From b98fc5b3cf9bee656c16cfe985a629abeb84c8e4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Florian=20Priv=C3=A9?= <florian.prive.21@gmail.com>
Date: Tue, 20 Aug 2024 14:34:08 +0200
Subject: [PATCH] minor updates to chapter 6

---
 docs/404.html           |  2 +-
 docs/packages.html      | 62 ++++++++++++++++-------------------------
 docs/reference-keys.txt |  1 +
 docs/search_index.json  |  2 +-
 packages.Rmd            | 20 ++++++-------
 5 files changed, 37 insertions(+), 50 deletions(-)

diff --git a/docs/404.html b/docs/404.html
index 633ebea..4bd9244 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -249,7 +249,7 @@
 <li class="chapter" data-level="6" data-path="packages.html"><a href="packages.html"><i class="fa fa-check"></i><b>6</b> Packages</a>
 <ul>
 <li class="chapter" data-level="6.1" data-path="packages.html"><a href="packages.html#resources"><i class="fa fa-check"></i><b>6.1</b> Resources</a></li>
-<li class="chapter" data-level="6.2" data-path="packages.html"><a href="packages.html#project-exercise"><i class="fa fa-check"></i><b>6.2</b> Project exercise</a></li>
+<li class="chapter" data-level="6.2" data-path="packages.html"><a href="packages.html#package-exercise"><i class="fa fa-check"></i><b>6.2</b> Package exercise</a></li>
 <li class="chapter" data-level="6.3" data-path="packages.html"><a href="packages.html#pkg-start"><i class="fa fa-check"></i><b>6.3</b> Quick start</a></li>
 <li class="chapter" data-level="6.4" data-path="packages.html"><a href="packages.html#pkg-basics"><i class="fa fa-check"></i><b>6.4</b> Basic stuff</a>
 <ul>
diff --git a/docs/packages.html b/docs/packages.html
index 92e7bac..133cb72 100644
--- a/docs/packages.html
+++ b/docs/packages.html
@@ -249,7 +249,7 @@
 <li class="chapter" data-level="6" data-path="packages.html"><a href="packages.html"><i class="fa fa-check"></i><b>6</b> Packages</a>
 <ul>
 <li class="chapter" data-level="6.1" data-path="packages.html"><a href="packages.html#resources"><i class="fa fa-check"></i><b>6.1</b> Resources</a></li>
-<li class="chapter" data-level="6.2" data-path="packages.html"><a href="packages.html#project-exercise"><i class="fa fa-check"></i><b>6.2</b> Project exercise</a></li>
+<li class="chapter" data-level="6.2" data-path="packages.html"><a href="packages.html#package-exercise"><i class="fa fa-check"></i><b>6.2</b> Package exercise</a></li>
 <li class="chapter" data-level="6.3" data-path="packages.html"><a href="packages.html#pkg-start"><i class="fa fa-check"></i><b>6.3</b> Quick start</a></li>
 <li class="chapter" data-level="6.4" data-path="packages.html"><a href="packages.html#pkg-basics"><i class="fa fa-check"></i><b>6.4</b> Basic stuff</a>
 <ul>
@@ -324,16 +324,16 @@ <h2><span class="header-section-number">6.1</span> Resources<a href="packages.ht
 <li><p><a href="https://github.com/jtleek/simplystats_posts_sisbid/blob/master/posts/2015-11-06-how-i-decide-when-to-trust-an-r-package.md">How to decide when to trust an R package?</a></p></li>
 </ul>
 </div>
-<div id="project-exercise" class="section level2 hasAnchor" number="6.2">
-<h2><span class="header-section-number">6.2</span> Project exercise<a href="packages.html#project-exercise" class="anchor-section" aria-label="Anchor link to header"></a></h2>
+<div id="package-exercise" class="section level2 hasAnchor" number="6.2">
+<h2><span class="header-section-number">6.2</span> Package exercise<a href="packages.html#package-exercise" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>Just to experiment with making an R package, we’ll try to make a small package that implements some of the features of package {dplyr} that we learned in chapter <a href="tidyverse.html#tidyverse">4</a>. We can call this package {minidplyr}.</p>
 <ol style="list-style-type: decimal">
