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Merge pull request #12 from PecanProject/mvp-betydata
Move datapackage.json to repo root (Frictionless spec)
2 parents 65ca70d + a6f793c commit 528739c

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‎.Rbuildignore‎

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^.*.Rproj$
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^.Rproj.user$
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^README.Rmd$
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^LICENSE.md$
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^.github$
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^data-raw$
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^_pkgdown.yml$
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^docs$
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^pkgdown$
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^.lintr$
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^codecov.yml$
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^.pre-commit-config.yaml$
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^renv$
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^renv.lock$
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^betydata\.Rproj$
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^\.Rproj\.user$
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^CITATION\.cff$
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^vignettes/.*_files$
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^_quarto\.yml$
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^_site$
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^_freeze$
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^index\.qmd$
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^_publish\.yml$
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^datapackage\.json$

‎.github/ISSUE_TEMPLATE/data_correction.md‎

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---
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name: Data correction
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about: Report an error in betydata and suggest a correction
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labels: data, correction
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---
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### Summary
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<!-- Brief description of the issue -->
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### Affected Record(s)
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| Field | Value |
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|-------|-------|
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| Dataset | traitsview / species / other |
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| Record ID(s) | |
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| Column(s) | |
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### Current Value
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<!-- What the data currently shows -->
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### Suggested Correction
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<!-- What the value should be -->
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### Source
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<!-- How you know the current value is wrong (publication, original data, etc.) -->
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- Citation/DOI:
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- Page/Table:
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- Additional evidence:
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### Additional Context
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<!-- Any other relevant information -->

‎.github/ISSUE_TEMPLATE/verified_record.md‎

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---
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name: Verified record report
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about: Report that you have verified a record matches its source
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labels: data, verification
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---
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### Summary
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<!-- Which record(s) have you verified? -->
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### Verified Record(s)
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| Field | Value |
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|-------|-------|
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| Dataset | traitsview / other |
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| Record ID(s) | |
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### Verification Details
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- Citation/DOI checked:
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- Page/Table/Figure:
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- Date verified:
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### Confirmation
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- [ ] I have compared the record(s) to the original source
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- [ ] The values match the source publication
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- [ ] The `checked` value should be updated to `1` (passed)
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### Notes
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<!-- Any discrepancies or observations -->

‎.github/PULL_REQUEST_TEMPLATE.md‎

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## Description
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<!-- Describe your changes in detail -->
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## Related Issue(s)
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<!-- Link to issue(s) this PR addresses -->
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## Type of Change
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<!-- Put an `x` in all boxes that apply -->
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- [ ] Bug fix (non-breaking change which fixes an issue)
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- [ ] New feature (non-breaking change which adds functionality)
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- [ ] Data update (changes to datasets)
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- [ ] Documentation update
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- [ ] Breaking change (fix or feature that would cause existing functionality to change)
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## Checklist
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<!-- Put an `x` in all boxes that apply -->
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- [ ] I have run `devtools::check()` with no errors or warnings
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- [ ] I have updated NEWS.md if applicable
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- [ ] I have updated documentation if applicable
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- [ ] I have added/updated tests if applicable
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## Data Changes (if applicable)
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<!-- If this PR modifies data, describe the changes -->
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- [ ] Data rebuilt from source using `data-raw/make-data.R`
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- [ ] datapackage.json updated
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- [ ] Row counts verified
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## Additional Notes
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<!-- Any other information reviewers should know -->

‎.github/PULL_REQUEST_TEMPLATE/data_correction.md‎

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## Data Correction
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### Summary
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<!-- Brief description of the correction -->
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### Affected Record(s)
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| Field | Value |
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|-------|-------|
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| Table | traitsview / species / other |
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| Record ID(s) | |
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| Column(s) | |
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### Current Value
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<!-- What the data currently shows -->
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### Corrected Value
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<!-- What the value should be -->
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### Source / Evidence
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<!-- How you verified the correction (publication DOI, original data, etc.) -->
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- Citation/DOI:
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- Page/Table:
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### Changes Made
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- [ ] Edited CSV in `data-raw/csv/`
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- [ ] Ran `source("data-raw/make-data.R")` to rebuild `.rda` files
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- [ ] Verified correction in the rebuilt data
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- [ ] Updated `NEWS.md`
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### Checklist
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- [ ] I have compared the corrected value to the original source
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- [ ] `devtools::check()` passes with no errors

‎.github/workflows/R-CMD-check.yaml‎

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on:
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push:
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branches: [main, develop]
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pull_request:
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branches: [main, develop]
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workflow_dispatch: # Allow manual triggers
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name: R-CMD-check
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permissions:
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contents: read
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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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- {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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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: quarto-dev/quarto-actions/setup@v2
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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, local::.
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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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args: 'c("--no-manual", "--as-cran")'

