Second full review cfr v0.1.0

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$
+^LICENSE\.md$
+^\.github$
+^codecov\.yml$
+^README\.Rmd$
+^\.lintr$
+^\_pkgdown.yml$
+^cran-comments\.md$
+^doc$
+^docs$
+^Meta$
+^pkgdown$
+^data-raw$
+^revdep$
+^CRAN-SUBMISSION$
+^_pkgdown\.yml$
+^CITATION\.cff$

.github/.gitignore

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+*.html

.github/CONTRIBUTING.md

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+# Contributing to _cfr_
+
+This outlines how to propose a change to _cfr_.
+
+## Making changes
+
+If you want to make a change, it's a good idea to first file an issue and make sure someone from the team agrees that it’s needed.
+If you’ve found a bug, please file an issue that illustrates the bug with a minimal 
+[reprex](https://www.tidyverse.org/help/#reprex) (this will also help you write a unit test, if needed). See [bug report template](https://github.com/epiverse-trace/cfr/issues/new?assignees=&labels=&template=bug_report.md&title=). If you have a feature request see [feature request](https://github.com/epiverse-trace/cfr/issues/new?assignees=&labels=&template=feature_request.md&title=).
+
+### Pull request process
+
+See [pull request template](https://github.com/epiverse-trace/cfr/blob/main/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md)
+
+*   Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("epiverse-trace/cfr", fork = TRUE)`.
+
+*   Install all development dependencies with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`. 
+    If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing. 
+*   Create a Git branch for your pull request (PR). We recommend using `usethis::pr_init("brief-description-of-change")`.
+
+*   Make your changes, commit to git, and then create a PR by running `usethis::pr_push()`, and following the prompts in your browser.
+    The title of your PR should briefly describe the change.
+    The body of your PR should contain `Fixes #issue-number`.
+
+*  For user-facing changes, add a bullet to the top of `NEWS.md` (i.e. just below the first header). Follow the style described in <https://style.tidyverse.org/news.html>.
+
+### Code style
+
+*   New code should follow the tidyverse [style guide](https://style.tidyverse.org). 
+    You can use the [styler](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.  
+
+*  We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html), for documentation.  
+
+*  We use [testthat](https://cran.r-project.org/package=testthat) for unit tests. 
+   Contributions with test cases included are easier to accept.  
+
+## Code of Conduct
+
+Please note that the _cfr_ project is released with a
+[Contributor Code of Conduct](https://github.com/epiverse-trace/.github/blob/main/CODE_OF_CONDUCT.md). By contributing to this
+project you agree to abide by its terms.

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+*Bugs* may include behaviour that does not impact package functionality, but which seems as though it might not be intended by the package developers.
+
+Please place an "x" in all the boxes that apply
+---------------------------------------------
+
+- [ ] I have the most recent version of _cfr_ and R
+- [ ] I have found a bug
+- [ ] I have a [reproducible example](https://reprex.tidyverse.org/articles/reprex-dos-and-donts.html)
+- [ ] I want to request a new feature
+
+--------
+
+Please include a brief description of the problem with a code example:
+
+```r
+# insert reprex here
+```
+
+---------

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest a feature to be added to this package
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. E.g. "When passing arguments as [...]"
+
+**Describe the solution you would like**
+A clear and concise description of what you want to happen.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/PULL_REQUEST_TEMPLATE/pull_request_template.md

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+* **Please check if the pull request fulfills these requirements**
+
+- [ ] I have read the CONTRIBUTING guidelines 
+- [ ] The commit message follows our guidelines
+- [ ] Tests for the changes have been added (for bug fixes / features)
+- [ ] Docs have been added / updated (for bug fixes / features)
+
+
+* **What kind of change does this PR introduce?** (Bug fix, feature, docs update, ...)
+
+* **What is the current behaviour?** (You can also link to an open issue here)
+
+* **What is the new behaviour (if this is a feature change)?**
+
+* **Does this PR introduce a breaking change?** (What changes might users need to make in their workflow due to this PR?)
+
+* **Other information**:

