diff --git a/README.md b/README.md
index 002d64e1..80aa6126 100644
--- a/README.md
+++ b/README.md
@@ -118,10 +118,11 @@ ci()
 #> No problems found
 #> 
 #> style_all()
-#> Styling  56  files:
+#> Styling  57  files:
 #>  .Rprofile                                               ✔ 
 #>  README.Rmd                                              ✔ 
 #>  inst/rmarkdown/templates/analysis/skeleton/skeleton.Rmd ✔ 
+#>  inst/templates/changelog.qmd                            ✔ 
 #>  inst/templates/index.qmd                                ✔ 
 #>  inst/templates/package.R                                ✔ 
 #>  inst/templates/README-analysis.Rmd                      ✔ 
@@ -177,7 +178,7 @@ ci()
 #>  vignettes/style-guide.Rmd                               ✔ 
 #> ───────────────────────────────────────────────────────
 #> Status   Count   Legend 
-#> ✔    56  File unchanged.
+#> ✔    57  File unchanged.
 #> ℹ    0   File changed.
 #> ✖    0   Styling threw an error.
 #> ───────────────────────────────────────────────────────
@@ -219,10 +220,10 @@ ci()
 #> * creating vignettes ... OK
 #> * checking for LF line-endings in source and make files and shell scripts
 #> * checking for empty or unneeded directories
-#> * building ‘rdev_1.9.8.tar.gz’
+#> * building ‘rdev_1.9.9.tar.gz’
 #> 
 #> ── R CMD check ─────────────────────────────────────────────────────────────────
-#> * using log directory ‘/private/var/folders/vn/cw5f9gws42v9m8mdsds_zbl00000gp/T/RtmpriAiu8/file3c30ca812b/rdev.Rcheck’
+#> * using log directory ‘/private/var/folders/vn/cw5f9gws42v9m8mdsds_zbl00000gp/T/RtmpUPErWo/file5f90121489b4/rdev.Rcheck’
 #> * using R version 4.3.2 (2023-10-31)
 #> * using platform: aarch64-apple-darwin20 (64-bit)
 #> * R was compiled by
@@ -232,7 +233,7 @@ ci()
 #> * using session charset: UTF-8
 #> * using option ‘--no-manual’
 #> * checking for file ‘rdev/DESCRIPTION’ ... OK
-#> * this is package ‘rdev’ version ‘1.9.8’
+#> * this is package ‘rdev’ version ‘1.9.9’
 #> * package encoding: UTF-8
 #> * checking package namespace information ... OK
 #> * checking package dependencies ... OK
@@ -292,8 +293,8 @@ ci()
 #> * DONE
 #> 
 #> Status: OK
-#> ── R CMD check results ───────────────────────────────────────── rdev 1.9.8 ────
-#> Duration: 30.2s
+#> ── R CMD check results ───────────────────────────────────────── rdev 1.9.9 ────
+#> Duration: 32.9s
 #> 
 #> 0 errors ✔ | 0 warnings ✔ | 0 notes ✔
 ```
diff --git a/docs/404.html b/docs/404.html
index 5c9cb292..a27cdcc9 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -32,7 +32,7 @@
     
     <a class="navbar-brand me-2" href="https://jabenninghoff.github.io/rdev/index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index 9329d22d..edadc65a 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
index 2079fa9a..023b0da8 100644
--- a/docs/LICENSE.html
+++ b/docs/LICENSE.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/TODO.html b/docs/TODO.html
index d0a72d74..3324b150 100644
--- a/docs/TODO.html
+++ b/docs/TODO.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -110,6 +110,7 @@ <h2 id="package">Package<a class="anchor" aria-label="anchor" href="#package"></
 <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">Remove <code>preset: bootstrap</code> if <a href="https://github.com/r-lib/pkgdown/issues/2376" class="external-link uri">https://github.com/r-lib/pkgdown/issues/2376</a> is accepted</label></li>
 <li><label><input type="checkbox">Replace <code>dev = TRUE</code> logic if <a href="https://github.com/rstudio/renv/issues/1695" class="external-link uri">https://github.com/rstudio/renv/issues/1695</a> is accepted</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>
diff --git a/docs/articles/analysis-package-layout.html b/docs/articles/analysis-package-layout.html
index 6187d8c1..266201c0 100644
--- a/docs/articles/analysis-package-layout.html
+++ b/docs/articles/analysis-package-layout.html
@@ -34,7 +34,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -137,7 +137,7 @@
 <tbody>
 <tr class="odd">
 <td align="left">.Rbuildignore</td>
-<td align="left"><code>x</code></td>
+<td align="left"></td>
 <td align="left"><code>x</code></td>
 <td align="left">Files excluded from the package, sorted using
 <code><a href="../reference/sort_rbuildignore.html">sort_rbuildignore()</a></code>
@@ -157,7 +157,7 @@
 </tr>
 <tr class="even">
 <td align="left">.Rprofile</td>
-<td align="left"><code>x</code></td>
+<td align="left"></td>
 <td align="left"><code>x</code></td>
 <td align="left">Used by <code>renv</code> and to <a href="https://r-pkgs.org/setup.html?#personal-startup-configuration" class="external-link">attach
 development tools</a> and set project options</td>
@@ -182,7 +182,7 @@
 </tr>
 <tr class="even">
 <td align="left">.gitignore</td>
-<td align="left"><code>x</code></td>
+<td align="left"></td>
 <td align="left"><code>x</code></td>
 <td align="left">git exclusions based on <a href="https://github.com/github/gitignore/blob/master/R.gitignore" class="external-link">GitHub
 R</a>. Generated files outside of <code>docs</code> (used by GitHub
@@ -247,7 +247,7 @@
 </tr>
 <tr class="even">
 <td align="left">NEWS.md</td>
-<td align="left"></td>
+<td align="left"><code>x</code></td>
 <td align="left"><code>x</code></td>
 <td align="left">Release notes, used by <code><a href="../reference/get_release.html">get_release()</a></code>, <a href="https://pkgdown.r-lib.org" class="external-link">pkgdown</a> and <a href="https://quarto.org" class="external-link">Quarto</a>
 </td>
@@ -260,7 +260,7 @@
 </tr>
 <tr class="even">
 <td align="left">README.Rmd</td>
-<td align="left"><code>x</code></td>
+<td align="left"></td>
 <td align="left"><code>x</code></td>
 <td align="left">Generated with <code><a href="https://usethis.r-lib.org/reference/use_readme_rmd.html" class="external-link">usethis::use_readme_md()</a></code> or
 rdev template</td>
@@ -307,33 +307,41 @@
 </tr>
 <tr class="even">
 <td align="left">analysis</td>
-<td align="left"></td>
+<td align="left"><code>x</code></td>
 <td align="left"><code>x</code></td>
 <td align="left">Exploratory data analysis in R Notebooks and R
 Presentations. Include functions from the R directory using
 <code><a href="https://rdrr.io/r/base/library.html" class="external-link">library()</a></code>, not <code><a href="https://rdrr.io/r/base/source.html" class="external-link">source()</a></code>.</td>
 </tr>
 <tr class="odd">
+<td align="left">analysis/_metadata.yml</td>
+<td align="left"><code>x</code></td>
+<td align="left"><code>x</code></td>
+<td align="left">Quarto <a href="https://quarto.org/docs/projects/quarto-projects.html#directory-metadata" class="external-link">directory
+configuration file</a>
+</td>
+</tr>
+<tr class="even">
 <td align="left">analysis/assets</td>
-<td align="left"></td>
+<td align="left"><code>x</code></td>
 <td align="left"><code>x</code></td>
 <td align="left">External assets (images, other files) included in R
 Notebooks</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td align="left">analysis/data</td>
-<td align="left"></td>
+<td align="left"><code>x</code></td>
 <td align="left"><code>x</code></td>
 <td align="left">Used to store small data sets used for analysis and
 exported data as <code>csv</code> files</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td align="left">analysis/import</td>
 <td align="left"></td>
 <td align="left"></td>
 <td align="left">Used for local storage of large data sets</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td align="left">analysis/rendered</td>
 <td align="left"></td>
 <td align="left"></td>
@@ -342,6 +350,12 @@
 files</a>
 </td>
 </tr>
+<tr class="even">
+<td align="left">changelog.qmd</td>
+<td align="left"><code>x</code></td>
+<td align="left"><code>x</code></td>
+<td align="left">Quarto front-end to NEWS.md</td>
+</tr>
 <tr class="odd">
 <td align="left">demos</td>
 <td align="left"><code>x</code></td>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index de0ceb82..9d476522 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/articles/rdev.html b/docs/articles/rdev.html
index 82a4fa71..97564b77 100644
--- a/docs/articles/rdev.html
+++ b/docs/articles/rdev.html
@@ -34,7 +34,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/articles/style-guide.html b/docs/articles/style-guide.html
index 1728dd8d..cf6abe56 100644
--- a/docs/articles/style-guide.html
+++ b/docs/articles/style-guide.html
@@ -34,7 +34,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/authors.html b/docs/authors.html
index 827ea2d4..c8fbe2eb 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -68,14 +68,14 @@ <h2 id="citation">Citation</h2>
 
       <p>Benninghoff J (2024).
 <em>rdev: R Development Tools</em>.
-R package version 1.9.8, 
+R package version 1.9.9, 
 https://github.com/jabenninghoff/rdev, <a href="https://jabenninghoff.github.io/rdev/">https://jabenninghoff.github.io/rdev/</a>. 
 </p>
       <pre>@Manual{,
   title = {rdev: R Development Tools},
   author = {John Benninghoff},
   year = {2024},
-  note = {R package version 1.9.8, 
+  note = {R package version 1.9.9, 
 https://github.com/jabenninghoff/rdev},
   url = {https://jabenninghoff.github.io/rdev/},
 }</pre>
diff --git a/docs/index.html b/docs/index.html
index 8730bd93..7b1f4fea 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -36,7 +36,7 @@
     
     <a class="navbar-brand me-2" href="index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -174,10 +174,11 @@ <h2 id="workflow">Workflow<a class="anchor" aria-label="anchor" href="#workflow"
 <span><span class="co">#&gt; No problems found</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; style_all()</span></span>
-<span><span class="co">#&gt; Styling  56  files:</span></span>
+<span><span class="co">#&gt; Styling  57  files:</span></span>
 <span><span class="co">#&gt;  .Rprofile                                               ✔ </span></span>
 <span><span class="co">#&gt;  README.Rmd                                              ✔ </span></span>
 <span><span class="co">#&gt;  inst/rmarkdown/templates/analysis/skeleton/skeleton.Rmd ✔ </span></span>
+<span><span class="co">#&gt;  inst/templates/changelog.qmd                            ✔ </span></span>
 <span><span class="co">#&gt;  inst/templates/index.qmd                                ✔ </span></span>
 <span><span class="co">#&gt;  inst/templates/package.R                                ✔ </span></span>
 <span><span class="co">#&gt;  inst/templates/README-analysis.Rmd                      ✔ </span></span>
@@ -233,7 +234,7 @@ <h2 id="workflow">Workflow<a class="anchor" aria-label="anchor" href="#workflow"
 <span><span class="co">#&gt;  vignettes/style-guide.Rmd                               ✔ </span></span>
 <span><span class="co">#&gt; ───────────────────────────────────────────────────────</span></span>
 <span><span class="co">#&gt; Status   Count   Legend </span></span>
-<span><span class="co">#&gt; ✔    56  File unchanged.</span></span>
+<span><span class="co">#&gt; ✔    57  File unchanged.</span></span>
 <span><span class="co">#&gt; ℹ    0   File changed.</span></span>
 <span><span class="co">#&gt; ✖    0   Styling threw an error.</span></span>
 <span><span class="co">#&gt; ───────────────────────────────────────────────────────</span></span>
@@ -275,10 +276,10 @@ <h2 id="workflow">Workflow<a class="anchor" aria-label="anchor" href="#workflow"
 <span><span class="co">#&gt; * creating vignettes ... OK</span></span>
 <span><span class="co">#&gt; * checking for LF line-endings in source and make files and shell scripts</span></span>
 <span><span class="co">#&gt; * checking for empty or unneeded directories</span></span>
-<span><span class="co">#&gt; * building ‘rdev_1.9.8.tar.gz’</span></span>
+<span><span class="co">#&gt; * building ‘rdev_1.9.9.tar.gz’</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; ── R CMD check ─────────────────────────────────────────────────────────────────</span></span>
-<span><span class="co">#&gt; * using log directory ‘/private/var/folders/vn/cw5f9gws42v9m8mdsds_zbl00000gp/T/RtmpriAiu8/file3c30ca812b/rdev.Rcheck’</span></span>
+<span><span class="co">#&gt; * using log directory ‘/private/var/folders/vn/cw5f9gws42v9m8mdsds_zbl00000gp/T/RtmpUPErWo/file5f90121489b4/rdev.Rcheck’</span></span>
 <span><span class="co">#&gt; * using R version 4.3.2 (2023-10-31)</span></span>
 <span><span class="co">#&gt; * using platform: aarch64-apple-darwin20 (64-bit)</span></span>
 <span><span class="co">#&gt; * R was compiled by</span></span>
@@ -288,7 +289,7 @@ <h2 id="workflow">Workflow<a class="anchor" aria-label="anchor" href="#workflow"
 <span><span class="co">#&gt; * using session charset: UTF-8</span></span>
 <span><span class="co">#&gt; * using option ‘--no-manual’</span></span>
 <span><span class="co">#&gt; * checking for file ‘rdev/DESCRIPTION’ ... OK</span></span>
-<span><span class="co">#&gt; * this is package ‘rdev’ version ‘1.9.8’</span></span>
+<span><span class="co">#&gt; * this is package ‘rdev’ version ‘1.9.9’</span></span>
 <span><span class="co">#&gt; * package encoding: UTF-8</span></span>
 <span><span class="co">#&gt; * checking package namespace information ... OK</span></span>
 <span><span class="co">#&gt; * checking package dependencies ... OK</span></span>
@@ -348,8 +349,8 @@ <h2 id="workflow">Workflow<a class="anchor" aria-label="anchor" href="#workflow"
 <span><span class="co">#&gt; * DONE</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; Status: OK</span></span>
-<span><span class="co">#&gt; ── R CMD check results ───────────────────────────────────────── rdev 1.9.8 ────</span></span>
-<span><span class="co">#&gt; Duration: 30.2s</span></span>
+<span><span class="co">#&gt; ── R CMD check results ───────────────────────────────────────── rdev 1.9.9 ────</span></span>
+<span><span class="co">#&gt; Duration: 32.9s</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; 0 errors ✔ | 0 warnings ✔ | 0 notes ✔</span></span></code></pre></div>
 </div>
diff --git a/docs/news/index.html b/docs/news/index.html
index 525d11b6..d5412062 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -54,6 +54,10 @@
       <small>Source: <a href="https://github.com/jabenninghoff/rdev/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
     </div>
 
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="1.9.9" id="rdev-199">rdev 1.9.9<a class="anchor" aria-label="anchor" href="#rdev-199"></a></h2>
+<ul><li>Updated quarto configuration (update: <code><a href="../reference/use_analysis_package.html">use_analysis_package()</a></code>)</li>
+</ul></div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="1.9.8" id="rdev-198">rdev 1.9.8<a class="anchor" aria-label="anchor" href="#rdev-198"></a></h2>
 <ul><li><p>Added quarto themes (flatly, darkly) (update: <code><a href="../reference/use_analysis_package.html">use_analysis_package()</a></code>)</p></li>
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 5ed75d66..4b409f9f 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -5,7 +5,7 @@ articles:
   analysis-package-layout: analysis-package-layout.html
   rdev: rdev.html
   style-guide: style-guide.html
-last_built: 2024-02-11T20:25Z
+last_built: 2024-02-15T22:10Z
 urls:
   reference: https://jabenninghoff.github.io/rdev/reference
   article: https://jabenninghoff.github.io/rdev/articles
diff --git a/docs/reference/build_analysis_site.html b/docs/reference/build_analysis_site.html
index 6281fb15..bdccd5c0 100644
--- a/docs/reference/build_analysis_site.html
+++ b/docs/reference/build_analysis_site.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/build_quarto_site.html b/docs/reference/build_quarto_site.html
index ca0b1601..f44362b1 100644
--- a/docs/reference/build_quarto_site.html
+++ b/docs/reference/build_quarto_site.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/build_rdev_site.html b/docs/reference/build_rdev_site.html
index 67a31ef4..06f074bd 100644
--- a/docs/reference/build_rdev_site.html
+++ b/docs/reference/build_rdev_site.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/check_renv.html b/docs/reference/check_renv.html
index 3f460764..ec0aff58 100644
--- a/docs/reference/check_renv.html
+++ b/docs/reference/check_renv.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/ci.html b/docs/reference/ci.html
index 41ceb119..19a2cd1a 100644
--- a/docs/reference/ci.html
+++ b/docs/reference/ci.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/create_github_repo.html b/docs/reference/create_github_repo.html
index b9586b4b..c3a20a2b 100644
--- a/docs/reference/create_github_repo.html
+++ b/docs/reference/create_github_repo.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/deps_check.html b/docs/reference/deps_check.html
index d1622b76..f3509e5a 100644
--- a/docs/reference/deps_check.html
+++ b/docs/reference/deps_check.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/get_license.html b/docs/reference/get_license.html
index 905423e7..fd61585f 100644
--- a/docs/reference/get_license.html
+++ b/docs/reference/get_license.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/get_release.html b/docs/reference/get_release.html
index 2093cfd7..8a79603d 100644
--- a/docs/reference/get_release.html
+++ b/docs/reference/get_release.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/html_url_check.html b/docs/reference/html_url_check.html
index 1861e999..3847980a 100644
--- a/docs/reference/html_url_check.html
+++ b/docs/reference/html_url_check.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 9fb5f85f..3824e589 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/init.html b/docs/reference/init.html
index 2f2880a0..f73b75f0 100644
--- a/docs/reference/init.html
+++ b/docs/reference/init.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/lint_all.html b/docs/reference/lint_all.html
index 613417c7..6fd3e3ef 100644
--- a/docs/reference/lint_all.html
+++ b/docs/reference/lint_all.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/local_temppkg.html b/docs/reference/local_temppkg.html
index 64bd06ab..fb301da3 100644
--- a/docs/reference/local_temppkg.html
+++ b/docs/reference/local_temppkg.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/merge_release.html b/docs/reference/merge_release.html
index a974ce01..5cbc7566 100644
--- a/docs/reference/merge_release.html
+++ b/docs/reference/merge_release.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/new_branch.html b/docs/reference/new_branch.html
index 6229af51..0e578c4f 100644
--- a/docs/reference/new_branch.html
+++ b/docs/reference/new_branch.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/open_files.html b/docs/reference/open_files.html
index ac4d5e54..ef6ac59e 100644
--- a/docs/reference/open_files.html
+++ b/docs/reference/open_files.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/quickstart.html b/docs/reference/quickstart.html
index 7ae26cd3..ba24a765 100644
--- a/docs/reference/quickstart.html
+++ b/docs/reference/quickstart.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/rdev-package.html b/docs/reference/rdev-package.html
index d443b5cd..00bdd878 100644
--- a/docs/reference/rdev-package.html
+++ b/docs/reference/rdev-package.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/rmd_metadata.html b/docs/reference/rmd_metadata.html
index 36252367..4cd6111f 100644
--- a/docs/reference/rmd_metadata.html
+++ b/docs/reference/rmd_metadata.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/setup_analysis.html b/docs/reference/setup_analysis.html
index 73562d7c..581771af 100644
--- a/docs/reference/setup_analysis.html
+++ b/docs/reference/setup_analysis.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/setup_rdev.html b/docs/reference/setup_rdev.html
index df528076..31d2d5e7 100644
--- a/docs/reference/setup_rdev.html
+++ b/docs/reference/setup_rdev.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/sort_file.html b/docs/reference/sort_file.html
index e7058d54..bef6a445 100644
--- a/docs/reference/sort_file.html
+++ b/docs/reference/sort_file.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/sort_rbuildignore.html b/docs/reference/sort_rbuildignore.html
index 262f039d..7a6f3f13 100644
--- a/docs/reference/sort_rbuildignore.html
+++ b/docs/reference/sort_rbuildignore.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/spell_check_notebooks.html b/docs/reference/spell_check_notebooks.html
index ab3dd2b5..4d14f43f 100644
--- a/docs/reference/spell_check_notebooks.html
+++ b/docs/reference/spell_check_notebooks.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/stage_release.html b/docs/reference/stage_release.html
index dac2def6..4430f6eb 100644
--- a/docs/reference/stage_release.html
+++ b/docs/reference/stage_release.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/style_all.html b/docs/reference/style_all.html
index 35377728..d7340a8d 100644
--- a/docs/reference/style_all.html
+++ b/docs/reference/style_all.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/to_document.html b/docs/reference/to_document.html
index b26ee9cb..acf3ca1f 100644
--- a/docs/reference/to_document.html
+++ b/docs/reference/to_document.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/unfreeze.html b/docs/reference/unfreeze.html
index e3e47426..e361a58e 100644
--- a/docs/reference/unfreeze.html
+++ b/docs/reference/unfreeze.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/update_wordlist_notebooks.html b/docs/reference/update_wordlist_notebooks.html
index 25cd7bfb..8fd9816e 100644
--- a/docs/reference/update_wordlist_notebooks.html
+++ b/docs/reference/update_wordlist_notebooks.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/urlchecker-reexports.html b/docs/reference/urlchecker-reexports.html
index 3446a7b8..32746bc0 100644
--- a/docs/reference/urlchecker-reexports.html
+++ b/docs/reference/urlchecker-reexports.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/use_analysis_package.html b/docs/reference/use_analysis_package.html
index f066cd04..745d4404 100644
--- a/docs/reference/use_analysis_package.html
+++ b/docs/reference/use_analysis_package.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -94,8 +94,8 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 <li><p>Adds <code>extra.css</code> to <code>analysis/assets</code> and <code>pkgdown</code> (when <code>use_quarto</code> is <code>FALSE</code>) to fix
 rendering of GitHub-style
 <a href="https://docs.github.com/en/get-started/writing-on-github/working-with-advanced-formatting/about-task-lists" class="external-link">task lists</a></p></li>
-<li><p>Adds <code>.nojekyll</code>, <code>_quarto.yml</code> and <code>index.qmd</code> from templates OR creates <code>_base.yml</code> in
-<code>pkgdown</code> from the first <code>URL</code> in <code>DESCRIPTION</code></p></li>
+<li><p>Adds <code>.nojekyll</code>, <code>_quarto.yml</code>, <code>changelog.qmd</code>, <code>index.qmd</code> and <code>analysis/_metadata.yml</code>
+from templates OR creates <code>_base.yml</code> in <code>pkgdown</code> from the first <code>URL</code> in <code>DESCRIPTION</code></p></li>