-<li><p>After having read the following two sections (<a href="packages.html#pkg-start">6.3</a> and <a href="packages.html#pkg-basics">6.4</a>), create a first function that helps you <code>select</code> variables of a data frame by using a character vector of variable names or an integer vector of variable positions. Which accessor could you use? Document this function and use it. Bonus (for later): can you use base R function <code>subset</code> to use variables names without quoting them?</p></li>
-<li><p>Check your package with <code>Ctrl/Cmd + Shift + E</code> and fix all problems. At this point, there should be no ERROR or WARNING, unless you did not document the previous function properly. However, you should still update the <em>DESCRIPTION</em> file with proper information. Do it, fix any problem, and run checks again. You could submit this package to CRAN in its present form; congratulations on your new R package!</p></li>
+<li><p>After having read the following two sections (<a href="packages.html#pkg-start">6.3</a> and <a href="packages.html#pkg-basics">6.4</a>), create a first function that helps you <code>select</code> variables of a data frame by using a character vector of variable names or an integer vector of variable positions. Which accessor could you use? Document this function and use it.</p></li>
+<li><p>Check your package with <code>Ctrl/Cmd + Shift + E</code> and fix all problems. At this point, there should be no ERROR or WARNING, unless you did not document the previous function properly. However, you should still update the <em>DESCRIPTION</em> file with proper information. Do it, fix any problem, and run checks again. You could almost submit this package to CRAN in its current form; congratulations on your new R package!</p></li>
 <li><p>Commit everything and push to GitHub. Try to install the package from someone else using <code>remotes::install_github("&lt;github-username&gt;/minidplyr")</code>.</p></li>
 <li><p>Learn how to make unit tests in section <a href="packages.html#pkg-tests">6.5.1</a> and do that for your new function <code>select2</code>. Which silly cases you should test? Here, you can use <code>usethis::use_package("dplyr", type = "Suggests")</code> to add package {dplyr} to the suggested packages (because you will use this package in tests only). You can see <a href="https://github.com/privefl/minidplyr/blob/master/tests/testthat/test-select.R">the unit tests I came up with for this function</a>.</p></li>
 <li><p>Make a function <code>filter2</code> that enables to filter rows of a data frame. Add some documentation and tests for this function as well.</p></li>
-<li><p>Learn about continuous checking of your package in section <a href="packages.html#pkg-ci">6.5.2</a>. Follow the instructions, commit and push your changes. Go check your new badges on GitHub!</p></li>
+<li><p>Learn about continuous checking of your package in section <a href="packages.html#pkg-ci">6.5.2</a>. Follow the instructions to set it up. Check your package locally, then commit and push your changes. Go check your new badges on GitHub!</p></li>
 <li><p>Learn how to make a website out of your package in section <a href="packages.html#pkgdown">6.5.3</a> and build one for this package (or another of your packages).</p></li>
 <li><p>Implement more functions if you find this project interesting. For example, make a function <code>mutate2</code> with the help of base R function <code>transform</code> (or <code>within</code>). Try to make the previous functions more general by taking many arguments at once (in <code>...</code>). <strong>Make sure to keep your existing code as internal functions in order to break your code in manageable parts.</strong></p></li>
 </ol>
@@ -345,11 +345,11 @@ <h2><span class="header-section-number">6.3</span> Quick start<a href="packages.
