v2.0.3

Fixes

• Update to ESP definition in glossary #423
• Update cheatsheet to reflect changes to accessibility functions
• Update special characters in glossary to prevent errors in rendering #425
• Fix issue with duplicated city for AFSC seattle office #426
• Update preamble prompt #430
• Update safe template table structure #432
• Provide temporary fix for gt::gt_split() while PR is awaiting approval in gt package #429
• Allow messages about tables when running create_template() #431
• Add float latex package to in-header tex as suggested when looking at NEFSC transition #427 . Thank you to @DHennen1 for helping shape this contribution!
• Add leading zeros into affiliation zip codes

Hotfix issues in create_template found during NSAW Workshop

There were a couple minor issues found with rerendering the skeleton and report type during the workshop and other testing in preparation for the upcoming workshop series. This release fixes these issues and allows users to have full functionality of create_template even when the non-standard template is selected.

Patch bugs found in v2.0.0

Summary

A series of minor bugs were found in create_template() when customizations were being made to the template and upon rerender. The following have been fixed:

• Authorship on rerender does not add a blank author section
• Adding in any new arguments when rerendering the skeleton works such as a new species, region, species name, office, ect
• Title is properly extracted and updated
• The parameters are updated properly in both the yaml and params chunk if any of them are updated
• Any new authors are now added to the citation
• New sections and custom sections are appropriately labelled and included

v2.0.0

What's Changed

In this major release, we have migrated convert_output() out of asar and into stockplotr. This large change was made due to the high dependency of the standardized output for the stockplotr package and only small role it has in `asar.

• Update cheatsheet for v2.0 by @sbreitbart-NOAA in #409

Full Changelog: v1.5.1...v2.0.0

v1.6.1

Hotfix Notes

• Users identified issue with alternative text not showing for the cover image. This is now fixed.
• Alternative text was not added under add_alttext() when users set a specified figure size in the quarto chunk which removed pandocbounded command. add_alttext() no longer relies on pandocbounded in it's process.

v1.6.0

Summary

We have made major strides in the accessibility in the documents produced from asar templates. All accessibility functions now operate as intended and document should reach the majority of federal section 508 accessibility standards.

Note: Tables made from flextable are not accessible and are not compatible with the methods use in asar.

What's Changed

• [Hotfix]: convert output for SS3 timeseries names and fleet names wrong (#379)
• [Hotfix]: uncertainty in improper location for conout BAM (#384)
• Replace rda item label "cap" with "caption", for clarity (#394)
• Update "tabsorder" to "page/tabsorder" (#395)
• Fix figure caption extraction (#397)
• Improve accessibility functions (#398)
• Default pdf document class is now set to "article"
• The glossary is expanded to contain the official survey names. The "acronym" is either/both the first initial of the survey or the common name used by assessment authors

Full Changelog: v1.5.1...v1.6.0

Patch bugs found in v1.5.0

Summary

There were a few minor bugs found after the release of v1.5.0. In response we performed a series of hotfixes to address the following bugs:

• Missing header in asar::create_figures_doc() in some instances
• Missing labels and additional 'X' column found in converted output
• Multiple missing standardized names
• BAM no longer working with minor adjustments
• Department of Commerce logo on the title page improperly marked as an mage when it should be an artifact tagging document

These issues were all addressed and fixed with this release.

v1.5.0

TLDR::

• Major improvements to asar::convert_output()
• New csl file for formatting citations
• Updated tagging
• Expanded information in vignettes (FAQs and alternative text guidance)

✍️ Summary

Since our last release, we have had identified various bugs and suggestions for improvement due to the increased use of asar across the country. The team has pushed a variety of hotfixes to v1.4.0, but we have made additional strides to improve the tool with this release, v1.5.0. We want to particularly highlight the improvements to the convert_output() function and improved formatting settings like adding a .csl file for citation formatting and improving add_tagging(). The team is in the midst of getting a pre-release ready for our sister package, stockplotr. We hope the improvements on this release only make the tool better! Additional contributions are welcome through a PR or feel free to file an issue if you find any bugs or have an idea for improvement to the tool.

🆕 Updates

Major Changes (user impact)

• New asar cheatsheet available!
• New code of conduct policy implemented for contributors and developers
• Major improvements to efficiency of convert_output() when running converting a Stock Synthesis model output
• convert_output() now recognizes which model the output originated
• FIMS is now compatible with convert_output()!
• Other quality of life improvements and bugs fixed in asar::convert_output
• stockplotr was removed as a dependency of asar
• Notation for tagging is updated to the most recent recommendation from the tagpdf LaTeX package
• Language is no longer set in the skeleton yaml. Instead, it is identified by tagpdf call when running asar::add_tagging()` (This is a required part of making documents section 508 compliant)
• Region is now an included parameter in the params chunk making it available to reference throughout the document by the author
• Explicit style guidelines identified for references to prevent errors in the form of a .csl file created when create_template() is run. Based on reference style guidelines from Canadian Journal of Fisheries and Aquatic Sciences
• More FAQs available
• Clearer messaging when author is missing or improperly added when making a template
• Updates to recommended addition of alternative text and captions when adding non-stockplotr tables and figures
• When adding more figures and tables from the same respective folders and the quarto files for these objects already exist, they are appended to the file

Minor Changes (dev)

• README example was updated
• Improved testing framework
• Updates to GitHub actions in the package repository
• returns() removed from the end of functions per best practice
• General changes to incorporate suggestions from {goodpractice} R package

🌟 Shout outs to our new contributors!