 <li><p>Installs the <code>README.Rmd</code> template for analysis packages, and the <code>dplyr</code>
 package needed for the <code>README.Rmd</code> template</p></li>
 </ol></div>
diff --git a/docs/reference/use_codecov.html b/docs/reference/use_codecov.html
index 052e7926..a5b55ac8 100644
--- a/docs/reference/use_codecov.html
+++ b/docs/reference/use_codecov.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/use_lintr.html b/docs/reference/use_lintr.html
index d7f92100..f7099e98 100644
--- a/docs/reference/use_lintr.html
+++ b/docs/reference/use_lintr.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/use_package_r.html b/docs/reference/use_package_r.html
index c872a108..eebe3034 100644
--- a/docs/reference/use_package_r.html
+++ b/docs/reference/use_package_r.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/use_rdev_package.html b/docs/reference/use_rdev_package.html
index 97b52fc9..82ad10b7 100644
--- a/docs/reference/use_rdev_package.html
+++ b/docs/reference/use_rdev_package.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/use_rdev_pkgdown.html b/docs/reference/use_rdev_pkgdown.html
index 1906bd9f..e1454505 100644
--- a/docs/reference/use_rdev_pkgdown.html
+++ b/docs/reference/use_rdev_pkgdown.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/use_rprofile.html b/docs/reference/use_rprofile.html
index 9473d77e..c47851f3 100644
--- a/docs/reference/use_rprofile.html
+++ b/docs/reference/use_rprofile.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/use_spelling.html b/docs/reference/use_spelling.html
index 8ec29272..01f76405 100644
--- a/docs/reference/use_spelling.html
+++ b/docs/reference/use_spelling.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/use_todo.html b/docs/reference/use_todo.html
index 9cbc8a6a..9f97d9dc 100644
--- a/docs/reference/use_todo.html
+++ b/docs/reference/use_todo.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rdev</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.8</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.9</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/search.json b/docs/search.json
index cf91d17d..04d68d39 100644
--- a/docs/search.json
+++ b/docs/search.json
@@ -1 +1 @@
-[{"path":"https://jabenninghoff.github.io/rdev/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2021 rdev authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/TODO.html","id":"content","dir":"","previous_headings":"","what":"Content","title":"TODO","text":"Add README.Rmd Update DESCRIPTION use description data README.Rmd Add ORCID Update ORCID details","code":""},{"path":"https://jabenninghoff.github.io/rdev/TODO.html","id":"package","dir":"","previous_headings":"","what":"Package","title":"TODO","text":"Write utility function sort .Rbuildignore Implement pkgdown Add links / update Rd formatting function documentation. Add dummy imports silence R CMD check note per tidyverse Migrate build_analysis_site() rdev Switch development version styler (1.3.2.9000) new release becomes available Validate lint_all works expected within ci Add ‘create package’ workflow example README, remove TODO section “Analysis package creation process” Move _pkgdown.yml repository root make projects discoverable pgkdown GitHub query Update README.Rmd template dynamically generate list notebooks analysis Automate release process Automate creation feature branches, including ‘Bump version’ using desc::desc_bump_version(\"dev\") Add check stage_release() look missing topics _pkgdown.yml reference section Update use_rdev_package() Handle .Rmd files already html_document section Move rmd_metadata() README-analysis.Rmd rdev package Add tests per comments R/ reading package book, documentation Update Roxygen comments reading package book, documentation, review merge duplicate Roxygen docs Write manual regression test script (notes R commands) vignette validate ‘Creating Packages’ ‘GitHub Releases’ Add messages, warnings build_analysis_site() report progress Add function spell check notebooks Automate branch protection Address issue https://github.com/r-lib/usethis/issues/1568, closed Add dplyr running use_analysis_package() Consider switching getOption(\"pkgType\") source per R options per R macOS FAQ, “CRAN build guaranteed compatible package binaries CRAN (Bioconductor).” Support creating repos organizations Consider incorporating GitHub description DESCRIPTION Create wrapper spelling includes notebooks package spell checking, WORDLIST Add spell_check_test_notebooks() function CI spellchecks notebooks Convert manual tests (Setup.Rmd) R Script can run within package created create_github_repo() Add function add missing (notebook) dependencies DESCRIPTION, see renv::dependencies() desc::desc_get_deps() Add check_renv() ci() stop renv::status() date Replace proof-docs urlchecker, support checking GitHub Pages docs directory using url_db_from_HTML_files (ask PR accepted) Move scripts tools inst/bin similar, per Stack Overflow R Packages Switch development versions styler (1.3.2.9000) lintr (2.0.1.9000) new release becomes available - needed address bugs current release versions, 1.3.2 2.0.1. Add trailing slash GitHub Pages URL Update lint_all() lint types, including .Rpres Add custom CSS files _site.yml analysis notebook templates control font size, described article, possibly using bs_theme(), since pkgdown customizes default using build_bslib() (issue exists unsupported Safari 14 Safari 15) Remove pkgdown/extra.css https://github.com/r-lib/pkgdown/issues/2377 accepted Establish default knitr options, including knitr::opts_chunk$set(fig.align = \"center\"), add analysis template, also review settings Advanced R Use Project Templates like vertical? Add CSS R Markdown Template instead assets/extra.css? Remove preset: bootstrap https://github.com/r-lib/pkgdown/issues/2376 accepted Replace dev = TRUE logic https://github.com/rstudio/renv/issues/1695 accepted Update errors messages reading Advanced R Conditions re-reading Tidyverse Style Guide Reduce number Imports, per R CMD check:","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."},{"path":"https://jabenninghoff.github.io/rdev/TODO.html","id":"github","dir":"","previous_headings":"","what":"GitHub","title":"TODO","text":"Use standard R CMD check Use lintr Faster CI checks Switch full R CMD check ? Update GitHub Actions r-lib examples Run test coverage Skip CI checks changes docs/ directory Add GitHub Action html/link checking using something like htmlproofer Autobuild docs/ like pkgdown ?","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Introduction to rdev","text":"rdev supports personal workflow, including creation traditional R packages R Analysis Packages (vignette(\"analysis-package-layout\")), enforcing consistency across packages, providing Continuous Integration/Continuous Delivery (CI/CD) automation. use tools rdev improve code quality, speed development R code, publish results analyses R Notebooks HTML make accessible non-R users.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Introduction to rdev","text":"current R development environment uses Homebrew, rig, RStudio, GitHub, collection R packages including rdev, Visual Studio Code, Vim.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"homebrew","dir":"Articles","previous_headings":"Installation","what":"Homebrew","title":"Introduction to rdev","text":"use Homebrew Bundle install software systems; basic macOS working environment published GitHub macos-env.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"installing-r","dir":"Articles","previous_headings":"Installation","what":"Installing R","title":"Introduction to rdev","text":"rig supports installation multiple versions official R binaries, use reproducibility. install R using rig, first install rig: install desired versions R. following installs R 3.4 4.3 Intel based macs (2023-11-13): don’t use pak, rig installs default, yet fully supported renv.","code":"brew tap r-lib/rig brew install --cask rig rig install oldrel/6 --without-pak rig install oldrel/5 --without-pak rig install oldrel/4 --without-pak rig install oldrel/3 --without-pak rig install oldrel/2 --without-pak rig install oldrel/1 --without-pak rig install oldrel --without-pak rig install release --without-pak rig default release"},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"development-tools","dir":"Articles","previous_headings":"Installation","what":"Development Tools","title":"Introduction to rdev","text":"Well, obviously, use RStudio. RStudio leading IDE R development integrates many R packages, although sometimes falls short; use GitHub command line Git, occasionally Visual Studio Code (better support markdown) Vim (faster types edits). RStudio, GitHub desktop client, Visual Studio Code easily installed using Homebrew: recommended change default settings .RData RStudio (Options > General > Basic > Workspace): Uncheck “Restore .Data workspace startup” Set “Save workspace .Data exit” “Never” Vim installed default macOS Unix-like systems.","code":"brew install --cask rstudio brew install --cask github brew install --cask visual-studio-code"},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"packages","dir":"Articles","previous_headings":"Installation","what":"Packages","title":"Introduction to rdev","text":"Managing packages environments challenge modern languages. Thankfully R doesn’t level challenge python, even ruby, managing packages available within project best practice. use renv purpose, use renv install manage packages projects. setup-r script rdev installs base set packages needed run rdev R User Library. streamlined version script included . chown command needed allow updating base packages using RStudio Packages “Update” function. generally update packages RStudio projects open starting development, update packages projects using renv::update(). ’re installing (development) versions packages GitHub, recommended set personal access token using usethis::create_github_token() adding .Renviron GITHUB_PAT= using usethis::edit_r_environ().","code":"# fix rig permissions sudo chown -R `whoami`:admin /Library/Frameworks/R.framework/Versions/*/Resources/library  RVERSION=`Rscript -e 'cat(as.character(getRversion()[1,1:2]))'` USERLIB=\"$HOME/Library/R/`uname -m`/${RVERSION}/library\" DEVPKG='c(\"renv\", \"styler\", \"lintr\", \"miniUI\", \"markdown\", \"rmarkdown\", \"devtools\", \"pkgdown\", \"available\", \"languageserver\")' GITPKG='c(\"jabenninghoff/rdev\")'  if [ ! -d \"${USERLIB}\" ] then     mkdir -p \"${USERLIB}\" fi  echo \"install.packages(${DEVPKG}, repos=\\\"https://cloud.r-project.org\\\", lib=\\\"${USERLIB}\\\")\" | R --no-save echo \"remotes::install_github(${GITPKG}, lib=\\\"${USERLIB}\\\")\" | R --no-save"},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"further-reading","dir":"Articles","previous_headings":"Installation","what":"Further Reading","title":"Introduction to rdev","text":"workflow heavily influenced DevOps movement research DevOps Research Assessment (DORA) team Google started Dr. Nicole Forsgren. research shows technical non-technical capabilities improve outcomes. functions included rdev support many technical capabilities, including: Code maintainability Continuous delivery Continuous integration Deployment automation Shifting left security Test automation Trunk-based development Version control outline SIRAcon 2022 talk, “Making R Work (Automation)” available GitHub siracon2022.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"rdev-conventions","dir":"Articles","previous_headings":"","what":"rdev conventions","title":"Style Guide","text":"rdev uses mix Google tidyverse conventions.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"naming-conventions","dir":"Articles","previous_headings":"rdev conventions","what":"Naming conventions","title":"Style Guide","text":"rdev follows tidyverse naming convention snake_case.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"right-hand-assignment","dir":"Articles","previous_headings":"rdev conventions","what":"Right-hand assignment","title":"Style Guide","text":"rdev follows Google’s style guide, use right-hand assignment.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"returns","dir":"Articles","previous_headings":"rdev conventions","what":"Returns","title":"Style Guide","text":"rdev typically uses implicit returns unless needed flow control construct specific return structure.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"qualifying-namespaces","dir":"Articles","previous_headings":"rdev conventions","what":"Qualifying namespaces","title":"Style Guide","text":"Use @import @importFrom discouraged, instead using :: functions defined R/. exception infix functions (%name%), always imported, using roxygen @importFrom. Within R Notebooks, use library() encouraged readability.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"package-level-documentation","dir":"Articles","previous_headings":"rdev conventions","what":"Package-level documentation","title":"Style Guide","text":"rdev package documentation lives R/package.R. Additionally, use base R encouraged within functions defined R/ (control dependencies), tidyverse R encouraged within notebooks readability. R Markdown documents generally wrap width code, exceptions R Notebook ‘description line’ (first non-blank line body), long hyperlinks.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"styler","dir":"Articles","previous_headings":"","what":"styler","title":"Style Guide","text":"rdev package implements styler using styler defaults, permanent caching enabled (options(styler.cache_root = \"styler-perm\")). style_all() function applies tidyverse style R files (R, Rprofile, Rmd, Rnw) package directory structure.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"lintr","dir":"Articles","previous_headings":"","what":"lintr","title":"Style Guide","text":"rdev uses opinionated lintr configuration (.lintr): settings deliberately chosen meet specific goals:","code":"linters: linters_with_tags(     tags = NULL,     extraction_operator_linter = NULL,     implicit_integer_linter = NULL,     line_length_linter(100),     missing_package_linter = NULL,     namespace_linter = NULL,     nonportable_path_linter = NULL,     paste_linter(allow_file_path = \"always\"),     todo_comment_linter = NULL,     undesirable_function_linter(       within(all_undesirable_functions, rm(ifelse, library, require, structure))     ),     undesirable_operator_linter(all_undesirable_operators),     unnecessary_concatenation_linter(allow_single_expression = FALSE),     unused_import_linter(       except_packages = c(\"bit64\", \"data.table\", \"tidyverse\", pkgload::pkg_name(\".\"))     )   )"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"use-all-linters","dir":"Articles","previous_headings":"lintr","what":"Use all linters","title":"Style Guide","text":"selects linters, including new Google linters. selecting linters, just defaults, forces evaluation new linters added lintr. Specific linters disabled configured per rdev style.","code":"linters: linters_with_tags(     tags = NULL,"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"allow-extraction-operator","dir":"Articles","previous_headings":"lintr","what":"Allow $ extraction operator","title":"Style Guide","text":"extraction operator linter enforces use [[ $. Since $ intended interactive use supports partial mapping, safer use [[. However, use $ common practice, including within lintr code, leads readable code.","code":"extraction_operator_linter = NULL,"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"allow-implicit-integers","dir":"Articles","previous_headings":"lintr","what":"Allow implicit integers","title":"Style Guide","text":"implicit integer linter checks integers explicitly typed using form 1L. , safer, implicit integers common practice, including output dput():","code":"implicit_integer_linter = NULL, dput(character(0L)) #> character(0)"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"set-line-length","dir":"Articles","previous_headings":"lintr","what":"Set line length","title":"Style Guide","text":"line length 100 reasonable width working RStudio IDE laptop.","code":"line_length_linter(100),"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"use-renv-for-missing-packages","dir":"Articles","previous_headings":"lintr","what":"Use renv for missing packages","title":"Style Guide","text":"missing package linter namespace linter check packages referenced code installed. rdev uses renv manage packages, better job detecting missing packages, including complaining current package (\".\") installed.","code":"missing_package_linter = NULL,     namespace_linter = NULL,"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"allow-non-portable-paths","dir":"Articles","previous_headings":"lintr","what":"Allow non-portable paths","title":"Style Guide","text":"non-portable path linter generates many false positives, including calls fs, essentially makes UNIX-style paths portable across operating systems. Similarly, allow_file_path default option \"double_slash\" generates false positives used fs.","code":"nonportable_path_linter = NULL,     paste_linter(allow_file_path = \"always\"),"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"allow-todo-comments","dir":"Articles","previous_headings":"lintr","what":"Allow TODO comments","title":"Style Guide","text":"rdev conventions encourage use # TODO comments convenient way identifying needed planned updates inline.","code":"todo_comment_linter = NULL,"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"disallow-almost-all-undesirable-functions-and-operators","dir":"Articles","previous_headings":"lintr","what":"Disallow almost all undesirable functions and operators","title":"Style Guide","text":"Enable undesirable functions operators, just defaults, except ifelse() succinct /else block, library(), require(), structure(). Use require() within .Rprofile library() within R Markdown documents appropriate common practice, although neither used within package code. structure() useful comparing test results values generated dput().","code":"undesirable_function_linter(       within(all_undesirable_functions, rm(ifelse, library, require, structure))     ),     undesirable_operator_linter(all_undesirable_operators),"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"enforce-strict-unnecessary-concatenation","dir":"Articles","previous_headings":"lintr","what":"Enforce strict unnecessary concatenation","title":"Style Guide","text":"Enforce stricter version unnecessary concatenation linter.","code":"unnecessary_concatenation_linter(allow_single_expression = FALSE),"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"verify-imported-packages-are-used","dir":"Articles","previous_headings":"lintr","what":"Verify imported packages are used","title":"Style Guide","text":"Verify imported packages used, except packages attached side effects, current package (support package development).","code":"unused_import_linter(       except_packages = c(\"bit64\", \"data.table\", \"tidyverse\", pkgload::pkg_name(\".\"))     )   )"},{"path":"https://jabenninghoff.github.io/rdev/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"John Benninghoff. Author, maintainer.","code":""},{"path":"https://jabenninghoff.github.io/rdev/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Benninghoff J (2024). rdev: R Development Tools. R package version 1.9.8,  https://github.com/jabenninghoff/rdev, https://jabenninghoff.github.io/rdev/.","code":"@Manual{,   title = {rdev: R Development Tools},   author = {John Benninghoff},   year = {2024},   note = {R package version 1.9.8,  https://github.com/jabenninghoff/rdev},   url = {https://jabenninghoff.github.io/rdev/}, }"},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/index.