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.