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VISCtemplates 1.3.2

Bug Fix

  • Fix issue with insert_break() not inserting page breaks at times (#216)

Other improvements

  • Reconcile differences between empty report template and other report templates (#204)
  • Remove dependency on the full tidyverse, per best practices (#213)

VISCtemplates 1.3.1

Bug Fix

  • Re-flip Fred Hutch and SCHARP header logos to fix regression from #196, restoring intended logo positions in #195 (#205)

VISCtemplates 1.3.0

Bug Fixes

  • Fix major bug that broke PDF knitting on pandoc >= 3.1.7 (#159)
  • Fix bug with latex packages (specifically etex's \reserveinserts command) that broke PDF knitting (#160)
  • Fix bug that occurred when a report subdirectory did not already exist, and add unit test (#173)
  • Fix insert_break() to actually create a page break (#188)
    • Update documentation to instruct users to use latex command instead in new code

Improvements to Report Templates

  • Update header logo for SCHARP/Fred Hutch branding compliance (#195)
  • Update templates and documentation for using correct syntax for multiple citations (#191)
  • Add section number to References section in PDF output (#176)
  • Clarify expectations for Background section of report (#143)
  • Fix BAMA positivity call definition (#144)
  • Add Acknowledgments section to report templates (#153)

Testing and Continuous Integration

  • Create unit tests to test knit all report templates to PDF and Word (#168, #182, #186, #187, #192)
    • Test locally via devtools::test(); files written to testthat/_snaps
    • On pull requests, test reports are written to file snapshots on GitHub Actions
  • Add GitHub Actions runner to test statsrv compatibility by matching its R and pandoc versions (#172)
  • Add interactive = FALSE option to interactive functions to facilitate automated unit testing (#168)
  • Speed up GitHub Action that renders skeleton.Rmd (#166)
    • But then remove it entirely once superseded by more thorough test knitting (#178)

Documentation and UI Improvements

  • Fix bad URL in GitHub setup instructions (#185)
  • Add guidance for where to install data packages (#154)
  • Add friendly error message to visc_load_pdata() when data package is not installed (#152)
  • Specify existence of NAb template in README and vignettes (#189)

Package Maintenance

  • Adjust filenames in R/ and tests/ to follow best practices (#175, #179)
  • Respect existing getOption('repos') instead of forcing CRAN installations (#163)
  • Adjust dependencies in DESCRIPTION (#164)
  • Update package authors and maintainer (#190)
  • Clean up latex template code, removing commented-out code and reorganizing for better readability (#196)

VISCtemplates 1.2.0

  • Update Fred Hutch logo in Word and PDF templates
  • Fix continuous integration issues (GitHub actions)
  • New GitHub action to auto-generate empty report template in Word and PDF (for verifying format with PRs) and associated template fixes
  • Fix double section numbering issue in Word doc template
  • Add visc_load_pdata and DataPackageR to Rmd template code

VISCtemplates 1.1.0

  • Improvements to use_visc_report():
    • A new NAb assay template.
    • This function reminds the user to use VISC's report naming convention.

VISCtemplates 1.0.0

The new release number is bumped to 1.0.0 because this version implements the structure needed for assay-specific templates.

  • New feature: use_visc_report() creates a VISC report template with assay-specific R Markdown files.
  • New vignette: a new vignette outlines how to set up a VISC analysis project (vignette("create_a_visc_analysis_project")).
  • Changes to the PT report README to make it easier to use.
  • Minor changes:
    • "*.zip" added to the .gitignore template
    • *.R template files created with create_visc_project() are saved to R/ in the analysis project template.
    • The study schema template is an R function.
    • New prompt with create_visc_project() asks about the project name.
    • Added \sloppy to .tex template to help with antigen name formatting.
  • Minor edits to template language and documentation throughout.

VISCtemplates 0.3.4

  • Bug fix: updated bibliography.bib file to fix citation format for R Core Team citation.

VISCtemplates 0.3.3

  • Bug fix: updated bibliography.bib file to fix issue with Mac using bib files.
  • Updated visc_report/skeleton.Rmd file in preparation of bug fix being addressed in VISCfunctions

VISCtemplates 0.3.2

  • Bug fix: fixed pandoc error that complains about cslreferences.

VISCtemplates 0.3.1

  • Bug fix:
    • Fixed biber/bibtex issue with pdf output.

VISCtemplates 0.3.0

  • New "empty" report template without the boilerplate PT report text.
    • Go to File > New File > Rmarkdown... > From Template and select the "Empty Report" template.
    • Or use template = "visc_empty" argument in rmarkdown::draft().
    • See the updated vignette for more info.
  • Changes to bibliography.bib file.
    • Shortened file contains only citations used in VISC reports.
    • A project-level bibliography.bib file is written to the docs/ directory. Previously there was one file generated for each report.
  • New Github PR text links to the documentation for writing and code review.
  • Bug fixes:
    • Footnote hyperlinks fixed: Footnote text (^[MY_FOOTNOTE]).

VISCtemplates 0.2.0

  • Changes to VISC Report (PDF & Word Output) template.
    • Example text updated.
    • Functions defined in report are now exported functions from {VISCtemplates}. Use insert_ref() to insert a reference to a table or figure.
    • Vignette updated to reflect these changes.

VISCtemplates 0.1.2

  • Minor fix to the VISC report template for compatibility with pandoc upgrade.

VISCtemplates 0.1.1

  • Added a NEWS.md file to track changes to the package.
  • Added CONDUCT.md and CONTRIBUTING.md to the package.
  • Improved README.Rmd.
  • You can now drop the VISC logo from the PT report template with dropVISClogo: true.