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Merge branch 'dev' into ml-99-panel-data-vignette
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‎.Rbuildignore

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^renv$
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^renv\.lock$
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^epipredict\.Rproj$
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^\.Rproj\.user$
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^LICENSE\.md$
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^drafts$
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^\.Rprofile$
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^man-roxygen$
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^README\.Rmd$
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^\.github$
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^musings$
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^data-raw$
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^vignettes/articles$
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^.git-blame-ignore-revs$
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^doc$
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^Meta$

‎.git-blame-ignore-revs

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# using styler at all
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aca7d5e7b66d8bac9d9fbcec3acdb98a087d58fa
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f12fcc2bf3fe0a75ba2b10eaaf8a1f1d22486a17

‎.github/pull_request_template.md

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### Checklist
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Please:
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- [ ] Make sure this PR is against "dev", not "main".
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- [ ] Request a review from one of the current epipredict main reviewers:
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dajmcdon.
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- [ ] Makes sure to bump the version number in `DESCRIPTION` and `NEWS.md`.
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Always increment the patch version number (the third number), unless you are
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making a release PR from dev to main, in which case increment the minor
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version number (the second number).
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- [ ] Describe changes made in NEWS.md, making sure breaking changes
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(backwards-incompatible changes to the documented interface) are noted.
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Collect the changes under the next release number (e.g. if you are on
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0.7.2, then write your changes under the 0.8 heading).
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### Change explanations for reviewer
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### Magic GitHub syntax to mark associated Issue(s) as resolved when this is merged into the default branch
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- Resolves #{issue number}

‎.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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# Created with usethis + edited to use API key.
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on:
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push:
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branches: [main, frosting]
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branches: [main, dev]
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pull_request:
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branches: [main, frosting]
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branches: [main, dev]
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name: R-CMD-check
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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@v2
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- uses: actions/checkout@v3
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- uses: r-lib/actions/setup-r@v2
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with:
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needs: check
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- uses: r-lib/actions/check-r-package@v2
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env:
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DELPHI_EPIDATA_KEY: ${{ secrets.SECRET_EPIPREDICT_GHACTIONS_DELPHI_EPIDATA_KEY }}

‎.github/workflows/pkgdown.yaml

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# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
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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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# Created with usethis + edited to run on PRs to dev, use API key.
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on:
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push:
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branches: [main, master]
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branches: [dev, main]
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pull_request:
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branches: [dev, main]
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release:
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types: [published]
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workflow_dispatch:
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jobs:
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pkgdown:
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# only build docs on the main repository and not forks
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if: github.repository_owner == 'cmu-delphi'
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runs-on: ubuntu-latest
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# Only restrict concurrency for non-PR jobs
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concurrency:
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group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
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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: actions/checkout@v3
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- uses: r-lib/actions/setup-pandoc@v2
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needs: website
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- name: Build site
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run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
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env:
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DELPHI_EPIDATA_KEY: ${{ secrets.SECRET_EPIPROCESS_GHACTIONS_DELPHI_EPIDATA_KEY }}
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run: |
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if (startsWith("${{ github.event_name }}", "pull_request")) {
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mode <- ifelse("${{ github.base_ref }}" == "main", "release", "devel")
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} else {
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mode <- ifelse("${{ github.ref_name }}" == "main", "release", "devel")
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}
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pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE, override=list(PKGDOWN_DEV_MODE=mode))
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shell: Rscript {0}
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- name: Deploy to GitHub pages 🚀
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if: github.event_name != 'pull_request'
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uses: JamesIves/[email protected].4
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uses: JamesIves/github-pages-deploy-action@v4.4.1
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with:
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clean: false
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branch: gh-pages

‎.github/workflows/styler.yml

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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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workflow_dispatch:
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pull_request:
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paths:
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[
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"**.[rR]",
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"**.[qrR]md",
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"**.[rR]markdown",
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"**.[rR]nw",
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"**.[rR]profile",
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]
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name: Style
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jobs:
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style:
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- name: Checkout repo
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uses: actions/checkout@v3
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with:
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fetch-depth: 0
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- name: Setup R
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uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- name: Install dependencies
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uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::styler, any::roxygen2
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needs: styler
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- name: Enable styler cache
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run: styler::cache_activate()
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shell: Rscript {0}
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- name: Determine cache location
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id: styler-location
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run: |
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cat(
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"location=",
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styler::cache_info(format = "tabular")$location,
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"\n",
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file = Sys.getenv("GITHUB_OUTPUT"),
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append = TRUE,
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sep = ""
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)
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shell: Rscript {0}
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- name: Cache styler
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uses: actions/cache@v3
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with:
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path: ${{ steps.styler-location.outputs.location }}
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key: ${{ runner.os }}-styler-${{ github.sha }}
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restore-keys: |
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${{ runner.os }}-styler-
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${{ runner.os }}-
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- name: Style
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run: styler::style_pkg()
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shell: Rscript {0}
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- name: Commit and push changes
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run: |
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if FILES_TO_COMMIT=($(git diff-index --name-only ${{ github.sha }} \
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| egrep --ignore-case '\.(R|[qR]md|Rmarkdown|Rnw|Rprofile)$'))
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then
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git config --local user.name "$GITHUB_ACTOR"
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git config --local user.email "[email protected]"
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git commit ${FILES_TO_COMMIT[*]} -m "Style code (GHA)"
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git pull --ff-only
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git push origin
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else
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echo "No changes to commit."
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fi