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"R Development Tools","text":"R Development Tools: opinionated collection development tools, packages, utilities. Feel free use /fork project!","code":""},{"path":"https://jabenninghoff.github.io/rdev/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"R Development Tools","text":"can install development version rdev GitHub : using renv:","code":"# install.packages(\"remotes\") remotes::install_github(\"jabenninghoff/rdev\") # install.packages(\"renv\") renv::install(\"jabenninghoff/rdev\")"},{"path":"https://jabenninghoff.github.io/rdev/index.html","id":"development","dir":"","previous_headings":"","what":"Development","title":"R Development Tools","text":"Changelog: See “Changelog” NEWS.md. Planned: TODO","code":""},{"path":"https://jabenninghoff.github.io/rdev/index.html","id":"creating-packages","dir":"","previous_headings":"","what":"Creating Packages","title":"R Development Tools","text":"rdev supports creation new R packages following rdev conventions well new R Analysis packages. typical setup workflow (per ?quickstart) : Use available::available() check package name project open, run create_github_repo() initialize GitHub R repository Without committing git, run init() newly created project Manually update Title Description fields DESCRIPTION file without committing Run setup_analysis() setup_rdev() configure package analysis package rdev package respectively. Update TODO.md, NEWS.md, README.Rmd, DESCRIPTION needed Re-run check_renv(), ci() validate package Commit git begin development","code":""},{"path":"https://jabenninghoff.github.io/rdev/index.html","id":"github-releases","dir":"","previous_headings":"","what":"GitHub Releases","title":"R Development Tools","text":"rdev automates workflow creating GitHub releases along updating GitHub pages either standard R packages R analysis packages, using release notes format NEWS.md. typical development workflow : Bump version create new feature branch new_branch() Write things Update release notes new version NEWS.md, following conventions described get_release() Finalize release merge changes git Run stage_release() create new pull request GitHub using details derived NEWS.md, including updating README GitHub pages pull request reviewed passes required status checks, accept staged release merge_release(), merges pull request, cleans branches, publishes new GitHub release Feature branches can merged without starting new release; stage_release() just requires everything committed, including new release notes NEWS.md running. ready release, stage_release() use existing branch feature branch, create new release branch default.","code":""},{"path":"https://jabenninghoff.github.io/rdev/index.html","id":"workflow","dir":"","previous_headings":"","what":"Workflow","title":"R Development Tools","text":"workflow, typically check renv start: also ci() function run continuous integration tests locally:","code":"library(rdev)  check_renv() #> renv::status(dev = TRUE) #> No issues found -- the project is in a consistent state. #>  #> renv::clean() #> - No stale package locks were found. #> - No temporary directories were found in the project library. #> - The project has been cleaned. ci() #> renv::status(dev = TRUE) #> No issues found -- the project is in a consistent state. #>  #> missing_deps() #> Finding R package dependencies ... Done! #> renv::dependencies() not in DESCRIPTION: #>  #> pkgdown::check_pkgdown() #> No problems found #>  #> style_all() #> Styling  56  files: #>  .Rprofile                                               ✔  #>  README.Rmd                                              ✔  #>  inst/rmarkdown/templates/analysis/skeleton/skeleton.Rmd ✔  #>  inst/templates/index.qmd                                ✔  #>  inst/templates/package.R                                ✔  #>  inst/templates/README-analysis.Rmd                      ✔  #>  inst/templates/README-rdev.Rmd                          ✔  #>  inst/templates/spelling.R                               ✔  #>  inst/templates/test-spelling.R                          ✔  #>  R/build.R                                               ✔  #>  R/ci.R                                                  ✔  #>  R/helpers.R                                             ✔  #>  R/init.R                                                ✔  #>  R/package.R                                             ✔  #>  R/release.R                                             ✔  #>  R/setup.R                                               ✔  #>  R/to_document.R                                         ✔  #>  R/urlchecker.R                                          ✔  #>  R/utils.R                                               ✔  #>  tests/spelling.R                                        ✔  #>  tests/testthat.R                                        ✔  #>  tests/manual/setup.Rmd                                  ✔  #>  tests/manual/test-new-repo-1.R                          ✔  #>  tests/manual/test-new-repo-2.R                          ✔  #>  tests/manual/test-new-repo-3-analysis.R                 ✔  #>  tests/manual/test-new-repo-3-package.R                  ✔  #>  tests/testthat/test-build.R                             ✔  #>  tests/testthat/test-ci.R                                ✔  #>  tests/testthat/test-helpers.R                           ✔  #>  tests/testthat/test-init.R                              ✔  #>  tests/testthat/test-inst.R                              ✔  #>  tests/testthat/test-release.R                           ✔  #>  tests/testthat/test-setup.R                             ✔  #>  tests/testthat/test-spelling.R                          ✔  #>  tests/testthat/test-to_document.R                       ✔  #>  tests/testthat/test-utils.R                             ✔  #>  tests/testthat/test-ci/test.Rprofile                    ✔  #>  tests/testthat/test-ci/testcode_1.R                     ✔  #>  tests/testthat/test-ci/testcode_2.R                     ✔  #>  tests/testthat/test-ci/testcode.Rmd                     ✔  #>  tests/testthat/test-ci/testcode.Rnw                     ✔  #>  tests/testthat/test-ci/packrat/test.R                   ✔  #>  tests/testthat/test-ci/R/RcppExports.R                  ✔  #>  tests/testthat/test-ci/renv/test.R                      ✔  #>  tests/testthat/test-to_document/document.Rmd            ✔  #>  tests/testthat/test-to_document/extra-spaces.Rmd        ✔  #>  tests/testthat/test-to_document/minimal-document.Rmd    ✔  #>  tests/testthat/test-to_document/minimal.Rmd             ✔  #>  tests/testthat/test-to_document/multiple.Rmd            ✔  #>  tests/testthat/test-to_document/no-front-matter.Rmd     ✔  #>  tests/testthat/test-to_document/no-yaml.Rmd             ✔  #>  tests/testthat/test-to_document/valid.Rmd               ✔  #>  tests/testthat/test-to_document/with-code.Rmd           ✔  #>  vignettes/analysis-package-layout.Rmd                   ✔  #>  vignettes/rdev.Rmd                                      ✔  #>  vignettes/style-guide.Rmd                               ✔  #> ─────────────────────────────────────────────────────── #> Status   Count   Legend  #> ✔    56  File unchanged. #> ℹ    0   File changed. #> ✖    0   Styling threw an error. #> ─────────────────────────────────────────────────────── #>  #> lint_all() #>  #> devtools::document() #> ℹ Updating rdev documentation #> ℹ Loading rdev #>  #> desc::desc_normalize() #>  #> extra_deps() #> Finding R package dependencies ... Done! #> desc::desc_get_deps() not found by renv: #> # A tibble: 3 × 3 #>   type     package    version #>   <chr>    <chr>      <chr>   #> 1 Suggests covr       *       #> 2 Suggests diffviewer *       #> 3 Suggests DT         *       #>  #> url_check() #> html_url_check() #> # A tibble: 3 × 9 #>   URL                        From  Status Message New   CRAN  Spaces R     root  #>   <chr>                      <nam> <chr>  <chr>   <chr> <chr> <chr>  <chr> <chr> #> 1 http://covr.r-lib.org/ref… <chr> 200    OK      http… \"\"    \"\"     \"\"    /Use… #> 2 http://r-lib.github.io/rc… <chr> 200    OK      http… \"\"    \"\"     \"\"    /Use… #> 3 https://opensource.org/li… <chr> 200    OK      http… \"\"    \"\"     \"\"    /Use… #>  #> Setting env vars: NOT_CRAN=\"true\", CI=\"true\" #> rcmdcheck::rcmdcheck(args = \"--no-manual\", error_on = \"warning\") #> ── R CMD build ───────────────────────────────────────────────────────────────── #> * checking for file ‘.../DESCRIPTION’ ... OK #> * preparing ‘rdev’: #> * checking DESCRIPTION meta-information ... OK #> * installing the package to build vignettes #> * creating vignettes ... OK #> * checking for LF line-endings in source and make files and shell scripts #> * checking for empty or unneeded directories #> * building ‘rdev_1.9.8.tar.gz’ #>  #> ── R CMD check ───────────────────────────────────────────────────────────────── #> * using log directory ‘/private/var/folders/vn/cw5f9gws42v9m8mdsds_zbl00000gp/T/RtmpriAiu8/file3c30ca812b/rdev.Rcheck’ #> * using R version 4.3.2 (2023-10-31) #> * using platform: aarch64-apple-darwin20 (64-bit) #> * R was compiled by #>     Apple clang version 14.0.0 (clang-1400.0.29.202) #>     GNU Fortran (GCC) 12.2.0 #> * running under: macOS Ventura 13.6.4 #> * using session charset: UTF-8 #> * using option ‘--no-manual’ #> * checking for file ‘rdev/DESCRIPTION’ ... OK #> * this is package ‘rdev’ version ‘1.9.8’ #> * package encoding: UTF-8 #> * checking package namespace information ... OK #> * checking package dependencies ... OK #> * checking if this is a source package ... OK #> * checking if there is a namespace ... OK #> * checking for executable files ... OK #> * checking for hidden files and directories ... OK #> * checking for portable file names ... OK #> * checking for sufficient/correct file permissions ... OK #> * checking whether package ‘rdev’ can be installed ... OK #> * checking installed package size ... OK #> * checking package directory ... OK #> * checking ‘build’ directory ... OK #> * checking DESCRIPTION meta-information ... OK #> * checking top-level files ... OK #> * checking for left-over files ... OK #> * checking index information ... OK #> * checking package subdirectories ... OK #> * checking R files for non-ASCII characters ... OK #> * checking R files for syntax errors ... OK #> * checking whether the package can be loaded ... OK #> * checking whether the package can be loaded with stated dependencies ... OK #> * checking whether the package can be unloaded cleanly ... OK #> * checking whether the namespace can be loaded with stated dependencies ... OK #> * checking whether the namespace can be unloaded cleanly ... OK #> * checking loading without being on the library search path ... OK #> * checking dependencies in R code ... OK #> * checking S3 generic/method consistency ... OK #> * checking replacement functions ... OK #> * checking foreign function calls ... OK #> * checking R code for possible problems ... OK #> * checking Rd files ... OK #> * checking Rd metadata ... OK #> * checking Rd cross-references ... OK #> * checking for missing documentation entries ... OK #> * checking for code/documentation mismatches ... OK #> * checking Rd \\usage sections ... OK #> * checking Rd contents ... OK #> * checking for unstated dependencies in examples ... OK #> * checking installed files from ‘inst/doc’ ... OK #> * checking files in ‘vignettes’ ... OK #> * checking examples ... OK #> * checking for unstated dependencies in ‘tests’ ... OK #> * checking tests ... #>   Running ‘spelling.R’ #>   Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ... OK #>   Running ‘testthat.R’ #>  OK #> * checking for unstated dependencies in vignettes ... OK #> * checking package vignettes in ‘inst/doc’ ... OK #> * checking running R code from vignettes ... #>   ‘analysis-package-layout.Rmd’ using ‘UTF-8’... OK #>   ‘rdev.Rmd’ using ‘UTF-8’... OK #>   ‘style-guide.Rmd’ using ‘UTF-8’... OK #>  NONE #> * checking re-building of vignette outputs ... OK #> * DONE #>  #> Status: OK #> ── R CMD check results ───────────────────────────────────────── rdev 1.9.8 ──── #> Duration: 30.2s #>  #> 0 errors ✔ | 0 warnings ✔ | 0 notes ✔"},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":null,"dir":"Reference","previous_headings":"","what":"Build Analysis Site — build_analysis_site","title":"Build Analysis Site — build_analysis_site","text":"build_analysis_site() wrapper pkgdown::build_site() adds 'Analysis' menu containing rendered versions .Rmd files analysis/.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build Analysis Site — build_analysis_site","text":"","code":"build_analysis_site(pkg = \".\", ...)"},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build Analysis Site — build_analysis_site","text":"pkg Path package. Currently, pkg = \".\" supported. ... additional arguments passed pkgdown::build_site() (implemented)","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build Analysis Site — build_analysis_site","text":"rmarkdown _site.yml yaml, invisibly","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Build Analysis Site — build_analysis_site","text":"run, build_analysis_site(): Reads base pkgdown settings pkgdown/_base.yml Writes base settings _pkgdown.yml Creates template using pkgdown::template_navbar() inserts analysis menu links html versions .Rmd file analysis/ Writes template _pkgdown.yml Updates README.md running devtools::build_readme() (README.Rmd exists) update list notebooks Runs pkgdown::clean_site() pkgdown::build_site() Creates _site.yml file based final _pkgdown.yml clones pkgdown navbar temporary build directory Copies following analysis/ build directory: *.Rmd, assets/, data/, import/, rendered/ Changes *.Rmd html_notebook html_document using to_document() Builds site using rmarkdown::render_site() using modified html_document output settings render files look feel html_notebook Moves rendered files docs/: *.html, assets/, rendered/, without overwriting build_analysis_site() fail error files analysis/*.Rmd, pkgdown/_base.yml exist.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":"continuous-integration","dir":"Reference","previous_headings":"","what":"Continuous Integration","title":"Build Analysis Site — build_analysis_site","text":"build_rdev_site() build_analysis_site() meant used part CI/CD workflow, temporarily set environment variable CI == \"TRUE\" build fail non-internal topics included reference index page per pkgdown::build_reference().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_quarto_site.html","id":null,"dir":"Reference","previous_headings":"","what":"Build Quarto Site — build_quarto_site","title":"Build Quarto Site — build_quarto_site","text":"build_quarto_site() wrapper quarto::quarto_render() also updates README.md optionally deletes Quarto _freeze directory fully re-render site.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_quarto_site.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build Quarto Site — build_quarto_site","text":"","code":"build_quarto_site(input = NULL, as_job = FALSE, unfreeze = FALSE, ...)"},{"path":"https://jabenninghoff.github.io/rdev/reference/build_quarto_site.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build Quarto Site — build_quarto_site","text":"input input file project directory rendered (defaults rendering project current working directory). as_job Render RStudio background job. Default \"auto\", render individual documents normally projects background jobs. Use quarto.render_as_job R option control default globally. unfreeze TRUE, delete Quarto _freeze directory fully re-render site. ... Arguments passed quarto::quarto_render().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_quarto_site.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Build Quarto Site — build_quarto_site","text":"run, build_quarto_site() calls: devtools::build_readme() unfreeze() (unfreeze = TRUE) quarto::quarto_render()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_rdev_site.html","id":null,"dir":"Reference","previous_headings":"","what":"Build rdev Site — build_rdev_site","title":"Build rdev Site — build_rdev_site","text":"build_rdev_site() wrapper pkgdown::build_site() optimized rdev workflow updates README.md performs clean build using pkgdown.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_rdev_site.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build rdev Site — build_rdev_site","text":"","code":"build_rdev_site(pkg = \".\", ...)"},{"path":"https://jabenninghoff.github.io/rdev/reference/build_rdev_site.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build rdev Site — build_rdev_site","text":"pkg Path package. Currently, pkg = \".\" supported. ... additional arguments passed pkgdown::build_site() (implemented)","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_rdev_site.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Build rdev Site — build_rdev_site","text":"run, build_rdev_site() calls: devtools::build_readme() pkgdown::clean_site() pkgdown::build_site()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_rdev_site.html","id":"continuous-integration","dir":"Reference","previous_headings":"","what":"Continuous Integration","title":"Build rdev Site — build_rdev_site","text":"build_rdev_site() build_analysis_site() meant used part CI/CD workflow, temporarily set environment variable CI == \"TRUE\" build fail non-internal topics included reference index page per pkgdown::build_reference().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/check_renv.html","id":null,"dir":"Reference","previous_headings":"","what":"Check renv — check_renv","title":"Check renv — check_renv","text":"Runs renv status(dev = TRUE), clean(), optionally update()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/check_renv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check renv — check_renv","text":"","code":"check_renv(update = rlang::is_interactive())"},{"path":"https://jabenninghoff.github.io/rdev/reference/check_renv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check renv — check_renv","text":"update run renv::update()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/check_renv.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check renv — check_renv","text":"","code":"if (FALSE) { check_renv() check_renv(update = FALSE) }"},{"path":"https://jabenninghoff.github.io/rdev/reference/ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Local CI — ci","title":"Local CI — ci","text":"Run continuous integration tests locally.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Local CI — ci","text":"","code":"ci(   renv = TRUE,   missing = TRUE,   pkgdown = TRUE,   styler = NULL,   lintr = TRUE,   document = TRUE,   normalize = TRUE,   extra = TRUE,   urls = TRUE,   rcmdcheck = TRUE )"},{"path":"https://jabenninghoff.github.io/rdev/reference/ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Local CI — ci","text":"renv check renv::status(dev = TRUE) missing run missing_deps() pkgdown check pkgdown::check_pkgdown() _pkgdown.yml exists styler style files using style_all(), see details lintr lint files using lint_all() document run devtools::document() normalize run desc::desc_normalize() extra run extra_deps() urls validate URLs url_check() html_url_check() rcmdcheck run R CMD check using: rcmdcheck::rcmdcheck(args = \"---manual\", error_on = \"warning\")","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/ci.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Local CI — ci","text":"renv::status(dev = TRUE) synchronized, ci() stop. missing_deps() returns missing dependencies, ci() stop. pkgdown::check_pkgdown() halt ci() error _pkgdown.yml invalid. styler set NULL (default), style_all() run uncommitted changes git. Setting value TRUE FALSE overrides check. lint_all() finds lints, ci() stop open RStudio markers pane. Output missing, extra, urls printed tibble improved readability console.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/ci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Local CI — ci","text":"","code":"if (FALSE) { ci() ci(styler = TRUE) ci(styler = FALSE, rcmdcheck = FALSE) }"},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":null,"dir":"Reference","previous_headings":"","what":"Create rdev GitHub repository — create_github_repo","title":"Create rdev GitHub repository — create_github_repo","text":"Create, configure, clone, open new GitHub R package repository following rdev conventions.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create rdev GitHub repository — create_github_repo","text":"","code":"create_github_repo(   repo_name,   repo_desc = \"\",   org = NULL,   host = getOption(\"rdev.host\") )"},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create rdev GitHub repository — create_github_repo","text":"repo_name name GitHub repository create repo_desc description GitHub repository create org organization create repository . NULL, create repository active user's account. host GitHub host target, passed .api_url argument gh::gh(). unspecified, gh defaults \"https://api.github.com\", although gh's default can customised setting GITHUB_API_URL environment variable. hypothetical GitHub Enterprise instance, either \"https://github.acme.com/api/v3\" \"https://github.acme.com\" acceptable.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create rdev GitHub repository — create_github_repo","text":"return value gh::gh() creating repository, invisibly","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create rdev GitHub repository — create_github_repo","text":"run, create_github_repo(): Creates new GitHub repository using gh::gh() license template get_license() Activates Dependabot alerts per getOption(\"rdev.dependabot\", default = TRUE) Activates Dependabot security updates per getOption(\"rdev.dependabot\", default = TRUE) Adds branch protection default branch Clones repository locally usethis::create_from_github() Creates basic package using usethis::create_package() running interactively macOS, repository automatically opened RStudio, GitHub Desktop, default browser","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":"github-actions","dir":"Reference","previous_headings":"","what":"GitHub Actions","title":"Create rdev GitHub repository — create_github_repo","text":"GitHub Actions can disabled setting rdev.github.actions FALSE: options(rdev.github.actions = FALSE)","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":"host","dir":"Reference","previous_headings":"","what":"Host","title":"Create rdev GitHub repository — create_github_repo","text":"Set rdev.host option using GitHub Enterprise server: options(rdev.host = \"https://github.example.com/api/v3\")","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/deps_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Check dependencies — missing_deps","title":"Check dependencies — missing_deps","text":"Check dependencies DESCRIPTION.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/deps_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check dependencies — missing_deps","text":"","code":"missing_deps(exclude_base = TRUE)  extra_deps()"},{"path":"https://jabenninghoff.github.io/rdev/reference/deps_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check dependencies — missing_deps","text":"exclude_base exclude packages installed R missing dependencies","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/deps_check.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check dependencies — missing_deps","text":"data.frame either renv::dependencies() desc::desc_get_deps().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/deps_check.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Check dependencies — missing_deps","text":"missing_deps() reports renv::dependencies() DESCRIPTION. extra_deps() reports desc::desc_get_deps() found renv. current package (pkgload::pkg_name(\".\")) renv (renv.lock ) automatically removed renv::dependencies(), along 'base' R packages exclude_base TRUE (base, compiler, datasets, grDevices, graphics, grid, methods, parallel, splines, stats, stats4, tcltk, tools, utils).","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_license.html","id":null,"dir":"Reference","previous_headings":"","what":"Get license option — get_license","title":"Get license option — get_license","text":"Retrieve validate rdev.license option.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_license.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get license option — get_license","text":"","code":"get_license()"},{"path":"https://jabenninghoff.github.io/rdev/reference/get_license.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get license option — get_license","text":"license string, one c(\"mit\", \"gpl\", \"lgpl\", \"proprietary\")","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_license.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get license option — get_license","text":"rdev.license must one c(\"mit\", \"gpl\", \"lgpl\", \"proprietary\"), defaults \"mit\". rdev.license \"proprietary\", rdev.license.copyright (name copyright holder) must also set.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_release.html","id":null,"dir":"Reference","previous_headings":"","what":"Get release details — get_release","title":"Get release details — get_release","text":"Extract release version release notes NEWS.md.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_release.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get release details — get_release","text":"","code":"get_release(pkg = \".\", filename = \"NEWS.md\")"},{"path":"https://jabenninghoff.github.io/rdev/reference/get_release.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get release details — get_release","text":"pkg path package. Currently, pkg = \".\" supported. filename name file containing release notes, defaults NEWS.md.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_release.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get release details — get_release","text":"list containing package, version release notes first release contained NEWS.md","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_release.