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Major changes including website and tests
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‎.Rbuildignore‎

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^LICENSE\.md$
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^data-raw$
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^README\.Rmd$
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^_pkgdown\.yml$
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^docs$
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^pkgdown$
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^\.github$

‎.github/.gitignore‎

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*.html

‎.github/workflows/Linux.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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branches: [main, master]
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pull_request:
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name: R-CMD-check.yaml
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permissions: read-all
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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: 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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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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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::rcmdcheck
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needs: check
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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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build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

‎.github/workflows/MacOS.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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branches: [main, master]
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pull_request:
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name: R-CMD-check.yaml
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permissions: read-all
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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: macos-latest, r: 'release'}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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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::rcmdcheck
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needs: check
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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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build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

‎.github/workflows/Windows.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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branches: [main, master]
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pull_request:
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name: R-CMD-check.yaml
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permissions: read-all
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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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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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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::rcmdcheck
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needs: check
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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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build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

‎.github/workflows/test-coverage.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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branches: [main, master]
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pull_request:
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name: test-coverage.yaml
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permissions: read-all
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jobs:
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test-coverage:
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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::covr, any::xml2
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needs: coverage
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- name: Test coverage
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run: |
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cov <- covr::package_coverage(
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quiet = FALSE,
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clean = FALSE,
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install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
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)
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print(cov)
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covr::to_cobertura(cov)
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shell: Rscript {0}
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- uses: codecov/codecov-action@v5
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with:
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# Fail if error if not on PR, or if on PR and token is given
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fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
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files: ./cobertura.xml
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plugins: noop
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disable_search: true
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token: ${{ secrets.CODECOV_TOKEN }}
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- name: Show testthat output
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if: always()
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run: |
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## --------------------------------------------------------------------
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find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
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shell: bash
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- name: Upload test results
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if: failure()
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uses: actions/upload-artifact@v4
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with:
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name: coverage-test-failures
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path: ${{ runner.temp }}/package

‎.gitignore‎

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Ancillary/*
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inst/doc
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docs

‎DESCRIPTION‎

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RoxygenNote: 7.3.2
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Suggests:
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knitr,
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rmarkdown
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rmarkdown,
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testthat (>= 3.0.0)
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VignetteBuilder: knitr
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Imports:
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assertthat,
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dplyr,
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ggplot2,
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patchwork,
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progress,
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purrr,
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readr,
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rlang,
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tibble,
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Depends:
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R (>= 3.5)
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LazyData: true
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Config/testthat/edition: 3

‎NAMESPACE‎

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# Generated by roxygen2: do not edit by hand
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export("%>%")
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export(averageTimeSeries)
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export(calculatePhytoParam)
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export(createEnviroData)
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export(createInputParams)
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export(extractPPMR)
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export(extractSizeRange)
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export(extractTrophicLevels)
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export(getBiomass)
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export(getGroups)
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export(plotEnvironment)
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export(plotPPMR)
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export(plotSizeSpectra)
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export(plotTimeSeries)
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export(reduceAll)
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export(reduceSize)
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export(reduceSpecies)
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export(untibble)
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export(zAveOutput)
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export(zBiomass)
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export(zCalculatePhytoParam)
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export(zCarbonBiomass)
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export(zConvert2Tibble)
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export(zCreateInputs)
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export(zCreateSimpleTimeSeries)
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export(zExtractAllSum)
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export(zExtractBiomassSize)
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export(zExtractBiomassSpecies)
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export(zExtractSizeRange)
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export(zExtractSizeSum)
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export(zExtractSpeciesSum)
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export(zExtractTrophicLevels)
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export(zExtract_PPMR)
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export(zGetGroups)
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export(zMakeDietTibble)
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export(zPlotEnvironment)
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export(zPlot_AbundTimeSeries)
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export(zPlot_BiomassTimeSeries)
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export(zPlot_GrowthTimeSeries)
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export(zPlot_PPMR)
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export(zPlot_PredTimeSeries)
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export(zPlot_SizeSpectra)
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export(zSpeciesCarbonBiomass)
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export(zValidateGroups)
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export(validateGroups)
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export(zoomss_model)
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export(zoomss_mvf)
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export(zoomss_params)
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export(zoomss_run)
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export(zoomss_setup)
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importFrom(magrittr,"%>%")
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importFrom(rlang,":=")
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importFrom(rlang,.data)

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