FIX[v1.0.2] - Add in nmfspalette dependency

nmfspalette was added back in as a dependency. Proper theming colors in plots is available again. Previously, changes with the nmfspalette package was causing an issue downloading asar. This is no longer the case.

As always, please report any issues to our issues page.

v1.0.1

What's Changed

Temporarily remove nmfspallete as a dependency and occurrences in add_theme function and tests. The package is currently not operating properly and the development team for that package is preparing a fix later this week.

v1.0.0

Welcome to asar

If you are a new user or have been using asar during initial development, thank you for trying out this package! We hope this will make a lasting impact into creating stock assessments and lay the framework for reporting at NOAA Fisheries. See below for major features of asar as well as changes since the last update!

Function of Package

Summary

• Major functions fully built allowing for customizations of stock assessment reports
• create_template() produces a modular structure to write a stock assessment report and incorporate pre-built tables and figures from satf
• users have the option to follow the workflow outlined in a tutorial or execute most of the necessary functions through create_template itself through specific arguments.
• convert_output() creates a standardized output file from BAM .rdat or SS3 Report.sso of key quantities and outputs (more functionality for other models planned for later)
• Built pkgdown site providing resources to use the tool to write stock assessment reports including short cuts for markdown notation and increasing accessibility in reports
• Pre-added cover images into the report (we are looking to expand this, so please leave an issue if the a specific species is missing!)
• Built in bibliography file which includes example references from the West Coast of the U.S.; however, a different file can be added.
• Template defaults to a LuaLaTex engine to accommodate greater accessibility features

What's changed

Minor Changes past v0.3.0

• Incorporate testing to provide sufficient coverage of the package
• Move post-dev0.3 changes from dev to dev-1.0 branch by @sbreitbart-NOAA in #101
• fix(cover image) by @Schiano-NOAA in #104
• added first draft of new FSC-specific citations by @sbreitbart-NOAA in #107
• change testthat parallel option to be false by @k-doering-NOAA in #109
• Render figures and tables qmds even if rdas are missing by @sbreitbart-NOAA in #110
• Faq vignette by @Schiano-NOAA in #112
• Integrate new fxns by @sbreitbart-NOAA in #114
• Add check when convert_output = TRUE by @Schiano-NOAA in #119
• Integrate failsafe for rda files by @Schiano-NOAA in #115

Notes

• All figures and tables imported into a template created using create_template include a pre-written caption and alternative text. The caption will be generated through base quarto after render, but currently, quarto does not support alternative text with render to anything other than HTML. asar is currently built for render to pdf.
• We have devoted considerable time building tools and resources to accompany this package. Please refer to the asar site or submit an issue when necessary.
• We welcome feedback and suggestions for improvement using our discussions page. A simple contribution to the package could be issued as a pull request if users are familiar with that process.

Full Changelog: v0.3...v1.0.0

v0.3

What's Changed

Major Updates

• GitHub Pages site is expanded and improved including a link to a tutorial for asar
• Fleets are now automatically identified when converting BAM output files (fleet names are still in acronym form)
• The skeleton now creates an R chunk referred to the preamble which loads the converted data frame and creates pre-calculated key quantities for users to reference throughout their report.
• Integrated an rda based approach to reading in figures and tables produced from satf into the template
• Improved the convert_output function where std naming is improved, module_name column has become a key factor in correctly converting the data frames, new and informative messages appear as the function processes, and other minor improvements
• The previous archiving focused folder structure was removed in favor of a single folder named "report"

Minor Updates

• Various updates to documentation of functions
• Improved testing
• Added working example to documentation and data for users
• Shorten create_template chunk labels by @sbreitbart-NOAA in #74
• Update(README.md): add pak installation instructions by @Schiano-NOAA in #79
• Add minor change to convert_output arg defaults and format latin name in title by @Schiano-NOAA in #88
• fixed bug in a11y vignette by @sbreitbart-NOAA in #95
• Codespaces was set up for those who have access
• Fixed error when rendering without a bib file - asar now contains a default bib file that can be replaced in the create_template function or later by the user.

Full Changelog: v0.2...v0.3

As of December 10th 2024, we are aware that the checks for the package are failing for ubuntu os; however, this is being worked on and should not impact the function of asar package

v0.2

v0.2 Improvements

In this release

Major changes impacting use

• Improvements to outline of GitHub page including added example and link to tutorial (in progress)

create_template

• Added option to convert output in create_template(convert_output = TRUE) by @Schiano-NOAA in #49
• build: added alt text to cover page's US Dept of Commerce seal by @sbreitbart-NOAA in #68* Add line in skeleton yaml to name pdf after render
• Added argument in create-template to add a .bib file
• the quarto skeleton produced by create_template now uses lualatex as its default engine
• Model results files (after conversion) are now read in as a chunk at the top of the quarto file
• Default figures and tables are set to eval = FALSE except for spawning_biomass

convert_output

• Add SS3 integration tests for testing convert_output() by @Bai-Li-NOAA in #45
• convert_output for BAM output files will now automatically recognize fleet names by @Schiano-NOAA in #72
• Other minor improvements to convert_output

other functions

• Added code to add_theme.R to use the nmfs color palette in plots by @sbreitbart-NOAA in #53

Minor Changes

• Authorship was fixed so that authorship follows the order entered into the argument rather than alphabetically

• Minor improvement to standard naming convention in convert_output

• Additional species images were added to the package

• fixed small typo to test branching/PR workflow works by @sbreitbart-NOAA in #41

• Small changes fixing a few bugs by @Schiano-NOAA in #43

• Style code and document by @github-actions in #33

• Add SS3 integration tests for testing convert_output() by @Bai-Li-NOAA in #45

• changed library in readme example (ASAR --> asar) by @sbreitbart-NOAA in #48

• fix(README): fix example by @Schiano-NOAA in #51

• fix failed GHA tests on main branch by @Bai-Li-NOAA in #57

• add issue templates by @Bai-Li-NOAA in #58

• Style code and document by @github-actions in #47

• fix add_chunk() tests by @Bai-Li-NOAA in #63

• fix(create_template): replace example with previous one developed by … by @Schiano-NOAA in #64

• Create working example and resources for users by @Schiano-NOAA in #54

• Pkgdown vignettes by @sbreitbart-NOAA in #65

• Revert "Pkgdown vignettes" by @sbreitbart-NOAA in #66

• Shorten create_template chunk labels by @sbreitbart-NOAA in #74

Full Changelog: v0.1.0-beta2...v0.1.0-beta3

Fix bugs in beta release 1 and add save for convert_output

Major change:

Add option to either save converted output or use it as a function to a global object.

Additional changes:

• Fix #35 minor problem when processing output from SS3 models: OVERALL_COMPS in files that have both age and length comps will now be properly converted.
• Fix minor problem in SS3 model output in CATCH
• Correct naming convention when reading in standard naming conventions
• Additional minor changes for improvement

Basic generation of pdf report

The package is now set up to generate a stock assessment report template. Associated functions can also be implemented including convert_output which has the ability to transform SS3 (Report.SSO) and BAM (xx.rdat) output data to a more standardized format. Some issues are still being sorted out, so we encourage testing and feedback of minor issues. The current built-in tables and figures are being reworked. While they are not in this package; however, they are prebuilt into the template for users to turn on and off. They are being adjusted to the standard output framework.