‎.gitignore

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docs
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inst/doc
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.DS_Store
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/doc/
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/Meta/
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.Rprofile
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renv.lock
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renv/

‎DESCRIPTION

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Package: epipredict
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Title: Basic epidemiology forecasting methods
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Version: 0.0.3
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Version: 0.0.9
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Authors@R: c(
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person("Daniel", "McDonald", , "[email protected]", role = c("aut", "cre")),
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person("Ryan", "Tibshirani", , "[email protected]", role = "aut"),
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person("Logan", "Brooks", role = "aut"),
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person("Rachel", "Lobay", role = "aut"),
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person("Maggie", "Liu", role = "aut"),
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person("Ken", "Mawer", role = "aut"),
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person("Chloe", "You", role = "aut"),
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person("Dmitry", "Shemetov", email = "[email protected]", role = "ctb"),
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person("David", "Weber", email = "[email protected]", role = "ctb"),
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person("Maggie", "Liu", role = "ctb"),
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person("Ken", "Mawer", role = "ctb"),
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person("Chloe", "You", role = "ctb"),
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person("Jacob", "Bien", role = "ctb")
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)
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Description: A forecasting "framework" for creating epidemiological
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URL: https://github.com/cmu-delphi/epipredict/,
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https://cmu-delphi.github.io/epipredict
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BugReports: https://github.com/cmu-delphi/epipredict/issues/
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Depends:
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epiprocess,
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Depends:
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epiprocess (>= 0.6.0),
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parsnip (>= 1.0.0),
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R (>= 3.5.0)
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Imports:
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Imports:
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checkmate,
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cli,
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distributional,
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dplyr,
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fs,
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generics,
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glue,
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hardhat (>= 1.2.0),
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hardhat (>= 1.3.0),
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lifecycle,
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magrittr,
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methods,
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quantreg,
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recipes (>= 1.0.0),
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recipes (>= 1.0.4),
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rlang,
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smoothqr,
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stats,
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tensr,
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tibble,
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tidyr,
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tidyselect,
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usethis,
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vctrs,
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workflows (>= 1.0.0)
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Suggests:
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Suggests:
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covidcast,
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data.table,
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epidatr,
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epidatr (>= 1.0.0),
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ggplot2,
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knitr,
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lubridate,
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rmarkdown,
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testthat (>= 3.0.0),
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xgboost
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VignetteBuilder:
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VignetteBuilder:
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knitr
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Remotes:
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cmu-delphi/epidatr,
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cmu-delphi/epiprocess
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cmu-delphi/epiprocess,
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dajmcdon/smoothqr
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Config/testthat/edition: 3
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Encoding: UTF-8
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LazyData: true
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Roxygen: list(markdown = TRUE)
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RoxygenNote: 7.2.3
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RoxygenNote: 7.3.0

‎DEVELOPMENT.md

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## Setting up the development environment
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```r
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install.packages(c('devtools', 'pkgdown', 'styler', 'lintr')) # install dev dependencies
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devtools::install_deps(dependencies = TRUE) # install package dependencies
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devtools::document() # generate package meta data and man files
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devtools::build() # build package
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```
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## Validating the package
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```r
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styler::style_pkg() # format code
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lintr::lint_package() # lint code
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devtools::test() # test package
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devtools::check() # check package for errors
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```
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## Developing the documentation site
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The [documentation site](https://cmu-delphi.github.io/epipredict/) is built off of the `main` branch. The `dev` version of the site is available at https://cmu-delphi.github.io/epipredict/dev.
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The documentation site can be previewed locally by running in R
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```r
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pkgdown::build_site(preview=TRUE)
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```
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The `main` version is available at `file:///<local path>/epidatr/epipredict/index.html` and `dev` at `file:///<local path>/epipredict/docs/dev/index.html`.
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You can also build the docs manually and launch the site with python. From the terminal, this looks like
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```bash
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R -e 'devtools::document()'
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python -m http.server -d docs
36+
```
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## Versioning
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40+
Please follow the guidelines in the PR template document (reproduced here):
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42+
- [ ] Make sure this PR is against "dev", not "main".
43+
- [ ] Request a review from one of the current epipredict main reviewers:
44+
dajmcdon.
45+
- [ ] Makes sure to bump the version number in `DESCRIPTION` and `NEWS.md`.
46+
Always increment the patch version number (the third number), unless you are
47+
making a release PR from dev to main, in which case increment the minor
48+
version number (the second number).
49+
- [ ] Describe changes made in NEWS.md, making sure breaking changes
50+
(backwards-incompatible changes to the documented interface) are noted.
51+
Collect the changes under the next release number (e.g. if you are on
52+
0.7.2, then write your changes under the 0.8 heading).
53+
54+
## Release process
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TBD

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