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Merge pull request #65 from r-spatialecology/main
shar v1.2
2 parents 05b9b23 + 3490cd0 commit a63e911

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‎.Rbuildignore

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^cran-comments\.md$
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^docs$
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^CODE_OF_CONDUCT.*$
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^LICENSE.*$
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^vignettes/articles$
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vignettes/articles
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^data-raw$
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^\.travis\.yml$
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^codecov\.yml$
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^CONTRIBUTING.*$
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^pkgdown$
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^\.github$
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^LICENSE\.md$

‎.github/.gitignore

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*.html

‎.github/workflows/Deploy-pkgdown.yaml

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on:
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push:
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branches:
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- master
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- CRAN
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name: Deploy-pkgdown
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jobs:
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pkgdown:
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runs-on: macOS-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-r@v1
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- uses: r-lib/actions/setup-pandoc@v1
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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shell: Rscript {0}
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- name: Cache R packages
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uses: actions/cache@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
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- name: Install dependencies
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run: |
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remotes::install_deps(dependencies = TRUE)
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install.packages("pkgdown", type = "binary")
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shell: Rscript {0}
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- name: Install package
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run: R CMD INSTALL .
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- name: Deploy package
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run: |
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git config --local user.email "[email protected]"
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git config --local user.name "GitHub Actions"
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Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'

‎.github/workflows/R-CMD-check.yaml

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# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
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# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
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on:
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push:
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branches:
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- master
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- CRAN
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pull_request:
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branches:
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- master
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- CRAN
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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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strategy:
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fail-fast: false
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matrix:
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config:
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- {os: windows-latest, r: 'release'}
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- {os: macOS-latest, r: 'release'}
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- {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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RSPM: ${{ matrix.config.rspm }}
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-r@v1
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with:
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r-version: ${{ matrix.config.r }}
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- uses: r-lib/actions/setup-pandoc@v1
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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shell: Rscript {0}
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- name: Cache R packages
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if: runner.os != 'Windows'
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uses: actions/cache@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
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- name: Install system dependencies
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if: runner.os == 'Linux'
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run: |
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while read -r cmd
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do
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eval sudo $cmd
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done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
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- name: Install dependencies
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run: |
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remotes::install_deps(dependencies = TRUE)
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remotes::install_cran("rcmdcheck")
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shell: Rscript {0}
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- name: Check
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env:
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_R_CHECK_CRAN_INCOMING_REMOTE_: false
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run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
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shell: Rscript {0}
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- name: Upload check results
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if: failure()
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uses: actions/upload-artifact@main
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with:
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name: ${{ runner.os }}-r${{ matrix.config.r }}-results
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path: check

‎.github/workflows/Render-README.yaml

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on:
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push:
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paths:
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- README.Rmd
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name: Render-README
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jobs:
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render:
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name: Render README
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runs-on: macOS-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@v2
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- uses: r-lib/actions/setup-r@v1
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- uses: r-lib/actions/setup-pandoc@v1
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- name: Install rmarkdown, remotes, and the local package
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run: |
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install.packages("remotes")
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remotes::install_local(".")
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remotes::install_cran("rmarkdown")
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shell: Rscript {0}
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- name: Render README
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run: Rscript -e 'rmarkdown::render("README.Rmd")'
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- name: Commit results
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run: |
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git config --local user.email "[email protected]"
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git config --local user.name "GitHub Actions"
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git add README.md man/figures/README-*
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git commit -m 'Re-build README.Rmd' || echo "No changes to commit"
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git push origin || echo "No changes to commit"

‎.github/workflows/Test-coverage.yaml

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on:
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push:
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branches:
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- master
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- CRAN
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pull_request:
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branches:
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- master
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- CRAN
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name: Test-coverage
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jobs:
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test-coverage:
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runs-on: macOS-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-r@v1
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- uses: r-lib/actions/setup-pandoc@v1
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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shell: Rscript {0}
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- name: Cache R packages
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uses: actions/cache@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
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- name: Install dependencies
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run: |
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install.packages(c("remotes"))
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remotes::install_deps(dependencies = TRUE)
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remotes::install_cran("covr")
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shell: Rscript {0}
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- name: Test coverage
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run: covr::codecov()
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shell: Rscript {0}

‎.gitignore

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.Rproj.user
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.Rhistory
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.RData
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.Ruserdata
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.DS_Store
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inst/doc
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Rplots.pdf
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.Rproj.user
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.Rhistory
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.RData
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.Ruserdata
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.DS_Store
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inst/doc
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Rplots.pdf

‎.travis.yml

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‎DESCRIPTION

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Type: Package
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Package: shar
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Title: Species-Habitat Associations
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Version: 1.1
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Authors@R: c(person("Maximillian H.K.", "Hesselbarth", email = "maximilian.hesselbarth@uni-goettingen.de",
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Version: 1.2
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Authors@R: c(person("Maximillian H.K.", "Hesselbarth", email = "mhk.hesselbarth@gmail.com",
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role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1125-9918")),
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person("Marco", "Sciaini", email = "[email protected]",
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role = "aut", comment = c(ORCID = '0000-0002-3042-5435')))
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Maintainer: Maximillian H.K. Hesselbarth <maximilian.hesselbarth@uni-goettingen.de>
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Maintainer: Maximillian H.K. Hesselbarth <mhk.hesselbarth@gmail.com>
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Description:
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Analyse species-habitat associations in R. Therefore, information about the
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location of the species is needed and about the environmental conditions. To test
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for significance habitat associations, one of the two components is randomized.
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Methods are mainly based on Plotkin et al. (2000) <doi:10.1006/jtbi.2000.2158> and
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Harms et al. (2001) <doi:10.1111/j.1365-2745.2001.00615.x>.
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License: GPL-3
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License: GPL (>= 3)
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URL: https://r-spatialecology.github.io/shar
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BugReports: https://github.com/r-spatialecology/shar/issues
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Depends: R (>= 3.1)
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grDevices,
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methods,
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raster,
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spatstat,
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spatstat.core,
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spatstat.geom,
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stats,
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utils,
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Rcpp
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RoxygenNote: 6.1.1
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RoxygenNote: 7.1.1
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Suggests:
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covr,
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dplyr,
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testthat (>= 2.1.0),
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knitr,
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rmarkdown
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rmarkdown,
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spatstat
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VignetteBuilder: knitr
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Encoding: UTF-8
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LazyData: true

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