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Integrate from master to main - #22

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Pakillo wants to merge 3 commits into
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Integrate from master to main#22
Pakillo wants to merge 3 commits into
mainfrom
master

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@Pakillo

@Pakillo Pakillo commented Feb 18, 2026

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Summary of Changes

Hello @Pakillo, I'm Gemini Code Assist1! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request performs a substantial overhaul of the 'RecruitNetP' package by removing a large portion of its existing R code, associated manual pages, and generated documentation. This action suggests a major refactoring, a significant reduction in scope, or preparation for a new version of the package. Concurrently, the PR updates project metadata and integrates modern development practices for documentation and continuous integration.

Highlights

  • Extensive Code and Documentation Removal: Most of the R source files, their corresponding manual pages, and all previously generated documentation files from the 'docs' directory have been removed, indicating a significant restructuring or cleanup of the package's functionality.
  • Documentation Infrastructure Update: The project's URL in the 'DESCRIPTION' file was updated, and a new '_pkgdown.yml' configuration file was added, along with 'docs' being added to '.gitignore', suggesting a fresh approach to documentation generation using 'pkgdown'.
  • CI/CD Integration: New badges for R-CMD-check and Codecov test coverage were added to the 'README.Rmd', indicating enhanced continuous integration and code quality monitoring.

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Changelog
  • .gitignore
    • Added 'docs' directory to the list of ignored files.
  • DESCRIPTION
    • Updated the project URL to include the GitHub Pages link.
  • R/RN_to_matrix.R
    • Removed the 'RN_to_matrix' function.
  • R/RecruitnetP-package.R
    • Removed the package definition file.
  • R/aggr_RN.R
    • Removed the 'aggr_RN' function.
  • R/aggr_cover.R
    • Removed the 'aggr_cover' function.
  • R/associndex.R
    • Removed the 'associndex' function.
  • R/canopy_level.R
    • Removed the 'canopy_level' function.
  • R/chisq.test2.R
    • Removed the 'chisq.test2' function.
  • R/comm_summary.R
    • Removed the 'comm_summary' function.
  • R/comm_to_RN.R
    • Removed the 'comm_to_RN' function.
  • R/datasets.R
    • Removed dataset definitions for 'RecruitNet' and 'CanopyCover'.
  • R/funtopol.R
    • Removed the 'funtopol' function.
  • R/globals.R
    • Removed global variable declarations.
  • R/link_completeness.R
    • Removed the 'link_completeness' function.
  • R/merge_RN_cover.R
    • Removed the 'merge_RN_cover' function.
  • R/plot_to_site.R
    • Removed the 'plot_to_site' function.
  • R/pre_asocindex.R
    • Removed the 'pre_asocindex' function.
  • R/recruit_level.R
    • Removed the 'recruit_level' function.
  • R/sig_test.R
    • Removed the 'sig_test' function.
  • R/sign_net.R
    • Removed the 'sign_net' function.
  • R/site_level.R
    • Removed the 'site_level' function.
  • README.Rmd
    • Added R-CMD-check workflow badge.
    • Added Codecov test coverage badge.
  • _pkgdown.yml
    • Added configuration file for pkgdown, specifying URL and bootstrap theme.
  • docs/404.html
    • Removed the generated 404 error page.
  • docs/LICENSE.html
    • Removed the generated license documentation page.
  • docs/articles/Completeness-of-the-recruitment-network.html
    • Removed generated article documentation.
  • docs/articles/The-RecruitNet-database.html
    • Removed generated article documentation.
  • docs/articles/index.html
    • Removed generated articles index page.
  • docs/authors.html
    • Removed generated authors documentation page.
  • docs/bootstrap-toc.css
    • Removed generated bootstrap table of contents CSS.
  • docs/bootstrap-toc.js
    • Removed generated bootstrap table of contents JavaScript.
  • docs/docsearch.css
    • Removed generated docsearch CSS.
  • docs/docsearch.js
    • Removed generated docsearch JavaScript.
  • docs/index.html
    • Removed generated main documentation index page.
  • docs/link.svg
    • Removed generated documentation asset.
  • docs/news/index.html
    • Removed generated news documentation page.
  • docs/pkgdown.css
    • Removed generated pkgdown CSS.
  • docs/pkgdown.js
    • Removed generated pkgdown JavaScript.
  • docs/pkgdown.yml
    • Removed generated pkgdown build configuration.
  • docs/reference/CanopyCover.html
    • Removed generated reference documentation for CanopyCover.
  • docs/reference/RN_to_matrix.html
    • Removed generated reference documentation for RN_to_matrix.
  • docs/reference/RecruitNet.html
    • Removed generated reference documentation for RecruitNet.
  • docs/reference/RecruitNetP-package.html
    • Removed generated reference documentation for RecruitNetP-package.
  • docs/reference/associndex.html
    • Removed generated reference documentation for associndex.
  • docs/reference/comm_subset.html
    • Removed generated reference documentation for comm_subset.
  • docs/reference/comm_summary.html
    • Removed generated reference documentation for comm_summary.
  • docs/reference/comm_to_RN.html
    • Removed generated reference documentation for comm_to_RN.
  • docs/reference/download_RN.html
    • Removed generated reference documentation for download_RN.
  • docs/reference/funtopol.html
    • Removed generated reference documentation for funtopol.
  • docs/reference/index.html
    • Removed generated reference documentation index page.
  • docs/reference/link_completeness.html
    • Removed generated reference documentation for link_completeness.
  • docs/reference/sign_net.html
    • Removed generated reference documentation for sign_net.
  • docs/sitemap.xml
    • Removed the generated sitemap file.
  • man/CanopyCover.Rd
    • Removed the manual page for CanopyCover.
  • man/RN_to_matrix.Rd
    • Removed the manual page for RN_to_matrix.
  • man/RecruitNet.Rd
    • Removed the manual page for RecruitNet.
  • man/RecruitNetP-package.Rd
    • Removed the manual page for RecruitNetP-package.
  • man/associndex.Rd
    • Removed the manual page for associndex.
  • man/comm_subset.Rd
    • Removed the manual page for comm_subset.
  • man/comm_summary.Rd
    • Removed the manual page for comm_summary.
  • man/comm_to_RN.Rd
    • Removed the manual page for comm_to_RN.
  • man/download_RN.Rd
    • Removed the manual page for download_RN.
  • man/funtopol.Rd
    • Removed the manual page for funtopol.
  • man/link_completeness.Rd
    • Removed the manual page for link_completeness.
  • man/sign_net.Rd
    • Removed the manual page for sign_net.
  • tests/testthat/test-RN_to_matrix.R
    • Removed the test file for 'RN_to_matrix'.
  • tests/testthat/test-comm_summary.R
    • Removed the test file for 'comm_summary'.
  • tests/testthat/test-comm_to_RN.R
    • Removed the test file for 'comm_to_RN'.
  • tests/testthat/test-link_completeness.R
    • Removed the test file for 'link_completeness'.
Ignored Files
  • Ignored by pattern: .github/workflows/** (3)
    • .github/workflows/R-CMD-check.yaml
    • .github/workflows/pkgdown.yaml
    • .github/workflows/test-coverage.yaml
Activity
  • Pakillo opened this pull request.
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Code Review