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get release details — get_release","text":"get_release() assumes NEWS.md contains markdown release notes, release header format: \"# <package> <version>\" followed release notes, expects first line NEWS.md release header.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/html_url_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Check URLs in HTML files — html_url_check","title":"Check URLs in HTML files — html_url_check","text":"Runs urlchecker::url_check() database created using url_db_from_HTML_files function tools package.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/html_url_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check URLs in HTML files — html_url_check","text":"","code":"html_url_check(   path = \"docs\",   parallel = TRUE,   pool = curl::new_pool(),   progress = TRUE )"},{"path":"https://jabenninghoff.github.io/rdev/reference/html_url_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check URLs in HTML files — html_url_check","text":"path Path directory HTML files parallel TRUE, check URLs parallel pool multi handle created curl::new_pool(). NULL use global pool. progress Whether show progress bar parallel checks","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/html_url_check.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check URLs in HTML files — html_url_check","text":"url_checker_db object (invisibly). check_url_db object added class custom print method.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/init.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialize rdev package — init","title":"Initialize rdev package — init","text":"Initialize rdev package within newly created create_github_repo() project creating new git branch, committing changes, running use_rdev_package().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/init.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialize rdev package — init","text":"","code":"init()"},{"path":"https://jabenninghoff.github.io/rdev/reference/init.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Initialize rdev package — init","text":"init() stop rlang::is_interactive() FALSE. running init(), update Title Description fields DESCRIPTION file without committing run either setup_analysis() setup_rdev() per quickstart.","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/lint_all.html","id":null,"dir":"Reference","previous_headings":"","what":"Lint all files — lint_all","title":"Lint all files — lint_all","text":"Lint files project. Implemented wrapper lintr::lint_dir().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/lint_all.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lint all files — lint_all","text":"","code":"lint_all(   pattern = \"(?i)[.](r|rmd|qmd|rnw|rhtml|rpres|rrst|rtex|rtxt)$\",   exclusions = list(\"renv\", \"packrat\", \"R/RcppExports.R\"),   ... )"},{"path":"https://jabenninghoff.github.io/rdev/reference/lint_all.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lint all files — lint_all","text":"pattern regex pattern files, default take files extensions .R, .Rmd, .qmd, .Rnw, .Rhtml, .Rpres, .Rrst, .Rtex, .Rtxt, ignoring case. exclusions exclusions exclude(), relative package path. ... Arguments passed lintr::lint_dir parse_settings Logical, default TRUE. Whether try parse settings; otherwise, default_settings() used. path base directory project (lint_dir()) package (lint_package()). relative_path TRUE, file paths printed using path relative base directory. FALSE, use full absolute path. show_progress Logical controlling whether show linting progress simple text progress bar via utils::txtProgressBar(). default behavior show progress interactive() sessions running testthat suite.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/lint_all.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lint all files — lint_all","text":"list lint objects.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/lint_all.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lint all files — lint_all","text":"","code":"if (FALSE) { lint_all() lint_all(\"analysis\") }"},{"path":"https://jabenninghoff.github.io/rdev/reference/local_temppkg.html","id":null,"dir":"Reference","previous_headings":"","what":"Temporary package — local_temppkg","title":"Temporary package — local_temppkg","text":"Temporarily create rdev R analysis package, automatically removed afterwards.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/local_temppkg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Temporary package — local_temppkg","text":"","code":"local_temppkg(dir = fs::file_temp(), type = \"usethis\", env = parent.frame())"},{"path":"https://jabenninghoff.github.io/rdev/reference/local_temppkg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Temporary package — local_temppkg","text":"dir Path package directory, created necessary, defaults fs::file_temp(). type type package create, one \"usethis\" - usethis::create_package(), \"rdev\" - use_rdev_package(), \"analysis\" - use_analysis_package(use_quarto = FALSE), \"quarto\" - use_analysis_package(use_quarto = TRUE). env Environment passed withr::defer(), defaults parent.frame().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/local_temppkg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Temporary package — local_temppkg","text":"Path temporary package directory.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/local_temppkg.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Temporary package — local_temppkg","text":"Used internally testing rdev automation. Based usethis case study testthat.","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/local_temppkg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Temporary package — local_temppkg","text":"","code":"if (FALSE) { test_that(\"local_temppkg creates a directory\", {   dir <- usethis::ui_silence(local_temppkg())   expect_true(fs::dir_exists(dir)) }) }"},{"path":"https://jabenninghoff.github.io/rdev/reference/merge_release.html","id":null,"dir":"Reference","previous_headings":"","what":"Merge staged GitHub release — merge_release","title":"Merge staged GitHub release — merge_release","text":"Merge pull request staged stage_release() create new release GitHub.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/merge_release.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Merge staged GitHub release — merge_release","text":"","code":"merge_release(pkg = \".\", filename = \"NEWS.md\", host = getOption(\"rdev.host\"))"},{"path":"https://jabenninghoff.github.io/rdev/reference/merge_release.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Merge staged GitHub release — merge_release","text":"pkg path package. Currently, pkg = \".\" supported. filename name file containing release notes, defaults NEWS.md. host GitHub host target, passed .api_url argument gh::gh(). unspecified, gh defaults \"https://api.github.com\", although gh's default can customised setting GITHUB_API_URL environment variable. hypothetical GitHub Enterprise instance, either \"https://github.acme.com/api/v3\" \"https://github.acme.com\" acceptable.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/merge_release.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Merge staged GitHub release — merge_release","text":"list containing results pull request merge GitHub release, invisibly","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/merge_release.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Merge staged GitHub release — merge_release","text":"Manually verify status checks completed running, merge_release() currently validate status checks successful. run, merge_release(): Determines staged release title NEWS.md using get_release() Selects GitHub pull request matches staged release title, stops less one matching PR using gh::gh() Verifies staged pull request ready merged checking locked, draft, mergeable, rebaseable flags Merges pull request default branch using \"Rebase merge\" using gh::gh() Deletes pull request branch remotely locally using gh::gh() gert::git_branch_delete() Updates default branch gert::git_pull() Adds version tag DESCRIPTION commit message \"GitHub release <version>\" gert::git_tag_create() pushes using gert::git_tag_push() Create GitHub release newly created tag, name \"<version>\" release notes body, using gh::gh()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/merge_release.html","id":"host","dir":"Reference","previous_headings":"","what":"Host","title":"Merge staged GitHub release — merge_release","text":"Set rdev.host option using GitHub Enterprise server: options(rdev.host = \"https://github.example.com/api/v3\")","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/new_branch.html","id":null,"dir":"Reference","previous_headings":"","what":"Start a new branch — new_branch","title":"Start a new branch — new_branch","text":"Create new \"feature\" branch current default branch project git repository using gert::git_branch_create() bump 'dev' version 9000 desc::desc_bump_version().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/new_branch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Start a new branch — new_branch","text":"","code":"new_branch(name, bump_ver = TRUE, current = FALSE)"},{"path":"https://jabenninghoff.github.io/rdev/reference/new_branch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Start a new branch — new_branch","text":"name name new branch. bump_ver TRUE, bump 'dev' version 9000, see details. current create new branch currently active branch (TRUE) default branch (FALSE), see details.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/new_branch.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Start a new branch — new_branch","text":"new branch created checked exist local remote. version DESCRIPTION 3 components (release version) bump_ver TRUE (default), fourth component, 'dev' bumped 9000 checked new branch. version already 4 components, changed. current = FALSE (default), new branch created default branch determined usethis::git_default_branch().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/open_files.html","id":null,"dir":"Reference","previous_headings":"","what":"Open rdev files — open_files","title":"Open rdev files — open_files","text":"Open standard set files editing RStudio.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/open_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Open rdev files — open_files","text":"","code":"open_files(files = c(\"TODO.md\", \"NEWS.md\", \"README.Rmd\", \"DESCRIPTION\"))"},{"path":"https://jabenninghoff.github.io/rdev/reference/open_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Open rdev files — open_files","text":"files vector files open.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/open_files.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Open rdev files — open_files","text":"named character vector files opened.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/open_files.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Open rdev files — open_files","text":"default, open_files() opens four documents RStudio: TODO.md, NEWS.md, README.Rmd, DESCRIPTION. open_files() stop error RStudio running.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/quickstart.html","id":null,"dir":"Reference","previous_headings":"","what":"rdev Quick Start — quickstart","title":"rdev Quick Start — quickstart","text":"Quick start guide creating new rdev analysis package.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/quickstart.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rdev Quick Start — quickstart","text":"quickly create configure new rdev analysis package, use following commands: project open, run create_github_repo() initialize GitHub R repository Without committing git, run init() newly created project Manually update Title Description fields DESCRIPTION file without committing Run setup_analysis() setup_rdev() configure package analysis package rdev package respectively. Manually update .gitignore: remove docs/ exclusion add line breaks , package configuration complete ready development.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/rdev-package.html","id":null,"dir":"Reference","previous_headings":"","what":"rdev: R Development Tools — rdev-package","title":"rdev: R Development Tools — rdev-package","text":"opinionated collection development tools, packages, utilities.","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/rdev-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rdev: R Development Tools — rdev-package","text":"Maintainer: John Benninghoff jbenninghoff@mac.com (ORCID)","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/rmd_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Get analysis notebook metadata — rmd_metadata","title":"Get analysis notebook metadata — rmd_metadata","text":"Extract YAML front matter 'description' line analysis notebook, construct URL notebook's location GitHub pages.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/rmd_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get analysis notebook metadata — rmd_metadata","text":"","code":"rmd_metadata(file_path)"},{"path":"https://jabenninghoff.github.io/rdev/reference/rmd_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get analysis notebook metadata — rmd_metadata","text":"file_path Path analysis notebook","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/rmd_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get analysis notebook metadata — rmd_metadata","text":"Named list containing analysis notebook title, URL, date, description","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/rmd_metadata.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get analysis notebook metadata — rmd_metadata","text":"'description' line first non-blank line body R notebook serves brief description work.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_analysis.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up analysis package — setup_analysis","title":"Set up analysis package — setup_analysis","text":"Set analysis package within rdev package newly initialized init(), updating Title Description DESCRIPTION, committing changes running use_analysis_package(), use_spelling(), ci().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_analysis.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up analysis package — setup_analysis","text":"","code":"setup_analysis(use_quarto = TRUE)"},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_analysis.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up analysis package — setup_analysis","text":"use_quarto TRUE (default), use Quarto publishing (build_quarto_site()), otherwise use build_analysis_site().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_analysis.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set up analysis package — setup_analysis","text":"setup_analysis() stop rlang::is_interactive() FALSE, run open_files() running RStudio.","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_rdev.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up rdev package — setup_rdev","title":"Set up rdev package — setup_rdev","text":"Set rdev package traditional package development running init() updating Title Description DESCRIPTION, committing changes running use_rdev_pkgdown(), use_spelling(), use_codecov(), ci().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_rdev.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up rdev package — setup_rdev","text":"","code":"setup_rdev()"},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_rdev.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set up rdev package — setup_rdev","text":"setup_rdev() stop rlang::is_interactive() FALSE, run open_files() running RStudio.","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/sort_file.html","id":null,"dir":"Reference","previous_headings":"","what":"Sort file — sort_file","title":"Sort file — sort_file","text":"Sorts file using R sort().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/sort_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sort file — sort_file","text":"","code":"sort_file(filename)"},{"path":"https://jabenninghoff.github.io/rdev/reference/sort_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sort file — sort_file","text":"filename file sorted","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/sort_file.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sort file — sort_file","text":"","code":"if (FALSE) { sort_file(\".Rbuildignore\") }"},{"path":"https://jabenninghoff.github.io/rdev/reference/sort_rbuildignore.html","id":null,"dir":"Reference","previous_headings":"","what":"Sort .Rbuildignore file — sort_rbuildignore","title":"Sort .Rbuildignore file — sort_rbuildignore","text":"Sorts .Rbuildignore file using sort_file().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/sort_rbuildignore.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sort .Rbuildignore file — sort_rbuildignore","text":"","code":"sort_rbuildignore()"},{"path":"https://jabenninghoff.github.io/rdev/reference/spell_check_notebooks.html","id":null,"dir":"Reference","previous_headings":"","what":"Spell Check Notebooks — spell_check_notebooks","title":"Spell Check Notebooks — spell_check_notebooks","text":"Perform spell check notebooks spelling::spell_check_files().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/spell_check_notebooks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spell Check Notebooks — spell_check_notebooks","text":"","code":"spell_check_notebooks(   path = \"analysis\",   glob = \"*.Rmd\",   use_wordlist = TRUE,   lang = NULL )"},{"path":"https://jabenninghoff.github.io/rdev/reference/spell_check_notebooks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spell Check Notebooks — spell_check_notebooks","text":"path character vector one paths. glob wildcard aka globbing pattern (e.g. *.csv) passed grep() filter paths. use_wordlist ignore words package WORDLIST file. lang set Language field DESCRIPTION e.g. \"en-US\" \"en-GB\". supporting languages, see hunspell vignette.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/spell_check_notebooks.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Spell Check Notebooks — spell_check_notebooks","text":"lang NULL (default), get language DESCRIPTION using desc::desc_get_field().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/stage_release.html","id":null,"dir":"Reference","previous_headings":"","what":"Stage a GitHub release — stage_release","title":"Stage a GitHub release — stage_release","text":"Open GitHub pull request new release NEWS.md. Approve, merge, create release using merge_release().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/stage_release.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Stage a GitHub release — stage_release","text":"","code":"stage_release(pkg = \".\", filename = \"NEWS.md\", host = getOption(\"rdev.host\"))"},{"path":"https://jabenninghoff.github.io/rdev/reference/stage_release.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Stage a GitHub release — stage_release","text":"pkg path package. Currently, pkg = \".\" supported. filename name file containing release notes, defaults NEWS.md. host GitHub host target, passed .api_url argument gh::gh(). unspecified, gh defaults \"https://api.github.com\", although gh's default can customised setting GITHUB_API_URL environment variable. hypothetical GitHub Enterprise instance, either \"https://github.acme.com/api/v3\" \"https://github.acme.com\" acceptable.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/stage_release.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Stage a GitHub release — stage_release","text":"results GitHub pull request, invisibly","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/stage_release.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Stage a GitHub release — stage_release","text":"run, stage_release(): Extracts release version release notes NEWS.md using get_release() Validates version conforms rdev conventions (#.#.#) release notes empty Verifies version tag already exist using gert::git_tag_list() Checks uncommitted changes stops exist using gert::git_status() Creates new branch default branch (gert::git_branch() == usethis::git_default_branch()) using gert::git_branch_create() Updates Version DESCRIPTION desc::desc_set_version(), commits push git message \"GitHub release <version>\" using gert::git_add(), gert::git_commit() gert::git_push() Runs build_quarto_site() (_quarto.yml exists), build_analysis_site() (pkgdown/_base.yml exists) build_rdev_site() (_pkgdown.yml exists), commits pushes changes () git message: \"<builder> release <version>\" Opens pull request title \"<package> <version>\" release notes body using gh::gh()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/stage_release.html","id":"host","dir":"Reference","previous_headings":"","what":"Host","title":"Stage a GitHub release — stage_release","text":"Set rdev.host option using GitHub Enterprise server: options(rdev.host = \"https://github.example.com/api/v3\")","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/style_all.html","id":null,"dir":"Reference","previous_headings":"","what":"Style all files — style_all","title":"Style all files — style_all","text":"Style files project. Implemented wrapper styler::style_dir() defaults styling .R, .Rprofile, .Rmd, .Rmarkdown, .Rnw, .Qmd files, excluding files packrat, renv, R/RcppExports.R.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/style_all.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Style all files — style_all","text":"","code":"style_all(   path = \".\",   filetype = c(\"R\", \"Rprofile\", \"Rmd\", \"Rmarkdown\", \"Rnw\", \"Qmd\"),   exclude_dirs = c(\"packrat\", \"renv\"),   exclude_files = \"R/RcppExports.R\",   ... )"},{"path":"https://jabenninghoff.github.io/rdev/reference/style_all.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Style all files — style_all","text":"path Path directory files transform. filetype Vector file extensions indicating file types styled. Case ignored, . optional, e.g. c(\".R\", \".Rmd\"), c(\"r\", \"rmd\"). Supported values (standardization) : \"r\", \"rprofile\", \"rmd\", \"rmarkdown\", \"rnw\", \"qmd\". Rmarkdown treated Rmd. exclude_dirs Character vector directories exclude (recursively). exclude_files Character vector paths files excluded styling. ... Arguments passed styler::style_dir style function creates style guide use, default tidyverse_style. used except construct argument transformers. See style_guides() details. transformers set transformer functions. argument conveniently constructed via style argument .... See 'Examples'. recursive logical value indicating whether files sub directories path styled well. include_roxygen_examples Whether style code roxygen examples. base_indention Integer scalar indicating many spaces whole output text indented. Note splitting line add base_indention spaces code case multi-line strings present. See 'Examples'. dry indicate whether styler run dry mode, .e. refrain writing back files .