 <ol style="list-style-type: decimal">
 <li><p>Create a new RStudio project (not a package). Here, I advise you to create a new project on GitHub (with a README) and then clone it as an RStudio project. It is a good practice to put all your (public) stuff on GitHub (as we learned in section <a href="good-practices.html#git">2.3</a>).</p></li>
 <li><p>Run the following lines of R code.</p>
-<div class="sourceCode" id="cb453"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb453-1"><a href="packages.html#cb453-1" tabindex="-1"></a>usethis<span class="sc">::</span><span class="fu">use_description</span>(<span class="fu">list</span>(<span class="at">License =</span> <span class="st">&quot;GPL-3&quot;</span>))</span>
-<span id="cb453-2"><a href="packages.html#cb453-2" tabindex="-1"></a>usethis<span class="sc">::</span><span class="fu">use_namespace</span>()</span>
-<span id="cb453-3"><a href="packages.html#cb453-3" tabindex="-1"></a><span class="fu">dir.create</span>(<span class="st">&quot;R&quot;</span>)</span>
-<span id="cb453-4"><a href="packages.html#cb453-4" tabindex="-1"></a>usethis<span class="sc">::</span><span class="fu">use_package_doc</span>()</span>
-<span id="cb453-5"><a href="packages.html#cb453-5" tabindex="-1"></a>usethis<span class="sc">::</span><span class="fu">use_roxygen_md</span>()</span></code></pre></div></li>
+<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="packages.html#cb1-1" tabindex="-1"></a>usethis<span class="sc">::</span><span class="fu">use_description</span>(<span class="fu">list</span>(<span class="at">License =</span> <span class="st">&quot;GPL-3&quot;</span>))</span>
+<span id="cb1-2"><a href="packages.html#cb1-2" tabindex="-1"></a>usethis<span class="sc">::</span><span class="fu">use_namespace</span>()</span>
+<span id="cb1-3"><a href="packages.html#cb1-3" tabindex="-1"></a><span class="fu">dir.create</span>(<span class="st">&quot;R&quot;</span>)</span>
+<span id="cb1-4"><a href="packages.html#cb1-4" tabindex="-1"></a>usethis<span class="sc">::</span><span class="fu">use_package_doc</span>()</span>
+<span id="cb1-5"><a href="packages.html#cb1-5" tabindex="-1"></a>usethis<span class="sc">::</span><span class="fu">use_roxygen_md</span>()</span></code></pre></div></li>
 <li><p><strong>Restart RStudio</strong> and change the following options. You should see a new “Build” panel next to the “Git” panel.</p>
 <p><img src="https://privefl.github.io/R-presentation/build-doc.png" width="60%" style="display: block; margin: auto;" /></p></li>
 <li><p>Then use <code>Ctrl/Cmd + Shift + B</code> to build and reload your package.</p></li>
@@ -369,8 +369,8 @@ <h3><span class="header-section-number">6.4.2</span> R code<a href="packages.htm
 <li><p>Never explicitly load a package with <code>library()</code> or <code>require()</code>. Use <code>usethis::use_package()</code> to add one package to your <em>DESCRIPTION</em> file. Then, refer to some function with <code>&lt;package&gt;::&lt;function&gt;()</code> in your code, or by using the <code>@import &lt;package&gt;</code> or <code>@importFrom &lt;package&gt; &lt;function&gt;</code> roxygen tags.</p></li>
 <li><p>If one R function need another function in another R file, use the <code>@import &lt;basename&gt;.R</code> to make sure it is built and documented before; it is for example useful if you define new generics and methods in different files.</p></li>
 <li><p>If you modify global <code>options()</code> or graphics <code>par()</code> in a function of your package (try to avoid it), save the old values and reset when you are done:</p>
-<div class="sourceCode" id="cb454"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb454-1"><a href="packages.html#cb454-1" tabindex="-1"></a>old <span class="ot">&lt;-</span> <span class="fu">options</span>(<span class="at">stringsAsFactors =</span> <span class="cn">FALSE</span>)</span>
-<span id="cb454-2"><a href="packages.html#cb454-2" tabindex="-1"></a><span class="fu">on.exit</span>(<span class="fu">options</span>(old), <span class="at">add =</span> <span class="cn">TRUE</span>)</span></code></pre></div></li>
+<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="packages.html#cb2-1" tabindex="-1"></a>old <span class="ot">&lt;-</span> <span class="fu">options</span>(<span class="at">stringsAsFactors =</span> <span class="cn">FALSE</span>)</span>
+<span id="cb2-2"><a href="packages.html#cb2-2" tabindex="-1"></a><span class="fu">on.exit</span>(<span class="fu">options</span>(old), <span class="at">add =</span> <span class="cn">TRUE</span>)</span></code></pre></div></li>