This pull request appears to be a major refactoring, removing a significant amount of functionality from the package by deleting numerous R files, documentation, and tests. The pull request title and empty description don't provide any context for these substantial changes, which makes it difficult to assess the overall impact and correctness of the PR. For future pull requests of this magnitude, a detailed description explaining the rationale behind the changes would be highly beneficial for reviewers. My review is focused on the files that were modified. I've found a minor casing inconsistency in the README.Rmd file that should be addressed.

Comment thread README.Rmd
Comment on lines +25 to +26
[![R-CMD-check](https://github.com/EcologyR/RecruitnetP/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/EcologyR/RecruitnetP/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/EcologyR/RecruitnetP/graph/badge.svg)](https://app.codecov.io/gh/EcologyR/RecruitnetP)

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medium

There's a casing inconsistency in the repository name within the URLs for the new badges. The repository appears to be named RecruitNetP, but the URLs use RecruitnetP. To ensure consistency and prevent potential issues with case-sensitive systems, it's recommended to use the correct casing.

Suggested change
[![R-CMD-check](https://github.com/EcologyR/RecruitnetP/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/EcologyR/RecruitnetP/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/EcologyR/RecruitnetP/graph/badge.svg)](https://app.codecov.io/gh/EcologyR/RecruitnetP)
[![R-CMD-check](https://github.com/EcologyR/RecruitNetP/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/EcologyR/RecruitNetP/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/EcologyR/RecruitNetP/graph/badge.svg)](https://app.codecov.io/gh/EcologyR/RecruitNetP)

@Pakillo Pakillo closed this Feb 18, 2026
@Pakillo
Pakillo deleted the master branch February 18, 2026 16:28
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