• @ClaireGonzales-NOAA made their first contribution in #333
• @Andrea-Havron-NOAA made their first contribution in #334
• @e-perl-NOAA ran {goodpractice} check

Full Changelog: v1.4.0...v1.5.0

v1.4.0

TLDR

• New templates
• Notation for author argument in create_template() changed
• Improvements to the converter
• Reduction in number of arguments in all functions
• Updated preamble
• Disclaimer added to outline (replaced "DRAFT" watermark)
• Improved messages and warnings to the console
• Tables and figures are now separated in their own respective folders

Summary

The asar team gathered feedback following the Workflows Workthrough activity done by NOAA's Stock Assessment Workflows Steering Committee. The team prioritized feedback from the activity which developed a full cleanup of the package with some minor tweaks to the workflow. The majority of these changes occurred on the backend of development, but minor impacts to the workflow resulted in a more modular workflow and need for explicit steps taken. We hope this workflow is easier to follow and more user friendly than the completely all-in-one approach we have taken in the past.

Updates

Major Changes (user impacts)

• Major reduction in the number of arguments in all functions used in the asar workflow
• Default arguments have now changed and are no longer hidden in some cases
• Folders for rda objects made by {stockplotr} are now called "tables" and "figures" (previously "rda_files")
• Improved messaging in the console
• If rdas made from {stockplotr} do exist, they are no longer loaded in automatically by create_template(). The user is required to run create_tables_doc() and create_figures_doc() to perform this action
• Improved documentation through expanded definitions of arguments and prioritized argument order
• Any rda can be added to the tables or figures qmd when running create_tables_doc() or create_figures_doc()
• Any .jpg or .png located in the figures folder will be formatted into the create_figures_doc()

`create_template()

• Three new templates to choose from! -- We understand that the standard guidelines found in asar are not yet widely accepted by regional SSCs and councils. In response, we have incorporated alternative templates the meet the stock assessment guidelines from the Pacific Fisheries Management Council (pfmc), Northeast Fisheries Science Center Management Track (nemt), and Stock Assessment and Fishery Evaluation documents (safe). Each of these templates can be called using the 'type' argument in create_template()

asar::create_template(type = "pfmc")
asar::create_template(type = "nemt")
asar::create_template(type = "safe")

Note: these templates will be deprecated in the future once asar guidelines are reviewed and formally approved for use in management.

• Authors are now called through c("name" = "affiliation") in a vector. We removed the use of a database of assessment authors across NOAA since there were many missing entries and the work to maintain this database is above the small team's capacity. If the office is not currently recognized or found in our database, we recommend users to leave an issue to submit a request to add an office.

asar::create_template(author = c("Jane Smith" = "AFSC"))

• Removed "DRAFT" watermark over documents
• Added in a disclaimer to the beginning of the document (alternative to watermark)
• Removed the option to convert output and produce .rda files all within create_template
• Fixed bug when re-rendering template. Previously, title or species cover image is was not updated when defined
• Quantities in the preamble are updated to include improvements suggested by the NWFSC and to reflect changes to convert_output() resulting data frame.
• model_results is still a path to the standard file; however, users must have saved it as either an rda object. Due to the limitations of Quarto, the file must be loaded into the document at some point in order to make the quantities available to the user to make a reproducible document.
• Minor changes updating our standard guidelines found in the default report

convert_output()

• Major improvements that fixed issues with some quantities and estimates in the data frame for both Stock Synthesis and BAM
• The option to save the resulting data frame as a csv was deprecated
• Fleet names are automatically extracted from converted stock synthesis Report.sso file (users still have the option to specify fleet names if they wish using fleet_names)
• The number of "keywords" from stock synthesis found in the converted data frame has increased
• Users now input a single file path as the model_results argument instead of having 2 separate arguments to input file name and file path
• The option to save a file has changed from a .csv to an .rda. Quarto requires the user to load in a saved file in order to process quantities referenced throughout the report. Rda is easily read in by R.

Minor Changes (dev info)

• Update messaging system to show user errors, messages, warnings, and stops
• add_chunk() has options to add both quarto and rmarkdown chunk options. The defaults for this function have remained the same, however, the method in which it is implemented has changed
• Automated the processing of keywords found in stock synthesis Report.sso in convert_output()
• Removed old, unused functions
• Removed 'the' from NWFC title
• The previous message when installing or loading the package has been removed

Full Changelog: v1.3.0...v1.4.0

v1.3.0

TLDR

• New global glossary - to reference an acronym in text use the notation \gls{acronym}
• On rerender, only things can be updates or added to when run
• Improved tagging and alternative text functions
• Additional Q&A added

Updates

• Add in a global glossary to allow users to add in acronyms using \gls{<acronym>}
• Fix feature when user rerenders the skeleton - function no longer overwrites old files
• Minor improvements to accessibility functions (add_tagging and add_alttext)
• New Q&A added regarding tinytex install
• Update notation for appendix labelling in the outline
• Code proceeds when not in an interactive environment
• Citation now contains dynamic page count
• Update citation to fix bug that prevents function from proceeding without it
• Change the default text of the document to remain consistent throughout and among all machine types

What's Changed

• Hotfix: custom section option in #211
• reflect changes to alttext fxn pushed into dev and pre-reviewed in #222
• Fix issue when rerendering and adding author creates invalid spacing in yaml in #220
• Fix issue page break rendering before citation in #221
• Fix issue with create_citation and multiple matches to last name in #226
• updated reference to asar in default acknowldgements per #230 in #240

Full Changelog: v1.2.0...v1.3.0