‎.github/workflows/quarto-publish.yml‎

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name: Deploy Quarto site to GitHub Pages
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on:
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push:
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branches: [main]
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workflow_dispatch:
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permissions:
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contents: write
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pages: write
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jobs:
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build-deploy:
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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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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Setup R
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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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- name: Install R dependencies
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uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: |
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local::.
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any::dplyr
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any::ggplot2
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any::knitr
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any::maps
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- name: Setup Quarto
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uses: quarto-dev/quarto-actions/setup@v2
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- name: Render and deploy to gh-pages
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uses: quarto-dev/quarto-actions/publish@v2
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with:
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target: gh-pages
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎.gitignore‎

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*.html
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.Rhistory
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.Rdata
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.RData
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.Ruserdata
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.Rproj.user
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*.tar.gz
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*.Rcheck/
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.DS_Store
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Thumbs.db
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.vscode/
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*.swp
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renv/library/
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renv/local/
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renv/cellar/
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renv/lock/
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renv/python/
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renv/sandbox/
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_site/
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_freeze/
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/.quarto/
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vignettes/*_files/

‎CITATION.cff‎

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cff-version: 1.2.0
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title: "betydata: Public Data from the BETYdb Database"
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version: 0.1.0
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abstract: >-
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An R data package providing offline access to public plant trait and
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crop yield data from the BETYdb (Biofuel Ecophysiological Traits and
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Yields) database.
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license: BSD-3-Clause
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# doi: -- will be assigned by Zenodo on first github release
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message: >-
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If you use this data package, please cite both this software and
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the BETYdb paper (see preferred-citation below).
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type: dataset
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date-released: "2026-02-11"
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repository-code: https://github.com/PecanProject/betydata
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url: https://betydb.org
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keywords:
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- plant traits
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- crop yields
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- bioenergy
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- ecosystem modeling
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- BETYdb
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- PEcAn
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- ecological data
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- R data package
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authors:
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- given-names: David
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family-names: LeBauer
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email: dlebauer@arizona.edu
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affiliation: University of Arizona
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orcid: 'https://orcid.org/0000-0001-7228-053X'
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- given-names: Akash
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family-names: BV
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email: www.divinehome12@gmail.com
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affiliation: CMR Institute of Technology, Bengaluru
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preferred-citation:
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type: article
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title: >-
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BETYdb: a yield, trait, and ecosystem service database applied to
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second-generation bioenergy feedstock production
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authors:
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- given-names: David
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family-names: LeBauer
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- given-names: Rob
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family-names: Kooper
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- given-names: Patrick
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family-names: Mulrooney
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- given-names: Scott
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family-names: Rohde
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- given-names: Dan
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family-names: Wang
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- given-names: Stephen P.
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family-names: Long
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- given-names: Michael C.
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family-names: Dietze
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journal: GCB Bioenergy
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year: 2018
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volume: 10
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issue: 1
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start: 61
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end: 71
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doi: "10.1111/gcbb.12420"

‎DESCRIPTION‎

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Package: betydata
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Title: What the Package Does (One Line, Title Case)
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Version: 0.0.0.9000
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Authors@R:
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person("First", "Last", , "first.last@example.com", role = c("aut", "cre"))
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Description: What the package does (one paragraph).
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License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
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license
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Type: Package
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Title: Public Data from the BETYdb Database
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Version: 0.1.0
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Authors@R: c(
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person("David", "LeBauer", email = "dlebauer@arizona.edu", role = c("aut", "cre")),
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person("Akash B V", email = "www.divinehome12@gmail.com", role = "aut")
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)
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Description: An R data package providing offline access to public data from
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the BETYdb database (betydb.org). Includes plant traits, crop yields,
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and supporting metadata for bioenergy and ecosystem research. This
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package enables reproducible analyses without requiring database access.
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License: BSD_3_clause + file LICENSE
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URL: https://github.com/PecanProject/betydata,
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https://betydb.org
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BugReports: https://github.com/PecanProject/betydata/issues
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Depends:
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R (>= 4.1.0)
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Suggests:
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dplyr (>= 1.1.0),
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ggplot2,
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jsonlite,
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knitr,
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maps,
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quarto,
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rmarkdown,
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testthat (>= 3.0.0)
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VignetteBuilder: quarto
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SystemRequirements: Quarto command line tool (https://github.com/quarto-dev/quarto-cli)
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Encoding: UTF-8
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LazyData: true
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LazyDataCompression: xz
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Roxygen: list(markdown = TRUE)
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RoxygenNote: 7.3.2
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RoxygenNote: 7.3.3
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Config/testthat/edition: 3

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