\"\" \"fail\" write back, latter returns error input code identical result styling. \"\", default, writes back input output styling identical.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/style_all.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Style all files — style_all","text":"","code":"if (FALSE) { style_all() style_all(\"analysis\", filetype = \"Rmd\") }"},{"path":"https://jabenninghoff.github.io/rdev/reference/to_document.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert R Notebook to html_document — to_document","title":"Convert R Notebook to html_document — to_document","text":"Copies file using fs::file_copy() changes output type yaml front matter html_notebook html_document, removing output types.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/to_document.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert R Notebook to html_document — to_document","text":"","code":"to_document(file_path, new_path, overwrite = FALSE)"},{"path":"https://jabenninghoff.github.io/rdev/reference/to_document.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert R Notebook to html_document — to_document","text":"file_path Path source file new_path Path copy converted file using fs::file_copy() overwrite Overwrite file exists, passed fs::file_copy()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/to_document.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert R Notebook to html_document — to_document","text":"Path new file","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/to_document.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert R Notebook to html_document — to_document","text":"","code":"if (FALSE) { to_document(\"notebook.Rmd\", \"document.Rmd\") to_document(\"notebooks_dir/notebook.Rmd\", \"documents_dir\") }"},{"path":"https://jabenninghoff.github.io/rdev/reference/unfreeze.html","id":null,"dir":"Reference","previous_headings":"","what":"Unfreeze Quarto site — unfreeze","title":"Unfreeze Quarto site — unfreeze","text":"Delete Quarto _freeze directory fully re-render site quarto::quarto_render() called.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/unfreeze.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Unfreeze Quarto site — unfreeze","text":"","code":"unfreeze()"},{"path":"https://jabenninghoff.github.io/rdev/reference/update_wordlist_notebooks.html","id":null,"dir":"Reference","previous_headings":"","what":"Update WORDLIST from notebooks — update_wordlist_notebooks","title":"Update WORDLIST from notebooks — update_wordlist_notebooks","text":"Update package inst/WORDLIST words spell_check_notebooks().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/update_wordlist_notebooks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update WORDLIST from notebooks — update_wordlist_notebooks","text":"","code":"update_wordlist_notebooks(   pkg = \".\",   vignettes = TRUE,   path = \"analysis\",   glob = \"*.Rmd\",   confirm = TRUE )"},{"path":"https://jabenninghoff.github.io/rdev/reference/update_wordlist_notebooks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update WORDLIST from notebooks — update_wordlist_notebooks","text":"pkg path package root directory containing DESCRIPTION file vignettes check rmd rnw files pkg root directory (e.g. readme.md) package vignettes folder. path character vector one paths. glob wildcard aka globbing pattern (e.g. *.csv) passed grep() filter paths. confirm show changes ask confirmation adding new words list","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/update_wordlist_notebooks.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Update WORDLIST from notebooks — update_wordlist_notebooks","text":"update_wordlist_notebooks customized version spelling::update_wordlist() using code wordlist.R.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/urlchecker-reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Functions re-exported from the urlchecker package — urlchecker-reexports","title":"Functions re-exported from the urlchecker package — urlchecker-reexports","text":"functions re-exported urlchecker package.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/urlchecker-reexports.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Functions re-exported from the urlchecker package — urlchecker-reexports","text":"","code":"url_check(   path = \".\",   db = NULL,   parallel = TRUE,   pool = curl::new_pool(),   progress = TRUE )  url_update(path = \".\", results = url_check(path))"},{"path":"https://jabenninghoff.github.io/rdev/reference/urlchecker-reexports.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Functions re-exported from the urlchecker package — urlchecker-reexports","text":"path Path package db url database parallel TRUE, check URLs parallel pool multi handle created curl::new_pool(). NULL use global pool. progress Whether show progress bar parallel checks results results url_check.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/urlchecker-reexports.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Functions re-exported from the urlchecker package — urlchecker-reexports","text":"Follow links see urlchecker documentation. urlchecker::url_check() urlchecker::url_update()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_analysis_package.html","id":null,"dir":"Reference","previous_headings":"","what":"Use Analysis Package Layout — use_analysis_package","title":"Use Analysis Package Layout — use_analysis_package","text":"Add Analysis Package Layout current package.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_analysis_package.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Use Analysis Package Layout — use_analysis_package","text":"","code":"use_analysis_package(use_quarto = TRUE, prompt = FALSE)"},{"path":"https://jabenninghoff.github.io/rdev/reference/use_analysis_package.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Use Analysis Package Layout — use_analysis_package","text":"use_quarto TRUE (default), use Quarto publishing (build_quarto_site()), otherwise use build_analysis_site(). prompt TRUE, prompt writing renv.lock, passed renv::snapshot().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_analysis_package.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Use Analysis Package Layout — use_analysis_package","text":"List containing dirs created, rbuildignore lines added .Rbuildignore, gitignore exclusions added .gitignore.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_analysis_package.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Use Analysis Package Layout — use_analysis_package","text":"run, use_analysis_package(): Creates analysis package directories Adds exclusions .gitignore .Rbuildignore Adds extra.css analysis/assets pkgdown (use_quarto FALSE) fix rendering GitHub-style task lists Adds .nojekyll, _quarto.yml index.qmd templates creates _base.yml pkgdown first URL DESCRIPTION Installs README.Rmd template analysis packages, dplyr package needed README.Rmd template","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_codecov.html","id":null,"dir":"Reference","previous_headings":"","what":"Use rdev code coverage — use_codecov","title":"Use rdev code coverage — use_codecov","text":"Install code coverage usethis::use_coverage(type = \"codecov\"), DT package covr::report(), rdev GitHub action test-coverage.yaml.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_codecov.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Use rdev code coverage — use_codecov","text":"","code":"use_codecov(prompt = FALSE)"},{"path":"https://jabenninghoff.github.io/rdev/reference/use_codecov.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Use rdev code coverage — use_codecov","text":"prompt TRUE, prompt writing renv.lock, passed renv::snapshot().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_codecov.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Use rdev code coverage — use_codecov","text":"use_rdev_package(), use_analysis_package() use_codecov() modify README.Rmd, use_codecov() must run last changes overwritten. use_codecov() run use_rdev_package(). Set option rdev.codecov FALSE skip installation codecov.io test-coverage.yaml: options(rdev.codecov = FALSE)","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_codecov.html","id":"github-actions","dir":"Reference","previous_headings":"","what":"GitHub Actions","title":"Use rdev code coverage — use_codecov","text":"GitHub Actions can disabled setting rdev.github.actions FALSE: options(rdev.github.actions = FALSE)","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_lintr.html","id":null,"dir":"Reference","previous_headings":"","what":"Use rdev .lintr — use_lintr","title":"Use rdev .lintr — use_lintr","text":"Install rdev .lintr template using usethis::use_template()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_lintr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Use rdev .lintr — use_lintr","text":"","code":"use_lintr(open = FALSE)"},{"path":"https://jabenninghoff.github.io/rdev/reference/use_lintr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Use rdev .lintr — use_lintr","text":"open Open newly created file editing? Happens RStudio, applicable, via utils::file.edit() otherwise.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_package_r.html","id":null,"dir":"Reference","previous_headings":"","what":"Use rdev package.R — use_package_r","title":"Use rdev package.R — use_package_r","text":"Install rdev package.R template using usethis::use_template()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_package_r.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Use rdev package.R — use_package_r","text":"","code":"use_package_r(open = FALSE)"},{"path":"https://jabenninghoff.github.io/rdev/reference/use_package_r.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Use rdev package.R — use_package_r","text":"open Open newly created file editing? Happens RStudio, applicable, via utils::file.edit() otherwise.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_package_r.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Use rdev package.R — use_package_r","text":"package.R saved \"R/package.R\".","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_rdev_package.html","id":null,"dir":"Reference","previous_headings":"","what":"Use rdev package conventions — use_rdev_package","title":"Use rdev package conventions — use_rdev_package","text":"Add rdev templates settings within active package. Normally invoked first setting package.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_rdev_package.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Use rdev package conventions — use_rdev_package","text":"","code":"use_rdev_package(quiet = TRUE)"},{"path":"https://jabenninghoff.github.io/rdev/reference/use_rdev_package.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Use rdev package conventions — use_rdev_package","text":"quiet TRUE, disable user prompts setting rlang::local_interactive() FALSE.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_rdev_package.html","id":"github-pages","dir":"Reference","previous_headings":"","what":"GitHub Pages","title":"Use rdev package conventions — use_rdev_package","text":"GitHub Pages can disabled setting rdev.github.pages FALSE: options(rdev.github.pages = FALSE)","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_rdev_package.html","id":"github-actions","dir":"Reference","previous_headings":"","what":"GitHub Actions","title":"Use rdev package conventions — use_rdev_package","text":"GitHub Actions can disabled setting rdev.github.actions FALSE: options(rdev.github.actions = FALSE)","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_rdev_pkgdown.html","id":null,"dir":"Reference","previous_headings":"","what":"Use rdev pkgdown — use_rdev_pkgdown","title":"Use rdev pkgdown — use_rdev_pkgdown","text":"Add pkgdown rdev customizations. Implemented wrapper usethis::use_pkgdown().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_rdev_pkgdown.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Use rdev pkgdown — use_rdev_pkgdown","text":"","code":"use_rdev_pkgdown(config_file = \"_pkgdown.yml\", destdir = \"docs\")"},{"path":"https://jabenninghoff.github.io/rdev/reference/use_rdev_pkgdown.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Use rdev pkgdown — use_rdev_pkgdown","text":"config_file Path pkgdown yaml config file, relative project. destdir Target directory pkgdown docs.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_rdev_pkgdown.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Use rdev pkgdown — use_rdev_pkgdown","text":"addition running usethis::use_pkgdown(), use_rdev_pkgdown adds extra.css pkgdown fix rendering GitHub-style task lists, adds GitHub Pages URL, disables bslib::bs_theme() \"shiny\" preset.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_rprofile.html","id":null,"dir":"Reference","previous_headings":"","what":"Use rdev .Rprofile — use_rprofile","title":"Use rdev .Rprofile — use_rprofile","text":"Install rdev .Rprofile template using usethis::use_template()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_rprofile.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Use rdev .Rprofile — use_rprofile","text":"","code":"use_rprofile(open = FALSE)"},{"path":"https://jabenninghoff.github.io/rdev/reference/use_rprofile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Use rdev .Rprofile — use_rprofile","text":"open Open newly created file editing? Happens RStudio, applicable, via utils::file.edit() otherwise.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_spelling.html","id":null,"dir":"Reference","previous_headings":"","what":"Use rdev spelling — use_spelling","title":"Use rdev spelling — use_spelling","text":"Install spelling rdev conventions.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_spelling.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Use rdev spelling — use_spelling","text":"","code":"use_spelling(lang = \"en-US\", prompt = FALSE)"},{"path":"https://jabenninghoff.github.io/rdev/reference/use_spelling.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Use rdev spelling — use_spelling","text":"lang Preferred spelling language. Usually either \"en-US\" \"en-GB\". prompt TRUE, prompt writing renv.lock, passed renv::snapshot().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_spelling.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Use rdev spelling — use_spelling","text":"Since spelling::spell_check_setup() requires user interaction, use_spelling() run use_rdev_package().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_todo.html","id":null,"dir":"Reference","previous_headings":"","what":"Use rdev TODO.md — use_todo","title":"Use rdev TODO.md — use_todo","text":"Install rdev TODO.md template using usethis::use_template()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_todo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Use rdev TODO.md — use_todo","text":"","code":"use_todo(open = rlang::is_interactive())"},{"path":"https://jabenninghoff.github.io/rdev/reference/use_todo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Use rdev TODO.md — use_todo","text":"open Open newly created file editing? Happens RStudio, applicable, via utils::file.edit() otherwise.","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-198","dir":"Changelog","previous_headings":"","what":"rdev 1.9.8","title":"rdev 1.9.8","text":"Added quarto themes (flatly, darkly) (update: use_analysis_package()) Updated analysis template","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-197","dir":"Changelog","previous_headings":"","what":"rdev 1.9.7","title":"rdev 1.9.7","text":"Maintenance updates","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-196","dir":"Changelog","previous_headings":"","what":"rdev 1.9.6","title":"rdev 1.9.6","text":"Add new rdev hex sticker logo stickers man/figures/logo.png per roxygen2 README.Rmd per pkgdown Fixed bugs quickstart functions","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-195","dir":"Changelog","previous_headings":"","what":"rdev 1.9.5","title":"rdev 1.9.5","text":"Updated TODO","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-194","dir":"Changelog","previous_headings":"","what":"rdev 1.9.4","title":"rdev 1.9.4","text":"Updated lintr.yaml GitHub Action match lint_all() (update: run use_rdev_package())","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-193","dir":"Changelog","previous_headings":"","what":"rdev 1.9.3","title":"rdev 1.9.3","text":"lint_all() style_all() now (properly) exclude R/RcppExports.R","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-192","dir":"Changelog","previous_headings":"","what":"rdev 1.9.2","title":"rdev 1.9.2","text":"Updated manual tests Bug fixes","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-191","dir":"Changelog","previous_headings":"","what":"rdev 1.9.1","title":"rdev 1.9.1","text":"Maintenance updates","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-190","dir":"Changelog","previous_headings":"","what":"rdev 1.9.0","title":"rdev 1.9.0","text":"Adjusted Quarto margins _quarto.yml Added ?quickstart rdev Quick Start guide creating new rdev analysis package updated related functions (create_github_repo(), init(), setup_analysis()) README Added function setup_rdev(): set rdev package traditional package development Added function open_files(): open standard set files editing RStudio setup_analysis() setup_rdev() now call open_files() running RStudio","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-186","dir":"Changelog","previous_headings":"","what":"rdev 1.8.6","title":"rdev 1.8.6","text":"Check function arguments checkmate","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-185","dir":"Changelog","previous_headings":"","what":"rdev 1.8.5","title":"rdev 1.8.5","text":"Changed use_analysis_package() store _freeze directory git per Quarto guide","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-184","dir":"Changelog","previous_headings":"","what":"rdev 1.8.4","title":"rdev 1.8.4","text":"Also set GitHub Pages URL use_rdev_pkgdown()","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-183","dir":"Changelog","previous_headings":"","what":"rdev 1.8.3","title":"rdev 1.8.3","text":"Check pandoc PATH launch (update: use_rprofile())","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-182","dir":"Changelog","previous_headings":"","what":"rdev 1.8.2","title":"rdev 1.8.2","text":"Added rendering fixes use_analysis_package() (update: re-run use_analysis_package() update notebooks Analysis Notebook template) Added function use_rdev_pkgdown(): add pkgdown rdev 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0.4.4","title":"rdev 0.4.4","text":"Update build_analysis_site() work pkgdown version 2","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-043","dir":"Changelog","previous_headings":"","what":"rdev 0.4.3","title":"rdev 0.4.3","text":"maintenance, update TODO steps manually setting Analysis Package","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-042","dir":"Changelog","previous_headings":"","what":"rdev 0.4.2","title":"rdev 0.4.2","text":"maintenance release, update README GitHub Actions","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-041","dir":"Changelog","previous_headings":"","what":"rdev 0.4.1","title":"rdev 0.4.1","text":"bug fixes, maintenance","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-040","dir":"Changelog","previous_headings":"","what":"rdev 0.4.0","title":"rdev 0.4.0","text":"Add devtools::document() option ci(), turned default Add R Analysis Package layout definition, migrated rtraining Update ci() use style_all() lint_all() consistency Add import directory build_analysis_site() minor updates, improved tests, maintenance","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-031","dir":"Changelog","previous_headings":"","what":"rdev 0.3.1","title":"rdev 0.3.1","text":"maintenance release, updated R 4.1.0","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-030","dir":"Changelog","previous_headings":"","what":"rdev 0.3.0","title":"rdev 0.3.0","text":"build_analysis_site(), new function migrated rtraining: wrapper pkgdown::build_site() adds ‘Analysis’ menu containing rendered versions .Rmd files analysis/. still considered Experimental, due lack test coverage features implemented, work projects limited pkgdown customization. update also includes function convert notebooks html_document, to_document().","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-022","dir":"Changelog","previous_headings":"","what":"rdev 0.2.2","title":"rdev 0.2.2","text":"minor updates, maintenance","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-021","dir":"Changelog","previous_headings":"","what":"rdev 0.2.1","title":"rdev 0.2.1","text":"bug fixes","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-020","dir":"Changelog","previous_headings":"","what":"rdev 0.2.0","title":"rdev 0.2.0","text":"installing rdev now automatically install preferred development tools ‘meta-package’ (like tidyverse), including: styler, lintr, rcmdcheck, renv, miniUI (RStudio Addin support), devtools, rmarkdown","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-012","dir":"Changelog","previous_headings":"","what":"rdev 0.1.2","title":"rdev 0.1.2","text":"minor updates package site (https://jabenninghoff.github.io/rdev/)","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-011","dir":"Changelog","previous_headings":"","what":"rdev 0.1.1","title":"rdev 0.1.1","text":"maintenance release","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"updates-0-1-1","dir":"Changelog","previous_headings":"","what":"Updates","title":"rdev 0.1.1","text":"ci(): updated match preferred GitHub workflow: use_github_action_check_standard() ---cran removed documentation updates functions (style, links)","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-010","dir":"Changelog","previous_headings":"","what":"rdev 0.1.0","title":"rdev 0.1.0","text":"Initial GitHub release","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"new-features-0-1-0","dir":"Changelog","previous_headings":"","what":"New Features","title":"rdev 0.1.0","text":"./tools/setup-r: shell script install development packages site repository macOS + Homebrew check_renv(): convenience function runs renv status(), clean(), optionally update() (default). style_all(): style .R .Rmd files project using styler lint_all(): lint .R .Rmd files project using lintr sort_file(): sort file using R sort(), similar unix sort command sort_rbuildignore(): sort .Rbuildignore file using sort_file(), unsorted annoying ci(): run continuous integration tests locally: lint, R CMD check, style (default).","code":""}]
