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<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en-US"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>TODO • rdev</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="apple-touch-icon.png"><link rel="icon" sizes="any" href="favicon.ico"><link rel="manifest" href="site.webmanifest"><script src="lightswitch.js"></script><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><link href="extra.css" rel="stylesheet"><meta property="og:title" content="TODO"><meta property="og:image" content="https://jabenninghoff.github.io/rdev/logo.png"></head><body>
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<img src="logo.png" class="logo" alt=""><h1>TODO</h1>
<small class="dont-index">Source: <a href="https://github.com/jabenninghoff/rdev/blob/HEAD/TODO.md" class="external-link"><code>TODO.md</code></a></small>
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<div id="todo" class="section level1">
<div class="section level2">
<h2 id="content">Content<a class="anchor" aria-label="anchor" href="#content"></a></h2>
<ul class="task-list"><li><label><input type="checkbox" checked>Add README.Rmd</label></li>
<li><label><input type="checkbox" checked>Update <code>DESCRIPTION</code> and use description data in <code>README.Rmd</code></label></li>
<li><label><input type="checkbox" checked>Add ORCID</label></li>
<li><label><input type="checkbox" checked>Update my ORCID details</label></li>
</ul></div>
<div class="section level2">
<h2 id="package">Package<a class="anchor" aria-label="anchor" href="#package"></a></h2>
<ul class="task-list"><li><label><input type="checkbox" checked>Write a utility function to sort <code>.Rbuildignore</code></label></li>
<li><label><input type="checkbox" checked>Implement <a href="https://pkgdown.r-lib.org" class="external-link">pkgdown</a></label></li>
<li><label><input type="checkbox" checked>Add links / update <a href="https://roxygen2.r-lib.org/articles/rd-formatting.html" class="external-link">Rd formatting</a> for all function documentation.</label></li>
<li><label><input type="checkbox" checked>Add dummy imports to silence R CMD check note per <a href="https://github.com/tidyverse/tidyverse/blob/main/R/tidyverse-package.R" class="external-link">tidyverse</a></label></li>
<li><label><input type="checkbox" checked>Migrate <code><a href="reference/build_analysis_site.html">build_analysis_site()</a></code> to rdev</label></li>
<li><label><input type="checkbox" checked>Switch from development version of <code>styler</code> (1.3.2.9000) when a new release becomes available</label></li>
<li><label><input type="checkbox" checked><del>Validate that <code>lint_all</code> works as expected within <code>ci</code></del></label></li>
<li><label><input type="checkbox" checked>Add ‘create package’ workflow example to README, remove TODO section “Analysis package creation process”</label></li>
<li><label><input type="checkbox" checked>Move <code>_pkgdown.yml</code> to repository root to make projects discoverable by the <a href="https://pkgdown.r-lib.org" class="external-link">pgkdown</a> GitHub <a href="https://github.com/search?q=filename%3Apkgdown.yml+path%3A%2F&type=Code" class="external-link">query</a></label></li>
<li><label><input type="checkbox" checked>Update <code>README.Rmd</code> template to dynamically generate list of notebooks in <code>analysis</code></label></li>
<li><label><input type="checkbox" checked>Automate release process</label></li>
<li><label><input type="checkbox" checked>Automate creation of feature branches, including ‘Bump version’ using <code>desc::desc_bump_version("dev")</code></label></li>
<li><label><input type="checkbox" checked>Add check to <code><a href="reference/stage_release.html">stage_release()</a></code> to look for missing topics in <code>_pkgdown.yml</code> reference section</label></li>
<li><label><input type="checkbox" checked>Update <code><a href="reference/use_rdev_package.html">use_rdev_package()</a></code></label></li>
<li><label><input type="checkbox" checked>Handle <code>.Rmd</code> files that already have an <code>html_document</code> section</label></li>
<li><label><input type="checkbox" checked>Move <code><a href="reference/rmd_metadata.html">rmd_metadata()</a></code> from README-analysis.Rmd to rdev package</label></li>
<li><label><input type="checkbox" checked>Add tests per comments in <code>R/</code> after reading package book, documentation</label></li>
<li><label><input type="checkbox" checked>Update Roxygen comments after reading package book, documentation, review and merge duplicate Roxygen docs</label></li>
<li><label><input type="checkbox" checked>Write a manual regression test script (notes with R commands) <del>as a vignette</del> to validate ‘Creating Packages’ <del>and ‘GitHub Releases’</del></label></li>
<li><label><input type="checkbox" checked>Add messages, warnings to <code><a href="reference/build_analysis_site.html">build_analysis_site()</a></code> to report on progress</label></li>
<li><label><input type="checkbox" checked>Add function to spell check notebooks</label></li>
