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feat: Add GitHub Actions workflow for R CMD check.
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‎.github/workflows/R-CMD-check.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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#
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# Matrix mirrors active CRAN check platforms:
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# https://cran.r-project.org/web/checks/check_flavors.html
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on:
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push:
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branches:
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- main
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- master
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- develop
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- development
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- performance
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- 'feature/**'
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- 'bugfix/**'
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- 'hotfix/**'
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- 'fix/**'
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pull_request:
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branches:
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- main
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- master
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- develop
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- development
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- performance
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- 'feature/**'
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- 'bugfix/**'
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- 'hotfix/**'
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- 'fix/**'
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name: R-CMD-check
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jobs:
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R-CMD-check:
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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name: ${{ matrix.config.cran_flavor }}
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strategy:
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fail-fast: false
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matrix:
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config:
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- {os: macos-latest, r: 'release'}
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- {os: windows-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
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- {os: ubuntu-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'oldrel-1'}
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# ── macOS ARM64 ─────────────────────────────────────────────────────
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- {os: macos-latest, r: 'devel', cran_flavor: 'r-devel-macos-arm64'}
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- {os: macos-latest, r: 'release', cran_flavor: 'r-release-macos-arm64'}
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- {os: macos-latest, r: 'oldrel-1', cran_flavor: 'r-oldrel-macos-arm64'}
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# ── macOS x86_64 ─────────────────────────────────────────────────────
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- {os: macos-26-intel, r: 'devel', cran_flavor: 'r-devel-macos-x86_64'}
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- {os: macos-26-intel, r: 'release', cran_flavor: 'r-release-macos-x86_64'}
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- {os: macos-26-intel, r: 'oldrel-1', cran_flavor: 'r-oldrel-macos-x86_64'}
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# ── Windows x86_64 ───────────────────────────────────────────────────
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- {os: windows-latest, r: 'devel', cran_flavor: 'r-devel-windows-x86_64'}
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- {os: windows-latest, r: 'release', cran_flavor: 'r-release-windows-x86_64'}
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- {os: windows-latest, r: 'oldrel-1', cran_flavor: 'r-oldrel-windows-x86_64'}
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# ── Windows ARM64 ────────────────────────────────────────────────────
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- {os: windows-11-arm, r: 'devel', cran_flavor: 'r-devel-windows-arm64'}
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- {os: windows-11-arm, r: 'release', cran_flavor: 'r-release-windows-arm64'}
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- {os: windows-11-arm, r: 'oldrel-1', cran_flavor: 'r-oldrel-windows-arm64'}
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# ── Linux x86_64 (covers all four Linux CRAN flavors) ────────────────
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- {os: ubuntu-latest, r: 'devel', cran_flavor: 'r-devel-linux-x86_64', http-user-agent: 'release'}
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- {os: ubuntu-latest, r: 'release', cran_flavor: 'r-release-linux-x86_64'}
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- {os: ubuntu-latest, r: 'oldrel-1', cran_flavor: 'r-oldrel-linux-x86_64'}
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# ── Linux ARM64 ──────────────────────────────────────────────────────
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- {os: ubuntu-24.04-arm, r: 'release', cran_flavor: 'r-release-linux-arm64'}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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- uses: r-lib/actions/check-r-package@v2
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with:
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upload-snapshots: true
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error-on: '"error"'

‎.github/workflows/pkgdown.yaml‎

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branches:
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- main
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- master
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- develop
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- development
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- performance
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- 'feature/**'
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- 'bugfix/**'
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- 'hotfix/**'
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- 'fix/**'
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pull_request:
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branches:
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- main
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- master
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- develop
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- development
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- performance
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- 'feature/**'
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- 'bugfix/**'
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- 'hotfix/**'
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- 'fix/**'
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release:
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types: [published]
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workflow_dispatch:

‎.github/workflows/spell-check.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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pull_request:
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workflow_dispatch:
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name: spell-check
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jobs:
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spell-check:
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::spelling
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needs: check
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- name: Spell check
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run: spelling::spell_check_package(error = TRUE)
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shell: Rscript {0}

‎.github/workflows/test-coverage.yaml‎

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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches:
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- main
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- master
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- develop
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- development
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- performance
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- 'feature/**'
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- 'bugfix/**'
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- 'hotfix/**'
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- 'fix/**'
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pull_request:
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branches:
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- main
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- master
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- develop
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- development
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- performance
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- 'feature/**'
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- 'bugfix/**'
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- 'hotfix/**'
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- 'fix/**'
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name: test-coverage
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‎DESCRIPTION‎

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Package: selection.index
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Type: Package
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Title: Analysis of Selection Index in Plant Breeding
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Version: 2.0.0.9000
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Version: 2.0.1
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Date: 2026-03-06
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Authors@R:
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c(person(given = "Zankrut",
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family = "Goyani",

‎NEWS.md‎

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# selection.index (development version)
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# selection.index 2.0.1
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* Fixed numerical stability in `ppg_esim` tests where `eigen()` could return complex values on certain hardware architectures (e.g., macOS ARM64).
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* Added automated documentation spell-checking via the `spelling` package in a dedicated GitHub Actions workflow.
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* Expanded the GitHub Actions CI matrix to 17 runners, mirroring all official CRAN check flavors.
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# selection.index 2.0.0
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‎README.Rmd‎