+[{"path":"https://jabenninghoff.github.io/rdev/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2021 rdev authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/TODO.html","id":"content","dir":"","previous_headings":"","what":"Content","title":"TODO","text":"Add README.Rmd Update DESCRIPTION use description data README.Rmd Add ORCID Update ORCID details","code":""},{"path":"https://jabenninghoff.github.io/rdev/TODO.html","id":"package","dir":"","previous_headings":"","what":"Package","title":"TODO","text":"Write utility function sort .Rbuildignore Implement pkgdown Add links / update Rd formatting function documentation. Add dummy imports silence R CMD check note per tidyverse Migrate build_analysis_site() rdev Switch development version styler (1.3.2.9000) new release becomes available Validate lint_all works expected within ci Add ‘create package’ workflow example README, remove TODO section “Analysis package creation process” Move _pkgdown.yml repository root make projects discoverable pgkdown GitHub query Update README.Rmd template dynamically generate list notebooks analysis Automate release process Automate creation feature branches, including ‘Bump version’ using desc::desc_bump_version(\"dev\") Add check stage_release() look missing topics _pkgdown.yml reference section Update use_rdev_package() Handle .Rmd files already html_document section Move rmd_metadata() README-analysis.Rmd rdev package Add tests per comments R/ reading package book, documentation Update Roxygen comments reading package book, documentation, review merge duplicate Roxygen docs Write manual regression test script (notes R commands) vignette validate ‘Creating Packages’ ‘GitHub Releases’ Add messages, warnings build_analysis_site() report progress Add function spell check notebooks Automate branch protection Address issue https://github.com/r-lib/usethis/issues/1568, closed Add dplyr running use_analysis_package() Consider switching getOption(\"pkgType\") source per R options per R macOS FAQ, “CRAN build guaranteed compatible package binaries CRAN (Bioconductor).” Support creating repos organizations Consider incorporating GitHub description DESCRIPTION Create wrapper spelling includes notebooks package spell checking, WORDLIST Add spell_check_test_notebooks() function CI spellchecks notebooks Convert manual tests (Setup.Rmd) R Script can run within package created create_github_repo() Add function add missing (notebook) dependencies DESCRIPTION, see renv::dependencies() desc::desc_get_deps() Add check_renv() ci() stop renv::status() date Replace proof-docs urlchecker, support checking GitHub Pages docs directory using url_db_from_HTML_files (ask PR accepted) Move scripts tools inst/bin similar, per Stack Overflow R Packages Switch development versions styler (1.3.2.9000) lintr (2.0.1.9000) new release becomes available - needed address bugs current release versions, 1.3.2 2.0.1. Add trailing slash GitHub Pages URL Update lint_all() lint types, including .Rpres Add custom CSS files _site.yml analysis notebook templates control font size, described article, possibly using bs_theme(), since pkgdown customizes default using build_bslib() (issue exists unsupported Safari 14 Safari 15) Remove pkgdown/extra.css https://github.com/r-lib/pkgdown/issues/2377 accepted Establish default knitr options, including knitr::opts_chunk$set(fig.align = \"center\"), add analysis template, also review settings Advanced R Use Project Templates like vertical? Add CSS R Markdown Template instead assets/extra.css? Move shift-heading-level-: 1 _quarto.yml analysis/_metadata.yml, TODO.md renders properly Remove preset: bootstrap https://github.com/r-lib/pkgdown/issues/2376 accepted Replace dev = TRUE logic https://github.com/rstudio/renv/issues/1695 accepted Update errors messages reading Advanced R Conditions re-reading Tidyverse Style Guide Reduce number Imports, per R CMD check:","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."},{"path":"https://jabenninghoff.github.io/rdev/TODO.html","id":"github","dir":"","previous_headings":"","what":"GitHub","title":"TODO","text":"Use standard R CMD check Use lintr Faster CI checks Switch full R CMD check ? Update GitHub Actions r-lib examples Run test coverage Skip CI checks changes docs/ directory Add GitHub Action html/link checking using something like htmlproofer Autobuild docs/ like pkgdown ?","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Introduction to rdev","text":"rdev supports personal workflow, including creation traditional R packages R Analysis Packages (vignette(\"analysis-package-layout\")), enforcing consistency across packages, providing Continuous Integration/Continuous Delivery (CI/CD) automation. use tools rdev improve code quality, speed development R code, publish results analyses R Notebooks HTML make accessible non-R users.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Introduction to rdev","text":"current R development environment uses Homebrew, rig, RStudio, GitHub, collection R packages including rdev, Visual Studio Code, Vim.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"homebrew","dir":"Articles","previous_headings":"Installation","what":"Homebrew","title":"Introduction to rdev","text":"use Homebrew Bundle install software systems; basic macOS working environment published GitHub macos-env.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"installing-r","dir":"Articles","previous_headings":"Installation","what":"Installing R","title":"Introduction to rdev","text":"rig supports installation multiple versions official R binaries, use reproducibility. install R using rig, first install rig: install desired versions R. following installs R 3.4 4.3 Intel based macs (2023-11-13): don’t use pak, rig installs default, yet fully supported renv.","code":"brew tap r-lib/rig brew install --cask rig rig install oldrel/6 --without-pak rig install oldrel/5 --without-pak rig install oldrel/4 --without-pak rig install oldrel/3 --without-pak rig install oldrel/2 --without-pak rig install oldrel/1 --without-pak rig install oldrel --without-pak rig install release --without-pak rig default release"},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"development-tools","dir":"Articles","previous_headings":"Installation","what":"Development Tools","title":"Introduction to rdev","text":"Well, obviously, use RStudio. RStudio leading IDE R development integrates many R packages, although sometimes falls short; use GitHub command line Git, occasionally Visual Studio Code (better support markdown) Vim (faster types edits). RStudio, GitHub desktop client, Visual Studio Code easily installed using Homebrew: recommended change default settings .RData RStudio (Options > General > Basic > Workspace): Uncheck “Restore .Data workspace startup” Set “Save workspace .Data exit” “Never” Vim installed default macOS Unix-like systems.","code":"brew install --cask rstudio brew install --cask github brew install --cask visual-studio-code"},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"packages","dir":"Articles","previous_headings":"Installation","what":"Packages","title":"Introduction to rdev","text":"Managing packages environments challenge modern languages. Thankfully R doesn’t level challenge python, even ruby, managing packages available within project best practice. use renv purpose, use renv install manage packages projects. setup-r script rdev installs base set packages needed run rdev R User Library. streamlined version script included . chown command needed allow updating base packages using RStudio Packages “Update” function. generally update packages RStudio projects open starting development, update packages projects using renv::update(). ’re installing (development) versions packages GitHub, recommended set personal access token using usethis::create_github_token() adding .Renviron GITHUB_PAT= using usethis::edit_r_environ().","code":"# fix rig permissions sudo chown -R `whoami`:admin /Library/Frameworks/R.framework/Versions/*/Resources/library  RVERSION=`Rscript -e 'cat(as.character(getRversion()[1,1:2]))'` USERLIB=\"$HOME/Library/R/`uname -m`/${RVERSION}/library\" DEVPKG='c(\"renv\", \"styler\", \"lintr\", \"miniUI\", \"markdown\", \"rmarkdown\", \"devtools\", \"pkgdown\", \"available\", \"languageserver\")' GITPKG='c(\"jabenninghoff/rdev\")'  if [ ! -d \"${USERLIB}\" ] then     mkdir -p \"${USERLIB}\" fi  echo \"install.packages(${DEVPKG}, repos=\\\"https://cloud.r-project.org\\\", lib=\\\"${USERLIB}\\\")\" | R --no-save echo \"remotes::install_github(${GITPKG}, lib=\\\"${USERLIB}\\\")\" | R --no-save"},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"further-reading","dir":"Articles","previous_headings":"Installation","what":"Further Reading","title":"Introduction to rdev","text":"workflow heavily influenced DevOps movement research DevOps Research Assessment (DORA) team Google started Dr. Nicole Forsgren. research shows technical non-technical capabilities improve outcomes. functions included rdev support many technical capabilities, including: Code maintainability Continuous delivery Continuous integration Deployment automation Shifting left security Test automation Trunk-based development Version control outline SIRAcon 2022 talk, “Making R Work (Automation)” available GitHub siracon2022.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"rdev-conventions","dir":"Articles","previous_headings":"","what":"rdev conventions","title":"Style Guide","text":"rdev uses mix Google tidyverse conventions.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"naming-conventions","dir":"Articles","previous_headings":"rdev conventions","what":"Naming conventions","title":"Style Guide","text":"rdev follows tidyverse naming convention snake_case.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"right-hand-assignment","dir":"Articles","previous_headings":"rdev conventions","what":"Right-hand assignment","title":"Style Guide","text":"rdev follows Google’s style guide, use right-hand assignment.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"returns","dir":"Articles","previous_headings":"rdev conventions","what":"Returns","title":"Style Guide","text":"rdev typically uses implicit returns unless needed flow control construct specific return structure.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"qualifying-namespaces","dir":"Articles","previous_headings":"rdev conventions","what":"Qualifying namespaces","title":"Style Guide","text":"Use @import @importFrom discouraged, instead using :: functions defined R/. exception infix functions (%name%), always imported, using roxygen @importFrom. Within R Notebooks, use library() encouraged readability.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"package-level-documentation","dir":"Articles","previous_headings":"rdev conventions","what":"Package-level documentation","title":"Style Guide","text":"rdev package documentation lives R/package.R. Additionally, use base R encouraged within functions defined R/ (control dependencies), tidyverse R encouraged within notebooks readability. R Markdown documents generally wrap width code, exceptions R Notebook ‘description line’ (first non-blank line body), long hyperlinks.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"styler","dir":"Articles","previous_headings":"","what":"styler","title":"Style Guide","text":"rdev package implements styler using styler defaults, permanent caching enabled (options(styler.cache_root = \"styler-perm\")). style_all() function applies tidyverse style R files (R, Rprofile, Rmd, Rnw) package directory structure.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"lintr","dir":"Articles","previous_headings":"","what":"lintr","title":"Style Guide","text":"rdev uses opinionated lintr configuration (.lintr): settings deliberately chosen meet specific goals:","code":"linters: linters_with_tags(     tags = NULL,     extraction_operator_linter = NULL,     implicit_integer_linter = NULL,     line_length_linter(100),     missing_package_linter = NULL,     namespace_linter = NULL,     nonportable_path_linter = NULL,     paste_linter(allow_file_path = \"always\"),     todo_comment_linter = NULL,     undesirable_function_linter(       within(all_undesirable_functions, rm(ifelse, library, require, structure))     ),     undesirable_operator_linter(all_undesirable_operators),     unnecessary_concatenation_linter(allow_single_expression = FALSE),     unused_import_linter(       except_packages = c(\"bit64\", \"data.table\", \"tidyverse\", pkgload::pkg_name(\".\"))     )   )"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"use-all-linters","dir":"Articles","previous_headings":"lintr","what":"Use all linters","title":"Style Guide","text":"selects linters, including new Google linters. selecting linters, just defaults, forces evaluation new linters added lintr. Specific linters disabled configured per rdev style.","code":"linters: linters_with_tags(     tags = NULL,"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"allow-extraction-operator","dir":"Articles","previous_headings":"lintr","what":"Allow $ extraction operator","title":"Style Guide","text":"extraction operator linter enforces use [[ $. Since $ intended interactive use supports partial mapping, safer use [[. However, use $ common practice, including within lintr code, leads readable code.","code":"extraction_operator_linter = NULL,"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"allow-implicit-integers","dir":"Articles","previous_headings":"lintr","what":"Allow implicit integers","title":"Style Guide","text":"implicit integer linter checks integers explicitly typed using form 1L. , safer, implicit integers common practice, including output dput():","code":"implicit_integer_linter = NULL, dput(character(0L)) #> character(0)"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"set-line-length","dir":"Articles","previous_headings":"lintr","what":"Set line length","title":"Style Guide","text":"line length 100 reasonable width working RStudio IDE laptop.","code":"line_length_linter(100),"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"use-renv-for-missing-packages","dir":"Articles","previous_headings":"lintr","what":"Use renv for missing packages","title":"Style Guide","text":"missing package linter namespace linter check packages referenced code installed. rdev uses renv manage packages, better job detecting missing packages, including complaining current package (\".\") installed.","code":"missing_package_linter = NULL,     namespace_linter = NULL,"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"allow-non-portable-paths","dir":"Articles","previous_headings":"lintr","what":"Allow non-portable paths","title":"Style Guide","text":"non-portable path linter generates many false positives, including calls fs, essentially makes UNIX-style paths portable across operating systems. Similarly, allow_file_path default option \"double_slash\" generates false positives used fs.","code":"nonportable_path_linter = NULL,     paste_linter(allow_file_path = \"always\"),"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"allow-todo-comments","dir":"Articles","previous_headings":"lintr","what":"Allow TODO comments","title":"Style Guide","text":"rdev conventions encourage use # TODO comments convenient way identifying needed planned updates inline.","code":"todo_comment_linter = NULL,"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"disallow-almost-all-undesirable-functions-and-operators","dir":"Articles","previous_headings":"lintr","what":"Disallow almost all undesirable functions and operators","title":"Style Guide","text":"Enable undesirable functions operators, just defaults, except ifelse() succinct /else block, library(), require(), structure(). Use require() within .Rprofile library() within R Markdown documents appropriate common practice, although neither used within package code. structure() useful comparing test results values generated dput().","code":"undesirable_function_linter(       within(all_undesirable_functions, rm(ifelse, library, require, structure))     ),     undesirable_operator_linter(all_undesirable_operators),"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"enforce-strict-unnecessary-concatenation","dir":"Articles","previous_headings":"lintr","what":"Enforce strict unnecessary concatenation","title":"Style Guide","text":"Enforce stricter version unnecessary concatenation linter.","code":"unnecessary_concatenation_linter(allow_single_expression = FALSE),"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"verify-imported-packages-are-used","dir":"Articles","previous_headings":"lintr","what":"Verify imported packages are used","title":"Style Guide","text":"Verify imported packages used, except packages attached side effects, current package (support package development).","code":"unused_import_linter(       except_packages = c(\"bit64\", \"data.table\", \"tidyverse\", pkgload::pkg_name(\".\"))     )   )"},{"path":"https://jabenninghoff.github.io/rdev/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"John Benninghoff. Author, maintainer.","code":""},{"path":"https://jabenninghoff.github.io/rdev/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Benninghoff J (2024). rdev: R Development Tools. R package version 1.9.9,  https://github.com/jabenninghoff/rdev, https://jabenninghoff.github.io/rdev/.","code":"@Manual{,   title = {rdev: R Development Tools},   author = {John Benninghoff},   year = {2024},   note = {R package version 1.9.9,  https://github.com/jabenninghoff/rdev},   url = {https://jabenninghoff.github.io/rdev/}, }"},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/index.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"R Development Tools","text":"R Development Tools: opinionated collection development tools, packages, utilities. Feel free use /fork project!","code":""},{"path":"https://jabenninghoff.github.io/rdev/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"R Development Tools","text":"can install development version rdev GitHub : using renv:","code":"# install.packages(\"remotes\") remotes::install_github(\"jabenninghoff/rdev\") # install.packages(\"renv\") renv::install(\"jabenninghoff/rdev\")"},{"path":"https://jabenninghoff.github.io/rdev/index.html","id":"development","dir":"","previous_headings":"","what":"Development","title":"R Development Tools","text":"Changelog: See “Changelog” NEWS.md. Planned: TODO","code":""},{"path":"https://jabenninghoff.github.io/rdev/index.html","id":"creating-packages","dir":"","previous_headings":"","what":"Creating Packages","title":"R Development Tools","text":"rdev supports creation new R packages following rdev conventions well new R Analysis packages. typical setup workflow (per ?quickstart) : Use available::available() check package name project open, run create_github_repo() initialize GitHub R repository Without committing git, run init() newly created project Manually update Title Description fields DESCRIPTION file without committing Run setup_analysis() setup_rdev() configure package analysis package rdev package respectively. Update TODO.md, NEWS.md, README.Rmd, DESCRIPTION needed Re-run check_renv(), ci() validate package Commit git begin development","code":""},{"path":"https://jabenninghoff.github.io/rdev/index.html","id":"github-releases","dir":"","previous_headings":"","what":"GitHub Releases","title":"R Development Tools","text":"rdev automates workflow creating GitHub releases along updating GitHub pages either standard R packages R analysis packages, using release notes format NEWS.md. typical development workflow : Bump version create new feature branch new_branch() Write things Update release notes new version NEWS.md, following conventions described get_release() Finalize release merge changes git Run stage_release() create new pull request GitHub using details derived NEWS.md, including updating README GitHub pages pull request reviewed passes required status checks, accept staged release merge_release(), merges pull request, cleans branches, publishes new GitHub release Feature branches can merged without starting new release; stage_release() just requires everything committed, including new release notes NEWS.md running. ready release, stage_release() use existing branch feature branch, create new release branch default.","code":""},{"path":"https://jabenninghoff.github.io/rdev/index.html","id":"workflow","dir":"","previous_headings":"","what":"Workflow","title":"R Development Tools","text":"workflow, typically check renv start: also ci() function run continuous integration tests locally:","code":"library(rdev)  check_renv() #> renv::status(dev = TRUE) #> No issues found -- the project is in a consistent state. #>  #> renv::clean() #> - No stale package locks were found. #> - No temporary directories were found in the project library. #> - The project has been cleaned. ci() #> renv::status(dev = TRUE) #> No issues found -- the project is in a consistent state. #>  #> missing_deps() #> Finding R package dependencies ... Done! #> renv::dependencies() not in DESCRIPTION: #>  #> pkgdown::check_pkgdown() #> No problems found #>  #> style_all() #> Styling  57  files: #>  .Rprofile                                               ✔  #>  README.Rmd                                              ✔  #>  inst/rmarkdown/templates/analysis/skeleton/skeleton.Rmd ✔  #>  inst/templates/changelog.qmd                            ✔  #>  inst/templates/index.qmd                                ✔  #>  inst/templates/package.R                                ✔  #>  inst/templates/README-analysis.Rmd                      ✔  #>  inst/templates/README-rdev.Rmd                          ✔  #>  inst/templates/spelling.R                               ✔  #>  inst/templates/test-spelling.R                          ✔  #>  R/build.R                                               ✔  #>  R/ci.R                                                  ✔  #>  R/helpers.R                                             ✔  #>  R/init.R                                                ✔  #>  R/package.R                                             ✔  #>  R/release.R                                             ✔  #>  R/setup.R                                               ✔  #>  R/to_document.R                                         ✔  #>  R/urlchecker.R                                          ✔  #>  R/utils.R                                               ✔  #>  tests/spelling.R                                        ✔  #>  tests/testthat.R                                        ✔  #>  tests/manual/setup.Rmd                                  ✔  #>  tests/manual/test-new-repo-1.R                          ✔  #>  tests/manual/test-new-repo-2.R                          ✔  #>  tests/manual/test-new-repo-3-analysis.R                 ✔  #>  tests/manual/test-new-repo-3-package.R                  ✔  #>  tests/testthat/test-build.R                             ✔  #>  tests/testthat/test-ci.R                                ✔  #>  tests/testthat/test-helpers.R                           ✔  #>  tests/testthat/test-init.R                              ✔  #>  tests/testthat/test-inst.R                              ✔  #>  