<li><label><input type="checkbox" checked>Automate branch protection</label></li>
<li><label><input type="checkbox" checked>Address issue <a href="https://github.com/r-lib/usethis/issues/1568" class="external-link uri">https://github.com/r-lib/usethis/issues/1568</a>, which has been closed</label></li>
<li><label><input type="checkbox" checked>Add dplyr when running <code><a href="reference/use_analysis_package.html">use_analysis_package()</a></code></label></li>
<li><label><input type="checkbox" checked><del>Consider switching <code>getOption("pkgType")</code> from <code>source</code> to <code>both</code> per R <a href="https://stat.ethz.ch/R-manual/R-devel/library/base/html/options.html" class="external-link">options</a></del> per the <a href="https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#What-is-the-difference-between-the-CRAN-build-and-a-vanilla-build_003f" class="external-link">R macOS FAQ</a>, “Only the CRAN build is guaranteed to be compatible with the package binaries on CRAN (or Bioconductor).”</label></li>
<li><label><input type="checkbox" checked>Support creating repos in organizations</label></li>
<li><label><input type="checkbox" checked><del>Consider incorporating the GitHub description into <code>DESCRIPTION</code></del></label></li>
<li><label><input type="checkbox" checked>Create a wrapper for <code>spelling</code> that includes notebooks in package spell checking, WORDLIST</label></li>
<li><label><input type="checkbox" checked>Add a <code>spell_check_test_notebooks()</code> function for CI spellchecks on notebooks</label></li>
<li><label><input type="checkbox" checked>Convert manual tests (<code>Setup.Rmd</code>) into an R Script that can be run from within the package created with <code><a href="reference/create_github_repo.html">create_github_repo()</a></code></label></li>
<li><label><input type="checkbox" checked>Add a function to add missing (notebook) dependencies to DESCRIPTION, see <code><a href="https://rstudio.github.io/renv/reference/dependencies.html" class="external-link">renv::dependencies()</a></code> and <code><a href="https://desc.r-lib.org/reference/desc_get_deps.html" class="external-link">desc::desc_get_deps()</a></code></label></li>
<li><label><input type="checkbox" checked>Add <code><a href="reference/check_renv.html">check_renv()</a></code> to <code><a href="reference/ci.html">ci()</a></code> and stop if <code><a href="https://rstudio.github.io/renv/reference/status.html" class="external-link">renv::status()</a></code> is not up to date</label></li>
<li><label><input type="checkbox" checked>Replace proof-docs with <a href="https://urlchecker.r-lib.org" class="external-link">urlchecker</a>, support checking GitHub Pages <code>docs</code> directory using <code>url_db_from_HTML_files</code> <del>(ask if a PR for this would be accepted)</del></label></li>
<li><label><input type="checkbox" checked>Move scripts from <code>tools</code> to <code>inst/bin</code> or similar, per <a href="https://stackoverflow.com/questions/26104709/is-there-any-special-functionality-in-r-package-exec-or-tools-directories" class="external-link">Stack Overflow</a> and <a href="https://r-pkgs.org/inst.html#inst-other-langs" class="external-link">R Packages</a></label></li>
<li><label><input type="checkbox" checked>Switch from development versions of <code>styler</code> (1.3.2.9000) and <code>lintr</code> (2.0.1.9000) when a new release becomes available - both were needed to address bugs in the current release versions, 1.3.2 and 2.0.1.</label></li>
<li><label><input type="checkbox" checked>Add trailing slash to GitHub Pages URL</label></li>
<li><label><input type="checkbox" checked>Update <code><a href="reference/lint_all.html">lint_all()</a></code> to lint all types, including <code>.Rpres</code></label></li>
<li><label><input type="checkbox" checked><del>Add custom CSS files to <a href="https://rmarkdown.rstudio.com/docs/reference/render_site.html" class="external-link"><code>_site.yml</code></a> and analysis notebook templates to control font size, as described in this <a href="https://medium.com/@HadrienD/how-to-customize-font-size-in-r-markdown-documents-f5adff36e2cc" class="external-link">article</a>, or possibly using <a href="https://rstudio.github.io/bslib/articles/theming.html" class="external-link"><code>bs_theme()</code></a>, since pkgdown customizes the default using <a href="https://github.com/r-lib/pkgdown/blob/main/R/theme.R" class="external-link"><code>build_bslib()</code></a></del> (issue exists in unsupported Safari 14 but not Safari 15)</label></li>
<li><label><input type="checkbox" checked><del>Remove <code>pkgdown/extra.css</code> if <a href="https://github.com/r-lib/pkgdown/issues/2377" class="external-link uri">https://github.com/r-lib/pkgdown/issues/2377</a> is accepted</del></label></li>
<li><label><input type="checkbox" checked><del>Establish default <a href="https://yihui.org/knitr/options/" class="external-link">knitr options</a>, including <code>knitr::opts_chunk$set(fig.align = "center")</code>, add to analysis template, also review <a href="https://github.com/hadley/adv-r/blob/master/common.R" class="external-link">settings</a> for <em>Advanced R</em></del></label></li>
