betydata R data package with BETYdb public data export

.Rbuildignore

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

.github/ISSUE_TEMPLATE/data_correction.md

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

.github/ISSUE_TEMPLATE/verified_record.md

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

.github/PULL_REQUEST_TEMPLATE.md

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

.github/PULL_REQUEST_TEMPLATE/data_correction.md

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

.github/workflows/R-CMD-check.yaml

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+on:
+  push:
+    branches: [main, develop]
+  pull_request:
+    branches: [main, develop]
+  workflow_dispatch:  # Allow manual triggers
+
+name: R-CMD-check
+
+permissions:
+  contents: read
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: quarto-dev/quarto-actions/setup@v2
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck, local::.
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          args: 'c("--no-manual", "--as-cran")'

.github/workflows/quarto-publish.yml

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

.gitignore

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

CITATION.cff

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

DESCRIPTION

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

LICENSE

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+YEAR: 2025
+COPYRIGHT HOLDER: David LeBauer