tests/testthat/test-release.R                           ✔  #>  tests/testthat/test-setup.R                             ✔  #>  tests/testthat/test-spelling.R                          ✔  #>  tests/testthat/test-to_document.R                       ✔  #>  tests/testthat/test-utils.R                             ✔  #>  tests/testthat/test-ci/test.Rprofile                    ✔  #>  tests/testthat/test-ci/testcode_1.R                     ✔  #>  tests/testthat/test-ci/testcode_2.R                     ✔  #>  tests/testthat/test-ci/testcode.Rmd                     ✔  #>  tests/testthat/test-ci/testcode.Rnw                     ✔  #>  tests/testthat/test-ci/packrat/test.R                   ✔  #>  tests/testthat/test-ci/R/RcppExports.R                  ✔  #>  tests/testthat/test-ci/renv/test.R                      ✔  #>  tests/testthat/test-to_document/document.Rmd            ✔  #>  tests/testthat/test-to_document/extra-spaces.Rmd        ✔  #>  tests/testthat/test-to_document/minimal-document.Rmd    ✔  #>  tests/testthat/test-to_document/minimal.Rmd             ✔  #>  tests/testthat/test-to_document/multiple.Rmd            ✔  #>  tests/testthat/test-to_document/no-front-matter.Rmd     ✔  #>  tests/testthat/test-to_document/no-yaml.Rmd             ✔  #>  tests/testthat/test-to_document/valid.Rmd               ✔  #>  tests/testthat/test-to_document/with-code.Rmd           ✔  #>  vignettes/analysis-package-layout.Rmd                   ✔  #>  vignettes/rdev.Rmd                                      ✔  #>  vignettes/style-guide.Rmd                               ✔  #> ─────────────────────────────────────────────────────── #> Status   Count   Legend  #> ✔    57  File unchanged. #> ℹ    0   File changed. #> ✖    0   Styling threw an error. #> ─────────────────────────────────────────────────────── #>  #> lint_all() #>  #> devtools::document() #> ℹ Updating rdev documentation #> ℹ Loading rdev #>  #> desc::desc_normalize() #>  #> extra_deps() #> Finding R package dependencies ... Done! #> desc::desc_get_deps() not found by renv: #> # A tibble: 3 × 3 #>   type     package    version #>   <chr>    <chr>      <chr>   #> 1 Suggests covr       *       #> 2 Suggests diffviewer *       #> 3 Suggests DT         *       #>  #> url_check() #> html_url_check() #> # A tibble: 3 × 9 #>   URL                        From  Status Message New   CRAN  Spaces R     root  #>   <chr>                      <nam> <chr>  <chr>   <chr> <chr> <chr>  <chr> <chr> #> 1 http://covr.r-lib.org/ref… <chr> 200    OK      http… \"\"    \"\"     \"\"    /Use… #> 2 http://r-lib.github.io/rc… <chr> 200    OK      http… \"\"    \"\"     \"\"    /Use… #> 3 https://opensource.org/li… <chr> 200    OK      http… \"\"    \"\"     \"\"    /Use… #>  #> Setting env vars: NOT_CRAN=\"true\", CI=\"true\" #> rcmdcheck::rcmdcheck(args = \"--no-manual\", error_on = \"warning\") #> ── R CMD build ───────────────────────────────────────────────────────────────── #> * checking for file ‘.../DESCRIPTION’ ... OK #> * preparing ‘rdev’: #> * checking DESCRIPTION meta-information ... OK #> * installing the package to build vignettes #> * creating vignettes ... OK #> * checking for LF line-endings in source and make files and shell scripts #> * checking for empty or unneeded directories #> * building ‘rdev_1.9.9.tar.gz’ #>  #> ── R CMD check ───────────────────────────────────────────────────────────────── #> * using log directory ‘/private/var/folders/vn/cw5f9gws42v9m8mdsds_zbl00000gp/T/RtmpUPErWo/file5f90121489b4/rdev.Rcheck’ #> * using R version 4.3.2 (2023-10-31) #> * using platform: aarch64-apple-darwin20 (64-bit) #> * R was compiled by #>     Apple clang version 14.0.0 (clang-1400.0.29.202) #>     GNU Fortran (GCC) 12.2.0 #> * running under: macOS Ventura 13.6.4 #> * using session charset: UTF-8 #> * using option ‘--no-manual’ #> * checking for file ‘rdev/DESCRIPTION’ ... OK #> * this is package ‘rdev’ version ‘1.9.9’ #> * package encoding: UTF-8 #> * checking package namespace information ... OK #> * checking package dependencies ... OK #> * checking if this is a source package ... OK #> * checking if there is a namespace ... OK #> * checking for executable files ... OK #> * checking for hidden files and directories ... OK #> * checking for portable file names ... OK #> * checking for sufficient/correct file permissions ... OK #> * checking whether package ‘rdev’ can be installed ... OK #> * checking installed package size ... OK #> * checking package directory ... OK #> * checking ‘build’ directory ... OK #> * checking DESCRIPTION meta-information ... OK #> * checking top-level files ... OK #> * checking for left-over files ... OK #> * checking index information ... OK #> * checking package subdirectories ... OK #> * checking R files for non-ASCII characters ... OK #> * checking R files for syntax errors ... OK #> * checking whether the package can be loaded ... OK #> * checking whether the package can be loaded with stated dependencies ... OK #> * checking whether the package can be unloaded cleanly ... OK #> * checking whether the namespace can be loaded with stated dependencies ... OK #> * checking whether the namespace can be unloaded cleanly ... OK #> * checking loading without being on the library search path ... OK #> * checking dependencies in R code ... OK #> * checking S3 generic/method consistency ... OK #> * checking replacement functions ... OK #> * checking foreign function calls ... OK #> * checking R code for possible problems ... OK #> * checking Rd files ... OK #> * checking Rd metadata ... OK #> * checking Rd cross-references ... OK #> * checking for missing documentation entries ... OK #> * checking for code/documentation mismatches ... OK #> * checking Rd \\usage sections ... OK #> * checking Rd contents ... OK #> * checking for unstated dependencies in examples ... OK #> * checking installed files from ‘inst/doc’ ... OK #> * checking files in ‘vignettes’ ... OK #> * checking examples ... OK #> * checking for unstated dependencies in ‘tests’ ... OK #> * checking tests ... #>   Running ‘spelling.R’ #>   Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ... OK #>   Running ‘testthat.R’ #>  OK #> * checking for unstated dependencies in vignettes ... OK #> * checking package vignettes in ‘inst/doc’ ... OK #> * checking running R code from vignettes ... #>   ‘analysis-package-layout.Rmd’ using ‘UTF-8’... OK #>   ‘rdev.Rmd’ using ‘UTF-8’... OK #>   ‘style-guide.Rmd’ using ‘UTF-8’... OK #>  NONE #> * checking re-building of vignette outputs ... OK #> * DONE #>  #> Status: OK #> ── R CMD check results ───────────────────────────────────────── rdev 1.9.9 ──── #> Duration: 32.9s #>  #> 0 errors ✔ | 0 warnings ✔ | 0 notes ✔"},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":null,"dir":"Reference","previous_headings":"","what":"Build Analysis Site — build_analysis_site","title":"Build Analysis Site — build_analysis_site","text":"build_analysis_site() wrapper pkgdown::build_site() adds 'Analysis' menu containing rendered versions .Rmd files analysis/.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build Analysis Site — build_analysis_site","text":"","code":"build_analysis_site(pkg = \".\", ...)"},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build Analysis Site — build_analysis_site","text":"pkg Path package. Currently, pkg = \".\" supported. ... additional arguments passed pkgdown::build_site() (implemented)","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build Analysis Site — build_analysis_site","text":"rmarkdown _site.yml yaml, invisibly","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Build Analysis Site — build_analysis_site","text":"run, build_analysis_site(): Reads base pkgdown settings pkgdown/_base.yml Writes base settings _pkgdown.yml Creates template using pkgdown::template_navbar() inserts analysis menu links html versions .Rmd file analysis/ Writes template _pkgdown.yml Updates README.md running devtools::build_readme() (README.Rmd exists) update list notebooks Runs pkgdown::clean_site() pkgdown::build_site() Creates _site.yml file based final _pkgdown.yml clones pkgdown navbar temporary build directory Copies following analysis/ build directory: *.Rmd, assets/, data/, import/, rendered/ Changes *.Rmd html_notebook html_document using to_document() Builds site using rmarkdown::render_site() using modified html_document output settings render files look feel html_notebook Moves rendered files docs/: *.html, assets/, rendered/, without overwriting build_analysis_site() fail error files analysis/*.Rmd, pkgdown/_base.yml exist.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":"continuous-integration","dir":"Reference","previous_headings":"","what":"Continuous Integration","title":"Build Analysis Site — build_analysis_site","text":"build_rdev_site() build_analysis_site() meant used part CI/CD workflow, temporarily set environment variable CI == \"TRUE\" build fail non-internal topics included reference index page per pkgdown::build_reference().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_quarto_site.html","id":null,"dir":"Reference","previous_headings":"","what":"Build Quarto Site — build_quarto_site","title":"Build Quarto Site — build_quarto_site","text":"build_quarto_site() wrapper quarto::quarto_render() also updates README.md optionally deletes Quarto _freeze directory fully re-render site.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_quarto_site.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build Quarto Site — build_quarto_site","text":"","code":"build_quarto_site(input = NULL, as_job = FALSE, unfreeze = FALSE, ...)"},{"path":"https://jabenninghoff.github.io/rdev/reference/build_quarto_site.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build Quarto Site — build_quarto_site","text":"input input file project directory rendered (defaults rendering project current working directory). as_job Render RStudio background job. Default \"auto\", render individual documents normally projects background jobs. Use quarto.render_as_job R option control default globally. unfreeze TRUE, delete Quarto _freeze directory fully re-render site. ... Arguments passed quarto::quarto_render().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_quarto_site.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Build Quarto Site — build_quarto_site","text":"run, build_quarto_site() calls: devtools::build_readme() unfreeze() (unfreeze = TRUE) quarto::quarto_render()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_rdev_site.html","id":null,"dir":"Reference","previous_headings":"","what":"Build rdev Site — build_rdev_site","title":"Build rdev Site — build_rdev_site","text":"build_rdev_site() wrapper pkgdown::build_site() optimized rdev workflow updates README.md performs clean build using pkgdown.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_rdev_site.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build rdev Site — build_rdev_site","text":"","code":"build_rdev_site(pkg = \".\", ...)"},{"path":"https://jabenninghoff.github.io/rdev/reference/build_rdev_site.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build rdev Site — build_rdev_site","text":"pkg Path package. Currently, pkg = \".\" supported. ... additional arguments passed pkgdown::build_site() (implemented)","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_rdev_site.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Build rdev Site — build_rdev_site","text":"run, build_rdev_site() calls: devtools::build_readme() pkgdown::clean_site() pkgdown::build_site()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_rdev_site.html","id":"continuous-integration","dir":"Reference","previous_headings":"","what":"Continuous Integration","title":"Build rdev Site — build_rdev_site","text":"build_rdev_site() build_analysis_site() meant used part CI/CD workflow, temporarily set environment variable CI == \"TRUE\" build fail non-internal topics included reference index page per pkgdown::build_reference().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/check_renv.html","id":null,"dir":"Reference","previous_headings":"","what":"Check renv — check_renv","title":"Check renv — check_renv","text":"Runs renv status(dev = TRUE), clean(), optionally update()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/check_renv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check renv — check_renv","text":"","code":"check_renv(update = rlang::is_interactive())"},{"path":"https://jabenninghoff.github.io/rdev/reference/check_renv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check renv — check_renv","text":"update run renv::update()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/check_renv.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check renv — check_renv","text":"","code":"if (FALSE) { check_renv() check_renv(update = FALSE) }"},{"path":"https://jabenninghoff.github.io/rdev/reference/ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Local CI — ci","title":"Local CI — ci","text":"Run continuous integration tests locally.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Local CI — ci","text":"","code":"ci(   renv = TRUE,   missing = TRUE,   pkgdown = TRUE,   styler = NULL,   lintr = TRUE,   document = TRUE,   normalize = TRUE,   extra = TRUE,   urls = TRUE,   rcmdcheck = TRUE )"},{"path":"https://jabenninghoff.github.io/rdev/reference/ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Local CI — ci","text":"renv check renv::status(dev = TRUE) missing run missing_deps() pkgdown check pkgdown::check_pkgdown() _pkgdown.yml exists styler style files using style_all(), see details lintr lint files using lint_all() document run devtools::document() normalize run desc::desc_normalize() extra run extra_deps() urls validate URLs url_check() html_url_check() rcmdcheck run R CMD check using: rcmdcheck::rcmdcheck(args = \"---manual\", error_on = \"warning\")","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/ci.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Local CI — ci","text":"renv::status(dev = TRUE) synchronized, ci() stop. missing_deps() returns missing dependencies, ci() stop. pkgdown::check_pkgdown() halt ci() error _pkgdown.yml invalid. styler set NULL (default), style_all() run uncommitted changes git. Setting value TRUE FALSE overrides check. lint_all() finds lints, ci() stop open RStudio markers pane. Output missing, extra, urls printed tibble improved readability console.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/ci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Local CI — ci","text":"","code":"if (FALSE) { ci() ci(styler = TRUE) ci(styler = FALSE, rcmdcheck = FALSE) }"},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":null,"dir":"Reference","previous_headings":"","what":"Create rdev GitHub repository — create_github_repo","title":"Create rdev GitHub repository — create_github_repo","text":"Create, configure, clone, open new GitHub R package repository following rdev conventions.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create rdev GitHub repository — create_github_repo","text":"","code":"create_github_repo(   repo_name,   repo_desc = \"\",   org = NULL,   host = getOption(\"rdev.host\") )"},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create rdev GitHub repository — create_github_repo","text":"repo_name name GitHub repository create repo_desc description GitHub repository create org organization create repository . NULL, create repository active user's account. host GitHub host target, passed .api_url argument gh::gh(). unspecified, gh defaults \"https://api.github.com\", although gh's default can customised setting GITHUB_API_URL environment variable. hypothetical GitHub Enterprise instance, either \"https://github.acme.com/api/v3\" \"https://github.acme.com\" acceptable.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create rdev GitHub repository — create_github_repo","text":"return value gh::gh() creating repository, invisibly","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create rdev GitHub repository — create_github_repo","text":"run, create_github_repo(): Creates new GitHub repository using gh::gh() license template get_license() Activates Dependabot alerts per getOption(\"rdev.dependabot\", default = TRUE) Activates Dependabot security updates per getOption(\"rdev.dependabot\", default = TRUE) Adds branch protection default branch Clones repository locally usethis::create_from_github() Creates basic package using usethis::create_package() running interactively macOS, repository automatically opened RStudio, GitHub Desktop, default browser","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":"github-actions","dir":"Reference","previous_headings":"","what":"GitHub Actions","title":"Create rdev GitHub repository — create_github_repo","text":"GitHub Actions can disabled setting rdev.github.actions FALSE: options(rdev.github.actions = FALSE)","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":"host","dir":"Reference","previous_headings":"","what":"Host","title":"Create rdev GitHub repository — create_github_repo","text":"Set rdev.host option using GitHub Enterprise server: options(rdev.host = \"https://github.example.com/api/v3\")","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/deps_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Check dependencies — missing_deps","title":"Check dependencies — missing_deps","text":"Check dependencies DESCRIPTION.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/deps_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check dependencies — missing_deps","text":"","code":"missing_deps(exclude_base = TRUE)  extra_deps()"},{"path":"https://jabenninghoff.github.io/rdev/reference/deps_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check dependencies — missing_deps","text":"exclude_base exclude packages installed R missing dependencies","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/deps_check.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check dependencies — missing_deps","text":"data.frame either renv::dependencies() desc::desc_get_deps().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/deps_check.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Check dependencies — missing_deps","text":"missing_deps() reports renv::dependencies() DESCRIPTION. extra_deps() reports desc::desc_get_deps() found renv. current package (pkgload::pkg_name(\".\")) renv (renv.lock ) automatically removed renv::dependencies(), along 'base' R packages exclude_base TRUE (base, compiler, datasets, grDevices, graphics, grid, methods, parallel, splines, stats, stats4, tcltk, tools, utils).","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_license.html","id":null,"dir":"Reference","previous_headings":"","what":"Get license option — get_license","title":"Get license option — get_license","text":"Retrieve validate rdev.license option.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_license.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get license option — get_license","text":"","code":"get_license()"},{"path":"https://jabenninghoff.github.io/rdev/reference/get_license.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get license option — get_license","text":"license string, one c(\"mit\", \"gpl\", \"lgpl\", \"proprietary\")","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_license.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get license option — get_license","text":"rdev.license must one c(\"mit\", \"gpl\", \"lgpl\", \"proprietary\"), defaults \"mit\". rdev.license \"proprietary\", rdev.license.copyright (name copyright holder) must also set.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_release.html","id":null,"dir":"Reference","previous_headings":"","what":"Get release details — get_release","title":"Get release details — get_release","text":"Extract release version release notes NEWS.md.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_release.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get release details — get_release","text":"","code":"get_release(pkg = \".\", filename = \"NEWS.md\")"},{"path":"https://jabenninghoff.github.io/rdev/reference/get_release.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get release details — get_release","text":"pkg path package. Currently, pkg = \".\" supported. filename name file containing release notes, defaults NEWS.md.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_release.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get release details — get_release","text":"list containing package, version release notes first release contained NEWS.md","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_release.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get release details — get_release","text":"get_release() assumes NEWS.md contains markdown release notes, release header format: \"# <package> <version>\" followed release notes, expects first line NEWS.md release header.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/html_url_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Check URLs in HTML files — html_url_check","title":"Check URLs in HTML files — html_url_check","text":"Runs urlchecker::url_check() database created using url_db_from_HTML_files function tools package.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/html_url_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check URLs in HTML files — html_url_check","text":"","code":"html_url_check(   path = \"docs\",   parallel = TRUE,   pool = curl::new_pool(),   progress = TRUE )"},{"path":"https://jabenninghoff.github.io/rdev/reference/html_url_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check URLs in HTML files — html_url_check","text":"path Path directory HTML files parallel TRUE, check URLs parallel pool multi handle created curl::new_pool(). NULL use global pool. progress Whether show progress bar parallel checks","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/html_url_check.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check URLs in HTML files — html_url_check","text":"url_checker_db object (invisibly). check_url_db object added class custom print method.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/init.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialize rdev package — init","title":"Initialize rdev package — init","text":"Initialize rdev package within newly created create_github_repo() project creating new git branch, committing changes, running use_rdev_package().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/init.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialize rdev package — init","text":"","code":"init()"},{"path":"https://jabenninghoff.github.io/rdev/reference/init.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Initialize rdev package — init","text":"init() stop rlang::is_interactive() FALSE. running init(), update Title Description fields DESCRIPTION file without committing run either setup_analysis() setup_rdev() per quickstart.","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/lint_all.html","id":null,"dir":"Reference","previous_headings":"","what":"Lint all files — lint_all","title":"Lint all files — lint_all","text":"Lint files project. Implemented wrapper lintr::lint_dir().