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[![Total downloads](https://cranlogs.r-pkg.org/badges/grand-total/selection.index?color=blue)](https://CRAN.R-project.org/package=selection.index)
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[![Monthly downloads](https://cranlogs.r-pkg.org/badges/last-month/selection.index?color=green)](https://cran.r-project.org/package=selection.index)
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[![Codecov test coverage](https://codecov.io/gh/zankrut20/selection.index/branch/master/graph/badge.svg)](https://app.codecov.io/gh/zankrut20/selection.index?branch=master)
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[![CodeFactor](https://www.codefactor.io/repository/github/zankrut20/selection.index/badge)](https://www.codefactor.io/repository/github/zankrut20/selection.index)
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[![CodeFactor](https://www.codefactor.io/repository/github/zankrut20/selection.index/badge/master)](https://www.codefactor.io/repository/github/zankrut20/selection.index/overview/master)
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[![GitHub stars](https://img.shields.io/github/stars/zankrut20/selection.index?style=social)](https://github.com/zankrut20/selection.index/stargazers)
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[![GitHub issues](https://img.shields.io/github/issues/zankrut20/selection.index)](https://github.com/zankrut20/selection.index/issues)
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[![GitHub forks](https://img.shields.io/github/forks/zankrut20/selection.index?style=social)](https://github.com/zankrut20/selection.index/network/members)

‎README.md‎

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downloads](https://cranlogs.r-pkg.org/badges/last-month/selection.index?color=green)](https://cran.r-project.org/package=selection.index)
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[![Codecov test
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coverage](https://codecov.io/gh/zankrut20/selection.index/branch/master/graph/badge.svg)](https://app.codecov.io/gh/zankrut20/selection.index?branch=master)
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[![CodeFactor](https://www.codefactor.io/repository/github/zankrut20/selection.index/badge)](https://www.codefactor.io/repository/github/zankrut20/selection.index)
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[![CodeFactor](https://www.codefactor.io/repository/github/zankrut20/selection.index/badge/master)](https://www.codefactor.io/repository/github/zankrut20/selection.index/overview/master)
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[![GitHub
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[![GitHub

‎cran-comments.md‎

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## Test environments
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* OS X (on GitHub Actions), R 4.3.2
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* ubuntu 20.04 (on GitHub Actions), R 4.3.2
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* local Windows 11, R 4.5.2
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* GitHub Actions:
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* macOS (arm64 and x86_64) — R devel, release, oldrel-1 (total 6 runners)
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* Windows (arm64 and x86_64) — R devel, release, oldrel-1 (total 6 runners)
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* Linux (x86_64 and arm64) — R devel, release, patched, oldrel-1 (total 5 runners)
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* win-builder (devel and release)
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## R CMD check results
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0 errors | 0 warnings | 0 notes
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0 errors | 0 warnings | 1 note
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* NOTE: Installed package size is 9.2Mb.
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Justification: The installed size is primarily driven by the `libs` directory (~8.0Mb). This is expected and due to the heavy C++ template metaprogramming from `RcppEigen` used in the core mathematical engine.
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## Reverse dependencies
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I have checked 0 reverse dependencies and found no issues.
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---
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## Submission Summary
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This is a major release (1.2.1 -> 2.0.0) reflecting a comprehensive rewrite of the mathematical engine, sweeping new feature additions for modern quantitative genetics, and API rationalization.
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This is a resubmission to address the CRAN check failures reported in version 2.0.0 (requested to be fixed by 2026-03-16).
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**Fixes for CRAN:**
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* **Fixed ERROR on macOS ARM64 (r-oldrel-macos-arm64):** Fixed the `invalid comparison with complex values` testing error in `ppg_esim`. The `eigen()` function returned tiny imaginary parts on macOS ARM64 for non-symmetric matrices; we now wrap the values in `Re()` before rank evaluation.
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**Major Changes in 2.0.0:**
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* **C++ Integration:** The core mathematical solvers (matrices, combinatorial index permutations) have been transitioned to C++ using `Rcpp` and `RcppEigen` for a structural performance overhaul.
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* **API Standardization:** Core functions transitioned from dot.notation to snake_case (e.g. `phen.varcov()` -> `phen_varcov()`) to comply with CRAN S3 dispatch recommendations and modernize the API.
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* **Modern Genetics Methodologies Added:** Substantial new functions handling Genomic Selection Indices, Marker-Assisted Selection, Eigen-based indices, Constrained/Restricted indices, and Multi-Stage selection.
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* **Simulation:** Added stochastic genetic advance simulation models explicitly tracking progressive selection over multiple generations.
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* **Vignettes:** 10 comprehensive vignettes added mathematically documenting the index formulations.
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**Other Enhancements in 2.0.1:**
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* **Expanded CI Coverage:** Integrated a comprehensive 17-runner GitHub Actions matrix mirroring all official CRAN check flavors including explicit ARM64 support for macOS, Windows, and Linux.
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* **Documentation:** Automated spell-checking integrated into the CI pipeline via the `spelling` package.
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Thank you to the CRAN team for reviewing this significant update.
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Thank you to the CRAN team for reviewing this update.

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