of its common name. * Stock ID (detailed description if appropriate and quantitative studies or data are behind the decision-making) -* Management history: Briefly describe the management history of the stock and status. Please only touch on historical policies that would have impacted modeling decisions or would be critical knowledge about the species that might affect its population dynamics. +* Management History: Briefly describe the management history of the stock and status. Please only touch on historical policies that would have impacted modeling decisions or would be critical knowledge about the species that might affect its population dynamics. * Assessment history * Fishery Description: Short summary of fleet composition (i.e., boat types), gear types, species targeted, and fishing grounds (one paragraph) * Ecosystem Considerations: If this section is not relevant, please ignore; however the default will state “Ecosystem considerations and/or climate indicators were not included in this assessment.” From 8a7dc9ab1c5fd76c86d1037d48159d9ddbc5ca89 Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Thu, 4 Jun 2026 08:59:56 -0400 Subject: [PATCH 18/24] Update vignettes/articles/std_guidelines.qmd Co-authored-by: Sophie Breitbart --- vignettes/articles/std_guidelines.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/articles/std_guidelines.qmd b/vignettes/articles/std_guidelines.qmd index 545c0641..98e32649 100644 --- a/vignettes/articles/std_guidelines.qmd +++ b/vignettes/articles/std_guidelines.qmd @@ -49,7 +49,7 @@ Please provide relevant data that entered the assessment model including tempora * Life History (growth, maturity, fecundity, natural mortality, meristics, etc.) * Catch (retained and discarded) -* Indices and standardization (Fishery dependent and independent) +* Indices and Standardization (Fishery dependent and independent) * Composition data - age, length (Description, aging error, reweighting) * Absolute abundance (if applicable) * Environmental/ecosystem indicator data. Please include a blanket statement if none are considered. From 9493b271956674a16231c46dd395f392399044cd Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Thu, 4 Jun 2026 09:00:09 -0400 Subject: [PATCH 19/24] Update vignettes/articles/std_guidelines.qmd Co-authored-by: Sophie Breitbart --- vignettes/articles/std_guidelines.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/articles/std_guidelines.qmd b/vignettes/articles/std_guidelines.qmd index 98e32649..3c6bf531 100644 --- a/vignettes/articles/std_guidelines.qmd +++ b/vignettes/articles/std_guidelines.qmd @@ -39,7 +39,7 @@ The intent is to keep this section to **2-3 pages** and **provide a high level s * Stock ID (detailed description if appropriate and quantitative studies or data are behind the decision-making) * Management History: Briefly describe the management history of the stock and status. Please only touch on historical policies that would have impacted modeling decisions or would be critical knowledge about the species that might affect its population dynamics. -* Assessment history +* Assessment History * Fishery Description: Short summary of fleet composition (i.e., boat types), gear types, species targeted, and fishing grounds (one paragraph) * Ecosystem Considerations: If this section is not relevant, please ignore; however the default will state “Ecosystem considerations and/or climate indicators were not included in this assessment.” From 8bc2d0a10bbed02e28ccebbcac887ae6833fbbab Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Thu, 4 Jun 2026 09:06:27 -0400 Subject: [PATCH 20/24] Update vignettes/articles/std_guidelines.qmd Co-authored-by: Sophie Breitbart --- vignettes/articles/std_guidelines.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/articles/std_guidelines.qmd b/vignettes/articles/std_guidelines.qmd index 3c6bf531..87297e64 100644 --- a/vignettes/articles/std_guidelines.qmd +++ b/vignettes/articles/std_guidelines.qmd @@ -50,7 +50,7 @@ Please provide relevant data that entered the assessment model including tempora * Life History (growth, maturity, fecundity, natural mortality, meristics, etc.) * Catch (retained and discarded) * Indices and Standardization (Fishery dependent and independent) -* Composition data - age, length (Description, aging error, reweighting) +* Composition Data - age, length (Description, aging error, reweighting) * Absolute abundance (if applicable) * Environmental/ecosystem indicator data. Please include a blanket statement if none are considered. From 79fe29fb8d1d01fc98f8ab8238c1d0e658f464ff Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Thu, 4 Jun 2026 09:06:39 -0400 Subject: [PATCH 21/24] Update vignettes/articles/std_guidelines.qmd Co-authored-by: Sophie Breitbart --- vignettes/articles/std_guidelines.