<li>
<label><input type="checkbox" checked><del>Consider using RStudio <a href="https://rstudio.github.io/rstudio-extensions/index.html" class="external-link">Extensions</a>:</del></label>
<ul class="task-list"><li><label><input type="checkbox" checked><del>Use Project <a href="https://rstudio.github.io/rstudio-extensions/rstudio_project_templates.html" class="external-link">Templates</a> like <a href="https://www.crumplab.com/vertical/" class="external-link">vertical</a>?</del></label></li>
<li><label><input type="checkbox" checked><del>Add CSS to R Markdown <a href="https://rstudio.github.io/rstudio-extensions/rmarkdown_templates.html" class="external-link">Template</a> instead of <code>assets/extra.css</code>?</del></label></li>
</ul></li>
<li><label><input type="checkbox" checked>Move <code>shift-heading-level-by: 1</code> from <code>_quarto.yml</code> to <code>analysis/_metadata.yml</code>, so <code>TODO.md</code> renders properly</label></li>
<li><label><input type="checkbox" checked>Remove <code>preset: bootstrap</code> workaround when pkgdown 2.0.8+ is released (per <a href="https://github.com/r-lib/pkgdown/issues/2376" class="external-link uri">https://github.com/r-lib/pkgdown/issues/2376</a>)</label></li>
<li><label><input type="checkbox" checked>Replace <code>GITHUB_PAT</code> in <code>.Renviron</code> with <a href="https://usethis.r-lib.org/articles/git-credentials.html" class="external-link">gitcreds</a></label></li>
<li><label><input type="checkbox" checked>Review use of <a href="https://usethis.r-lib.org/reference/index.html" class="external-link">usethis functions</a>, including <a href="https://usethis.r-lib.org/articles/pr-functions.html" class="external-link">pull request helpers</a></label></li>
<li><label><input type="checkbox">Update tests with new testthat features (<code><a href="https://testthat.r-lib.org/reference/auto_test.html" class="external-link">testthat::auto_test_package()</a></code>, <code><a href="https://testthat.r-lib.org/reference/describe.html" class="external-link">testthat::describe()</a></code>, Reporters, <code><a href="https://testthat.r-lib.org/reference/local_mocked_bindings.html" class="external-link">testthat::local_mocked_bindings()</a></code>)</label></li>
<li><label><input type="checkbox">Replace <code>dev = TRUE</code> logic after renv 1.1.6+ is released; see renv <a href="https://github.com/rstudio/renv/issues/1695" class="external-link">#1695</a>, <a href="https://github.com/rstudio/renv/pull/2190" class="external-link">#2190</a></label></li>
<li><label><input type="checkbox">Update errors and messages after reading Advanced R <a href="https://adv-r.hadley.nz/conditions.html" class="external-link">Conditions</a> and re-reading the Tidyverse <a href="https://style.tidyverse.org/index.html" class="external-link">Style Guide</a></label></li>
<li><label><input type="checkbox">Reduce the number of Imports, per R CMD check:</label></li>
</ul><pre><code>> devtools::check()
...
> checking package dependencies ... NOTE
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.</code></pre>
</div>
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<h2 id="github">GitHub<a class="anchor" aria-label="anchor" href="#github"></a></h2>
<ul class="task-list"><li>
<label><input type="checkbox" checked>Set up <a href="https://usethis.r-lib.org/reference/github_actions.html" class="external-link">GitHub Actions</a></label>
<ul class="task-list"><li><label><input type="checkbox" checked>Use <a href="https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml" class="external-link">standard</a> <code>R CMD check</code></label></li>
<li><label><input type="checkbox" checked>Use <a href="https://github.com/r-lib/actions/blob/master/examples/lint.yaml" class="external-link">lintr</a></label></li>
</ul></li>
<li><label><input type="checkbox" checked>Faster CI checks</label></li>
<li><label><input type="checkbox" checked><del>Switch to <a href="https://github.com/r-lib/actions/blob/master/examples/check-full.yaml" class="external-link">full</a> <code>R CMD check</code> ?</del></label></li>
<li><label><input type="checkbox" checked>Update GitHub Actions from r-lib <a href="https://github.com/r-lib/actions/tree/master/examples" class="external-link">examples</a></label></li>
<li><label><input type="checkbox" checked>Run <a href="https://github.com/r-lib/actions/blob/master/examples/test-coverage.yaml" class="external-link">test coverage</a></label></li>
<li><label><input type="checkbox" checked><del>Skip CI checks for changes in only the <code>docs/</code> directory</del></label></li>
<li><label><input type="checkbox" checked><del>Add GitHub Action for html/link checking using something like <a href="https://github.com/gjtorikian/html-proofer" class="external-link">htmlproofer</a></del></label></li>
<li><label><input type="checkbox" checked><del>Autobuild <code>docs/</code> like <a href="https://github.com/r-lib/actions/blob/master/examples/pkgdown.yaml" class="external-link">pkgdown</a> ?</del></label></li>
</ul></div>
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