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

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+#
+# Reproduce locally by running:
+# ```r
+# pak::pak(c("any::rcmdcheck", "."), dependencies = "Config/Needs/check")
+# rcmdcheck::rcmdcheck()
+# ```
+on:
+  push:
+    branches: [main, master]
+    paths:
+      - 'data/**'
+      - 'R/**'
+      - 'inst/**'
+      - 'man/**'
+      - 'src/**'
+      - 'tests/**'
+      - 'vignettes/**'
+      - 'DESCRIPTION'
+      - 'NAMESPACE'
+      - 'LICENSE'
+      - '.Rbuildignore'
+      - '.github/workflows/R-CMD-check.yaml'
+  pull_request:
+    paths:
+      - 'data/**'
+      - 'R/**'
+      - 'inst/**'
+      - 'man/**'
+      - 'src/**'
+      - 'tests/**'
+      - 'vignettes/**'
+      - 'DESCRIPTION'
+      - 'NAMESPACE'
+      - 'LICENSE'
+      - '.Rbuildignore'
+      - '.github/workflows/R-CMD-check.yaml'
+
+name: R-CMD-check
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+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
+      # Exists since R 4.3.0 but `false` by default
+      _R_CHECK_LENGTH_COLON_: true
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - 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
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        id: rcmdcheck
+        with:
+          upload-snapshots: true
+
+      # fail-fast but only if rcmdcheck step fails
+      - name: Manual fail-fast
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        if: always() && steps.rcmdcheck.outcome == 'failure'
+        run: gh run cancel ${{ github.run_id }}

.github/workflows/pkgdown.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+#
+# Reproduce locally by running:
+# ```r
+# pak::pak(c("any::pkgdown", "."), dependencies = "Config/Needs/website")
+# pkgdown::build_site()
+# ```
+on:
+  push:
+    branches: [main, master]
+    paths:
+      - 'README.Rmd'
+      - 'README.md'
+      - 'index.Rmd'
+      - 'index.md'
+      - 'man/**'
+      - 'vignettes/**'
+      - '_pkgdown.yml'
+      - 'pkgdown/**'
+      - 'DESCRIPTION'
+      - '.Rbuildignore'
+      - '.github/**'
+  pull_request:
+    paths:
+      - 'README.Rmd'
+      - 'README.md'
+      - 'index.Rmd'
+      - 'index.md'
+      - 'man/**'
+      - 'vignettes/**'
+      - '_pkgdown.yml'
+      - 'pkgdown/**'
+      - 'DESCRIPTION'
+      - '.Rbuildignore'
+      - '.github/**'
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          # We clean on releases because we want to remove old vignettes,
+          # figures, etc. that have been deleted from the `main` branch.
+          # But we clean ONLY on releases because we want to be able to keep
+          # both the 'stable' and 'dev' websites.
+          # Also discussed in https://github.com/r-lib/actions/issues/484
+          clean: ${{ github.event_name == 'release' }}
+          branch: gh-pages
+          folder: docs

.github/workflows/render_readme.yml

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+name: render-readme
+
+# Controls when the action will run. Triggers include:
+#
+# - button trigger from github action page
+# - on changes to readme.Rmd
+
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - 'README.Rmd'
+      - '.github/workflows/render_readme.yml'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  render-readme:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repos
+        uses: actions/checkout@v3
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Setup pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rmarkdown, local::.
+
+      - name: Compile the readme
+        run: |
+          writeLines(
+            knitr::knit_expand(
+              "README.Rmd",
+              packagename = read.dcf("DESCRIPTION", "Package"),
+              gh_repo = Sys.getenv("GITHUB_REPOSITORY")
+            ),
+            "README_expanded.Rmd"
+          )
+          rmarkdown::render(
+            "README_expanded.Rmd",
+            output_file = "README.md",
+            output_dir = "."
+          )
+        shell: Rscript {0}
+
+      - name: Commit files
+        run: |
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Action"
+          git add README.md
+          # Also add README figures if they exist
+          if [ -d man/figures ]
+          then
+            git add man/figures/
+          fi
+          git diff-index --quiet HEAD || git commit -m "Automatic readme update"
+          git push origin || echo "No changes to push"