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/articles/std_guidelines.qmd b/vignettes/articles/std_guidelines.qmd index 87297e64..165a9bb7 100644 --- a/vignettes/articles/std_guidelines.qmd +++ b/vignettes/articles/std_guidelines.qmd @@ -51,7 +51,7 @@ Please provide relevant data that entered the assessment model including tempora * Catch (retained and discarded) * Indices and Standardization (Fishery dependent and independent) * Composition Data - age, length (Description, aging error, reweighting) -* Absolute abundance (if applicable) +* Absolute Abundance (if applicable) * Environmental/ecosystem indicator data. Please include a blanket statement if none are considered. ### Assessment From 4658798e3a77cb140473cab10a9c02ddb740671a Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Thu, 4 Jun 2026 09:08:05 -0400 Subject: [PATCH 22/24] Apply suggestions from code review Co-authored-by: Sophie Breitbart --- vignettes/articles/std_guidelines.qmd | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/vignettes/articles/std_guidelines.qmd b/vignettes/articles/std_guidelines.qmd index 165a9bb7..a89c138e 100644 --- a/vignettes/articles/std_guidelines.qmd +++ b/vignettes/articles/std_guidelines.qmd @@ -1,5 +1,5 @@ --- -title: "NMFS Stock Assessment Guidelines" +title: "NMFS Stock Assessment Report Guidelines" format: html: toc: true @@ -52,7 +52,7 @@ Please provide relevant data that entered the assessment model including tempora * Indices and Standardization (Fishery dependent and independent) * Composition Data - age, length (Description, aging error, reweighting) * Absolute Abundance (if applicable) -* Environmental/ecosystem indicator data. Please include a blanket statement if none are considered. +* Environmental/Ecosystem Indicator Data. Please include a blanket statement if none are considered. ### Assessment @@ -79,11 +79,11 @@ Dependent on analyst/assessment/region; please include sub sections discussing e ### Tables -At minimum, please include the following tables into the report (when applicable to the stock). Pre-made figures can be found in the {stockplotr} package downloaded from GitHub. +At minimum, please include the following tables in the report (when applicable to the stock). Semi-automated tables can be made using the [{stockplotr}](github.com/nmfs-ost/stockplotr) package. ### Figures -At minimum, please include the following figures into the report (when applicable to the stock). Pre-made figures can be found in the {stockplotr} package downloaded from GitHub. +At minimum, please include the following figures in the report (when applicable to the stock). Semi-automated figures can be made using the [{stockplotr}](github.com/nmfs-ost/stockplotr) package. ### Appendices Any information relevant for evaluation of the stock either during SSC or statistical 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. It is not intended for the appendices to be a catch-all. We highly encourage authors to review the need and irreplaceable value of the report's content when it comes to addressing the audience. From 8f0c4220fd4fa48e2cf06dc8709681d21d900526 Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Thu, 4 Jun 2026 09:09:02 -0400 Subject: [PATCH 23/24] Apply suggestions from code review Co-authored-by: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> --- vignettes/articles/std_guidelines.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/articles/std_guidelines.qmd b/vignettes/articles/std_guidelines.qmd index a89c138e..f761c679 100644 --- a/vignettes/articles/std_guidelines.qmd +++ b/vignettes/articles/std_guidelines.qmd @@ -66,7 +66,7 @@ Current modeling approach: short general overview of modeling platform including * Model Fits * Model Diagnostics * Sensitivity Analyses -* Management Benchmarks: decisions on management metrics/benchmarks (i.e. provide a rationale for why a specific F-proxy was recommended for management) +* Management Benchmarks: decisions on management metrics/benchmarks (e.g. provide a rationale for why a specific F-proxy was recommended for management) * Projections: Description of stock status, biological reference points (BRPs), and trends for each scenario; rebuilding times ### Discussion From 91eb373834583e95cf9072efca9a4346d7ea760b Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Thu, 4 Jun 2026 10:57:34 -0400 Subject: [PATCH 24/24] Apply suggestions from code review Co-authored-by: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> --- vignettes/articles/std_guidelines.qmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/vignettes/articles/std_guidelines.qmd b/vignettes/articles/std_guidelines.qmd index f761c679..6a13ee6c 100644 --- a/vignettes/articles/std_guidelines.qmd +++ b/vignettes/articles/std_guidelines.qmd @@ -79,11 +79,11 @@ Dependent on analyst/assessment/region; please include sub sections discussing e ### Tables -At minimum, please include the following tables in the report (when applicable to the stock). Semi-automated tables can be made using the [{stockplotr}](github.com/nmfs-ost/stockplotr) package. +Please include report tables in this section. Semi-automated tables can be made using the [{stockplotr}](github.com/nmfs-ost/stockplotr) package. ### Figures -At minimum, please include the following figures in the report (when applicable to the stock). Semi-automated figures can be made using the [{stockplotr}](github.com/nmfs-ost/stockplotr) package. +Please include report figures in this section. Semi-automated figures can be made using the [{stockplotr}](github.com/nmfs-ost/stockplotr) package. ### Appendices Any information relevant for evaluation of the stock either during SSC or statistical 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. It is not intended for the appendices to be a catch-all. We highly encourage authors to review the need and irreplaceable value of the report's content when it comes to addressing the audience.