Release/1.0.0 #72
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Release/1.0.0 #72
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…de and Stopnisek 2019
…loseq was not working correctly, no I fixed it.
Add abundance occupancy and core distribution plot functions
… with 50 samples as a base test dataset for the package, other small fixes and check messaging implementations
new pre-rarefaction functions and other fixes
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
linewidth Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
refining some plot function and fixing minor errors
…`importFrom` more. Importing only what we use. - Change from %>% pipe to |> base pipe. Plotting functions don't wrangle the data that much so we don't need the added benefits of %>%. This will be applied to other functions throughout. - identify_core() gains some clarity in function description as well as header cleanup (this helps when viewing outline in VS Code or Positron). - identify_core()'s "fo_diffs" output parameter updated to "elbow_slope_diffs" as it is more informative of the proccess applied to the data. - identify_core() changes pipe from %>% to |> - NAMESPACE cleans up a little bit after all this - corresponding function tests reformatted usint Air styler
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
- Added imports via `importFrom` that were missing - Removed %>% in other functions where it was unnecessary. - Only `do-phyloseq()` retains %>% in subsection - Updated NAMESPACE
…ction is due to failure to connect to Bioconductor.
…r the more explicit `@examples
#' \donttest{
#' library(phyloseq)
#' library(BRCore)` To convey the importance and relience of this package on "phyloseq".
- Kept \dontrun{} in some functions' documentation, like plot_neutral_model() that are only illustrative and depend on other functions.
- Changed name: `do_phyloseq()` is now `update_otu_table()
- `precompile.R` builds static vignette from "vignettes/BRCore-vignette.Rmd.orig" --> "vignettes/BRCore-vignette.Rmd - `prcompile.R` cleans directory and moves images to necessary direcotry for `devtools::build_vignette()`
Gains cli::cli_progress_bar
Package cleanup
…art example Co-authored-by: jibarozzo <64099468+jibarozzo@users.noreply.github.com>
Co-authored-by: jibarozzo <64099468+jibarozzo@users.noreply.github.com>
…adges Create brief README.Rmd for GitHub rendering
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Pull request overview
This pull request upgrades BRCore from v0.1.0 to v1.0.0, introducing significant new functionality for microbiome core analysis and visualization. The major changes include new plotting functions, rarefaction utilities, and a comprehensive static vignette for package documentation.
- Addition of five new visualization and analysis functions:
add_rarefaction_metrics(),plot_abundance_occupancy(),plot_core_distribution(),plot_rarefaction_metrics(), and renamedupdate_otu_table()(formerlydo_phyloseq()) - Implementation of a static vignette system to avoid failures in GitHub Actions macOS runners
- Enhanced test coverage for the new functions
- Improved progress messaging in
identify_core()with named list outputs
Reviewed changes
Copilot reviewed 50 out of 67 changed files in this pull request and generated 6 comments.
Show a summary per file
| File | Description |
|---|---|
| vignettes/BRCore-vignette.Rmd.orig | Source file for the static vignette containing comprehensive documentation and examples |
| vignettes/precompile.R | Script for pre-compiling the computationally intensive vignette and managing image files |
| vignettes/references.bib | Bibliography file with references for rarefaction, neutral models, and core microbiome concepts |
| vignettes/images/*.png | Pre-compiled visualization outputs for the vignette (4 image files) |
| vignettes/.gitignore | Excludes HTML output from version control |
| tests/testthat/test-update_otu_table.R | Updated tests using bcse dataset instead of test_phyloseq |
| tests/testthat/test-plot_*.R | New and updated test files for plotting functions with improved formatting |
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jibarozzo
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Dec 23, 2025
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Suggestions by Copilot resolved.
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@Gian77 once approved, I'll merge to |
Gian77
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Dec 23, 2025
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Looks great! What are we going to do for the vignette?
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Vignette #66 has already been merged to develop. It renders. |
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Increment to v1.0.0 from v0.1.0
New visualization functions bring new functionality to package and improve workflow. New workflow is captured in vignette and summarized in README.md. Some functionalities are still evolving, but this version represents a major change in workflow and API capabilities.
Highlights
Added functions:
R/
add_rarefaction_metrics()plot_abundance_occupancy()plot_core_distribution()plot_rarefaction_metrics()update_otu_table()(previouslydo_phyloseq())vignettes/
Static vignette for package documentation. This avoids failures in GH actions (macos runners).
BRCore-vignette.RmdBRCore-vignette.Rmd.origimages/precompile.Rreferences.bibChanged:
identify_corehas improved progress messaging, and named list outputsTests:
Added suites for added functions.
Selected commits
Contributors
Special thanks to @Gian77 for improvements in visualizations functions, tests, and vignette.