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/lint_all.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lint all files — lint_all","text":"","code":"lint_all(   pattern = \"(?i)[.](r|rmd|qmd|rnw|rhtml|rpres|rrst|rtex|rtxt)$\",   exclusions = list(\"renv\", \"packrat\", \"R/RcppExports.R\"),   ... )"},{"path":"https://jabenninghoff.github.io/rdev/reference/lint_all.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lint all files — lint_all","text":"pattern regex pattern files, default take files extensions .R, .Rmd, .qmd, .Rnw, .Rhtml, .Rpres, .Rrst, .Rtex, .Rtxt, ignoring case. exclusions exclusions exclude(), relative package path. ... Arguments passed lintr::lint_dir parse_settings Logical, default TRUE. Whether try parse settings; otherwise, default_settings() used. path base directory project (lint_dir()) package (lint_package()). relative_path TRUE, file paths printed using path relative base directory. FALSE, use full absolute path. show_progress Logical controlling whether show linting progress simple text progress bar via utils::txtProgressBar(). default behavior show progress interactive() sessions running testthat suite.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/lint_all.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lint all files — lint_all","text":"list lint objects.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/lint_all.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lint all files — lint_all","text":"","code":"if (FALSE) { lint_all() lint_all(\"analysis\") }"},{"path":"https://jabenninghoff.github.io/rdev/reference/local_temppkg.html","id":null,"dir":"Reference","previous_headings":"","what":"Temporary package — local_temppkg","title":"Temporary package — local_temppkg","text":"Temporarily create rdev R analysis package, automatically removed afterwards.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/local_temppkg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Temporary package — local_temppkg","text":"","code":"local_temppkg(dir = fs::file_temp(), type = \"usethis\", env = parent.frame())"},{"path":"https://jabenninghoff.github.io/rdev/reference/local_temppkg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Temporary package — local_temppkg","text":"dir Path package directory, created necessary, defaults fs::file_temp(). type type package create, one \"usethis\" - usethis::create_package(), \"rdev\" - use_rdev_package(), \"analysis\" - use_analysis_package(use_quarto = FALSE), \"quarto\" - use_analysis_package(use_quarto = TRUE). env Environment passed withr::defer(), defaults parent.frame().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/local_temppkg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Temporary package — local_temppkg","text":"Path temporary package directory.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/local_temppkg.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Temporary package — local_temppkg","text":"Used internally testing rdev automation. Based usethis case study testthat.","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/local_temppkg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Temporary package — local_temppkg","text":"","code":"if (FALSE) { test_that(\"local_temppkg creates a directory\", {   dir <- usethis::ui_silence(local_temppkg())   expect_true(fs::dir_exists(dir)) }) }"},{"path":"https://jabenninghoff.github.io/rdev/reference/merge_release.html","id":null,"dir":"Reference","previous_headings":"","what":"Merge staged GitHub release — merge_release","title":"Merge staged GitHub release — merge_release","text":"Merge pull request staged stage_release() create new release GitHub.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/merge_release.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Merge staged GitHub release — merge_release","text":"","code":"merge_release(pkg = \".\", filename = \"NEWS.md\", host = getOption(\"rdev.host\"))"},{"path":"https://jabenninghoff.github.io/rdev/reference/merge_release.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Merge staged GitHub release — merge_release","text":"pkg path package. Currently, pkg = \".\" supported. filename name file containing release notes, defaults NEWS.md. host GitHub host target, passed .api_url argument gh::gh(). unspecified, gh defaults \"https://api.github.com\", although gh's default can customised setting GITHUB_API_URL environment variable. hypothetical GitHub Enterprise instance, either \"https://github.acme.com/api/v3\" \"https://github.acme.com\" acceptable.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/merge_release.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Merge staged GitHub release — merge_release","text":"list containing results pull request merge GitHub release, invisibly","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/merge_release.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Merge staged GitHub release — merge_release","text":"Manually verify status checks completed running, merge_release() currently validate status checks successful. run, merge_release(): Determines staged release title NEWS.md using get_release() Selects GitHub pull request matches staged release title, stops less one matching PR using gh::gh() Verifies staged pull request ready merged checking locked, draft, mergeable, rebaseable flags Merges pull request default branch using \"Rebase merge\" using gh::gh() Deletes pull request branch remotely locally using gh::gh() gert::git_branch_delete() Updates default branch gert::git_pull() Adds version tag DESCRIPTION commit message \"GitHub release <version>\" gert::git_tag_create() pushes using gert::git_tag_push() Create GitHub release newly created tag, name \"<version>\" release notes body, using gh::gh()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/merge_release.html","id":"host","dir":"Reference","previous_headings":"","what":"Host","title":"Merge staged GitHub release — merge_release","text":"Set rdev.host option using GitHub Enterprise server: options(rdev.host = \"https://github.example.com/api/v3\")","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/new_branch.html","id":null,"dir":"Reference","previous_headings":"","what":"Start a new branch — new_branch","title":"Start a new branch — new_branch","text":"Create new \"feature\" branch current default branch project git repository using gert::git_branch_create() bump 'dev' version 9000 desc::desc_bump_version().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/new_branch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Start a new branch — new_branch","text":"","code":"new_branch(name, bump_ver = TRUE, current = FALSE)"},{"path":"https://jabenninghoff.github.io/rdev/reference/new_branch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Start a new branch — new_branch","text":"name name new branch. bump_ver TRUE, bump 'dev' version 9000, see details. current create new branch currently active branch (TRUE) default branch (FALSE), see details.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/new_branch.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Start a new branch — new_branch","text":"new branch created checked exist local remote. version DESCRIPTION 3 components (release version) bump_ver TRUE (default), fourth component, 'dev' bumped 9000 checked new branch. version already 4 components, changed. current = FALSE (default), new branch created default branch determined usethis::git_default_branch().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/open_files.html","id":null,"dir":"Reference","previous_headings":"","what":"Open rdev files — open_files","title":"Open rdev files — open_files","text":"Open standard set files editing RStudio.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/open_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Open rdev files — open_files","text":"","code":"open_files(files = c(\"TODO.md\", \"NEWS.md\", \"README.Rmd\", \"DESCRIPTION\"))"},{"path":"https://jabenninghoff.github.io/rdev/reference/open_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Open rdev files — open_files","text":"files vector files open.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/open_files.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Open rdev files — open_files","text":"named character vector files opened.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/open_files.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Open rdev files — open_files","text":"default, open_files() opens four documents RStudio: TODO.md, NEWS.md, README.Rmd, DESCRIPTION. open_files() stop error RStudio running.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/quickstart.html","id":null,"dir":"Reference","previous_headings":"","what":"rdev Quick Start — quickstart","title":"rdev Quick Start — quickstart","text":"Quick start guide creating new rdev analysis package.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/quickstart.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rdev Quick Start — quickstart","text":"quickly create configure new rdev analysis package, use following commands: project open, run create_github_repo() initialize GitHub R repository Without committing git, run init() newly created project Manually update Title Description fields DESCRIPTION file without committing Run setup_analysis() setup_rdev() configure package analysis package rdev package respectively. Manually update .gitignore: remove docs/ exclusion add line breaks , package configuration complete ready development.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/rdev-package.html","id":null,"dir":"Reference","previous_headings":"","what":"rdev: R Development Tools — rdev-package","title":"rdev: R Development Tools — rdev-package","text":"opinionated collection development tools, packages, utilities.","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/rdev-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rdev: R Development Tools — rdev-package","text":"Maintainer: John Benninghoff jbenninghoff@mac.com (ORCID)","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/rmd_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Get analysis notebook metadata — rmd_metadata","title":"Get analysis notebook metadata — rmd_metadata","text":"Extract YAML front matter 'description' line analysis notebook, construct URL notebook's location GitHub pages.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/rmd_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get analysis notebook metadata — rmd_metadata","text":"","code":"rmd_metadata(file_path)"},{"path":"https://jabenninghoff.github.io/rdev/reference/rmd_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get analysis notebook metadata — rmd_metadata","text":"file_path Path analysis notebook","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/rmd_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get analysis notebook metadata — rmd_metadata","text":"Named list containing analysis notebook title, URL, date, description","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/rmd_metadata.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get analysis notebook metadata — rmd_metadata","text":"'description' line first non-blank line body R notebook serves brief description work.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_analysis.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up analysis package — setup_analysis","title":"Set up analysis package — setup_analysis","text":"Set analysis package within rdev package newly initialized init(), updating Title Description DESCRIPTION, committing changes running use_analysis_package(), use_spelling(), ci().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_analysis.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up analysis package — setup_analysis","text":"","code":"setup_analysis(use_quarto = TRUE)"},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_analysis.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up analysis package — setup_analysis","text":"use_quarto TRUE (default), use Quarto publishing (build_quarto_site()), otherwise use build_analysis_site().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_analysis.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set up analysis package — setup_analysis","text":"setup_analysis() stop rlang::is_interactive() FALSE, run open_files() running RStudio.","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_rdev.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up rdev package — setup_rdev","title":"Set up rdev package — setup_rdev","text":"Set rdev package traditional package development running init() updating Title Description DESCRIPTION, committing changes running use_rdev_pkgdown(), use_spelling(), use_codecov(), ci().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_rdev.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up rdev package — setup_rdev","text":"","code":"setup_rdev()"},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_rdev.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set up rdev package — setup_rdev","text":"setup_rdev() stop rlang::is_interactive() FALSE, run open_files() running RStudio.","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/sort_file.html","id":null,"dir":"Reference","previous_headings":"","what":"Sort file — sort_file","title":"Sort file — sort_file","text":"Sorts file using R sort().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/sort_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sort file — sort_file","text":"","code":"sort_file(filename)"},{"path":"https://jabenninghoff.github.io/rdev/reference/sort_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sort file — sort_file","text":"filename file sorted","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/sort_file.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sort file — sort_file","text":"","code":"if (FALSE) { sort_file(\".Rbuildignore\") }"},{"path":"https://jabenninghoff.github.io/rdev/reference/sort_rbuildignore.html","id":null,"dir":"Reference","previous_headings":"","what":"Sort .Rbuildignore file — sort_rbuildignore","title":"Sort .Rbuildignore file — sort_rbuildignore","text":"Sorts .Rbuildignore file using sort_file().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/sort_rbuildignore.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sort .Rbuildignore file — sort_rbuildignore","text":"","code":"sort_rbuildignore()"},{"path":"https://jabenninghoff.github.io/rdev/reference/spell_check_notebooks.html","id":null,"dir":"Reference","previous_headings":"","what":"Spell Check Notebooks — spell_check_notebooks","title":"Spell Check Notebooks — spell_check_notebooks","text":"Perform spell check notebooks spelling::spell_check_files().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/spell_check_notebooks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spell Check Notebooks — spell_check_notebooks","text":"","code":"spell_check_notebooks(   path = \"analysis\",   glob = \"*.Rmd\",   use_wordlist = TRUE,   lang = NULL )"},{"path":"https://jabenninghoff.github.io/rdev/reference/spell_check_notebooks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spell Check Notebooks — spell_check_notebooks","text":"path character vector one paths. glob wildcard aka globbing pattern (e.g. *.csv) passed grep() filter paths. use_wordlist ignore words package WORDLIST file. lang set Language field DESCRIPTION e.g. \"en-US\" \"en-GB\". supporting languages, see hunspell vignette.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/spell_check_notebooks.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Spell Check Notebooks — spell_check_notebooks","text":"lang NULL (default), get language DESCRIPTION using desc::desc_get_field().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/stage_release.html","id":null,"dir":"Reference","previous_headings":"","what":"Stage a GitHub release — stage_release","title":"Stage a GitHub release — stage_release","text":"Open GitHub pull request new release NEWS.md. Approve, merge, create release using merge_release().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/stage_release.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Stage a GitHub release — stage_release","text":"","code":"stage_release(pkg = \".\", filename = \"NEWS.md\", host = getOption(\"rdev.host\"))"},{"path":"https://jabenninghoff.github.io/rdev/reference/stage_release.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Stage a GitHub release — stage_release","text":"pkg path package. Currently, pkg = \".\" supported. filename name file containing release notes, defaults NEWS.md. host GitHub host target, passed .api_url argument gh::gh(). unspecified, gh defaults \"https://api.github.com\", although gh's default can customised setting GITHUB_API_URL environment variable. hypothetical GitHub Enterprise instance, either \"https://github.acme.com/api/v3\" \"https://github.acme.com\" acceptable.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/stage_release.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Stage a GitHub release — stage_release","text":"results GitHub pull request, invisibly","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/stage_release.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Stage a GitHub release — stage_release","text":"run, stage_release(): Extracts release version release notes NEWS.md using get_release() Validates version conforms rdev conventions (#.#.#) release notes empty Verifies version tag already exist using gert::git_tag_list() Checks uncommitted changes stops exist using gert::git_status() Creates new branch default branch (gert::git_branch() == usethis::git_default_branch()) using gert::git_branch_create() Updates Version DESCRIPTION desc::desc_set_version(), commits push git message \"GitHub release <version>\" using gert::git_add(), gert::git_commit() gert::git_push() Runs build_quarto_site() (_quarto.yml exists), build_analysis_site() (pkgdown/_base.yml exists) build_rdev_site() (_pkgdown.yml exists), commits pushes changes () git message: \"<builder> release <version>\" Opens pull request title \"<package> <version>\" release notes body using gh::gh()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/stage_release.html","id":"host","dir":"Reference","previous_headings":"","what":"Host","title":"Stage a GitHub release — stage_release","text":"Set rdev.host option using GitHub Enterprise server: options(rdev.host = \"https://github.example.com/api/v3\")","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/style_all.html","id":null,"dir":"Reference","previous_headings":"","what":"Style all files — style_all","title":"Style all files — style_all","text":"Style files project. Implemented wrapper styler::style_dir() defaults styling .R, .Rprofile, .Rmd, .Rmarkdown, .Rnw, .Qmd files, excluding files packrat, renv, R/RcppExports.R.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/style_all.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Style all files — style_all","text":"","code":"style_all(   path = \".\",   filetype = c(\"R\", \"Rprofile\", \"Rmd\", \"Rmarkdown\", \"Rnw\", \"Qmd\"),   exclude_dirs = c(\"packrat\", \"renv\"),   exclude_files = \"R/RcppExports.R\",   ... )"},{"path":"https://jabenninghoff.github.io/rdev/reference/style_all.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Style all files — style_all","text":"path Path directory files transform. filetype Vector file extensions indicating file types styled. Case ignored, . optional, e.g. c(\".R\", \".Rmd\"), c(\"r\", \"rmd\"). Supported values (standardization) : \"r\", \"rprofile\", \"rmd\", \"rmarkdown\", \"rnw\", \"qmd\". Rmarkdown treated Rmd. exclude_dirs Character vector directories exclude (recursively). exclude_files Character vector paths files excluded styling. ... Arguments passed styler::style_dir style function creates style guide use, default tidyverse_style. used except construct argument transformers. See style_guides() details. transformers set transformer functions. argument conveniently constructed via style argument .... See 'Examples'. recursive logical value indicating whether files sub directories path styled well. include_roxygen_examples Whether style code roxygen examples. base_indention Integer scalar indicating many spaces whole output text indented. Note splitting line add base_indention spaces code case multi-line strings present. See 'Examples'. dry indicate whether styler run dry mode, .e. refrain writing back files .\"\" \"fail\" write back, latter returns error input code identical result styling. \"\", default, writes back input output styling identical.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/style_all.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Style all files — style_all","text":"","code":"if (FALSE) { style_all() style_all(\"analysis\", filetype = \"Rmd\") }"},{"path":"https://jabenninghoff.github.io/rdev/reference/to_document.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert R Notebook to html_document — to_document","title":"Convert R Notebook to html_document — to_document","text":"Copies file using fs::file_copy() changes output type yaml front matter html_notebook html_document, removing output 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(https://jabenninghoff.github.io/rdev/)","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-011","dir":"Changelog","previous_headings":"","what":"rdev 0.1.1","title":"rdev 0.1.1","text":"maintenance release","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"updates-0-1-1","dir":"Changelog","previous_headings":"","what":"Updates","title":"rdev 0.1.1","text":"ci(): updated match preferred GitHub workflow: use_github_action_check_standard() ---cran removed documentation updates functions (style, links)","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-010","dir":"Changelog","previous_headings":"","what":"rdev 0.1.0","title":"rdev 0.1.0","text":"Initial GitHub release","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"new-features-0-1-0","dir":"Changelog","previous_headings":"","what":"New Features","title":"rdev 0.1.0","text":"./tools/setup-r: shell script install development packages site repository macOS + Homebrew check_renv(): convenience function runs renv status(), clean(), optionally update() (default). style_all(): style .R .Rmd files project using styler lint_all(): lint .R .Rmd files project using lintr sort_file(): sort file using R sort(), similar unix sort command sort_rbuildignore(): sort .Rbuildignore file using sort_file(), unsorted annoying ci(): run continuous integration tests locally: lint, R CMD check, style (default).","code":""}]