nmfs-ost · Schiano-NOAA · Jun 1, 2026 · Jun 2, 2026 · Jun 2, 2026 · Jun 2, 2026
diff --git 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
@@ -74,15 +75,17 @@ findability
 flextable
 flextables
 frac
-goa
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+goa
 hardcoding
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 knitr
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 labelled
 le
+meristics
+modelling
 modularized
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 nefsc
@@ -105,6 +108,7 @@ rdas
 rdat
 rda’s
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+reweighting
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 saltatrix
 sar

diff --git 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

diff --git a/vignettes/articles/std_guidelines.qmd b/vignettes/articles/std_guidelines.qmd
@@ -0,0 +1,87 @@
+---
+title: "NMFS Stock Assessment Guidelines"
-title: "NMFS Stock Assessment Guidelines"
+title: "NMFS Stock Assessment Report Guidelines"
-title: "NMFS Stock Assessment Guidelines"
+title: "NMFS Stock Assessment Report 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.  
-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.  
-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. 
+
+## Outline for Stock Assessment Reports
+
+### Executive Summary:
-### Executive Summary:
+### Executive Summary
-### Executive Summary:
+### Executive Summary
+
+Where possible the executive summary should paraphrase the shared content of the body of the report to minimize redundancy.
-Where possible the executive summary should paraphrase the shared content of the body of the report to minimize redundancy.
+The executive summary should paraphrase the shared content of the body of the report to minimize redundancy.
-Where possible the executive summary should paraphrase the shared content of the body of the report to minimize redundancy.
+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:
-### Introduction:
+### Introduction
-### 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.
-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.
-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.
-* 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.
-* 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
-* Assessment history
+* Assessment History
-* 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.”
+
+### Data:
-### Data:
+### Data
-### 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:
+
+* 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)
+* Indices and Standardization (Fishery dependent and independent)
-* Indices and standardization (Fishery dependent and independent)
+* Indices and Standardization (Fishery dependent and independent)
+* Composition data - age, length (Description, aging error, reweighting)
-* Composition data - age, length (Description, aging error, reweighting)
+* Composition Data - age, length (Description, aging error, reweighting)
-* Composition data - age, length (Description, aging error, reweighting)
+* Composition Data - age, length (Description, aging error, reweighting)
+* Absolute abundance (if applicable)
-* Absolute abundance (if applicable)
+* Absolute Abundance (if applicable)
-* Absolute abundance (if applicable)
+* 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.
+* 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.
+* 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:
-### Discussion:
+### Discussion
-### Discussion:
+### 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:
-### Tables:
+### Tables
-### 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.
-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.
-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:
-### Figures:
+### Figures
-### 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.
-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.
-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 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 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.
-### 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.
+