 </ul>
 </div>
 <div id="documentation" class="section level3 hasAnchor" number="6.4.3">
@@ -379,9 +379,9 @@ <h3><span class="header-section-number">6.4.3</span> Documentation<a href="packa
 <p>Forget about the <code>man/</code> (manual) directory, files in this directory will be automatically generated thanks to the roxygen comments you use on top of your R functions.</p>
 <p>Learn more with <a href="http://r-pkgs.had.co.nz/man.html">this chapter</a>. Note that you can now use the Markdown syntax in the documentation. For example, instead of having to use <code>\code{foo}</code>, you can directly use <code>`foo`</code> in the roxygen comments.</p>
 <p>To use (and export) functions already implemented in other packages, for example the pipe from package {magrittr}, you can use <code>usethis::use_package("magrittr")</code> and put the following code somewhere in an R file of your package.</p>
-<div class="sourceCode" id="cb455"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb455-1"><a href="packages.html#cb455-1" tabindex="-1"></a><span class="co">#&#39; @importFrom magrittr %&gt;%</span></span>
-<span id="cb455-2"><a href="packages.html#cb455-2" tabindex="-1"></a><span class="co">#&#39; @export</span></span>
-<span id="cb455-3"><a href="packages.html#cb455-3" tabindex="-1"></a>magrittr<span class="sc">::</span><span class="st">`</span><span class="at">%&gt;%</span><span class="st">`</span></span></code></pre></div>
+<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="packages.html#cb3-1" tabindex="-1"></a><span class="co">#&#39; @importFrom magrittr %&gt;%</span></span>
+<span id="cb3-2"><a href="packages.html#cb3-2" tabindex="-1"></a><span class="co">#&#39; @export</span></span>
+<span id="cb3-3"><a href="packages.html#cb3-3" tabindex="-1"></a>magrittr<span class="sc">::</span><span class="st">`</span><span class="at">%&gt;%</span><span class="st">`</span></span></code></pre></div>
 <p>Fun: <a href="http://colinfay.me/dancing-banana-r-package-doc/">[How to] Include a dancing banana in your R package documentation</a>.</p>
 </div>
 <div id="namespace-file" class="section level3 hasAnchor" number="6.4.4">
@@ -402,9 +402,9 @@ <h3><span class="header-section-number">6.5.1</span> Testing<a href="packages.ht
 <h3><span class="header-section-number">6.5.2</span> Continuous checking<a href="packages.html#pkg-ci" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <p>I would rarely trust a package that doesn’t use these continuous integration services.
 It’s good practice to check your package regularly and on different Operating Systems (OS). Learn more about the different checks <a href="http://r-pkgs.had.co.nz/check.html">there</a>.</p>
-<p>An easy way to regularly check your package on GitHub is to use <a href="https://github.com/features/actions">GitHub Actions</a>. Indeed, each time you push to your GitHub repository, checks are run on different OS. To use this service, you can run <code>usethis::use_github_action_check_standard()</code>.</p>
+<p>An easy way to regularly check your package on GitHub is to use <a href="https://github.com/features/actions">GitHub Actions</a>. Indeed, each time you push to your GitHub repository, checks are run on different OS. To use this service, you can run <code>usethis::use_github_action("check-standard")</code>.</p>
 <p>To get the coverage of your tests, use <a href="https://codecov.io/">Codecov</a> by running <code>usethis::use_coverage()</code> and <code>usethis::use_github_action("test-coverage")</code>.</p>
-<p>Finally, to prevent typos in your package and especially for non-native English speakers, it can be useful to check the spelling in your package. If you think that the word “programmation” exists and that “prefered” has only one ‘r’ at the end (I did!), you should definitely use package {spelling}. Just run <code>spelling::spell_check_setup()</code>; this will check spelling in your package at the end of checks. If it reports words you want to ignore, just put these words in a text file <code>inst/WORDLIST</code> (with one word by line).</p>
+<p>Finally, to prevent typos in your package and especially for non-native English speakers, it can be useful to check the spelling in your package. If you think that the word “programmation” exists and that “prefered” has only one ‘r’ at the end (I did!), you should definitely use package {spelling}. Just run <code>spelling::spell_check_setup()</code>; this will check spelling in your package at the end of checks. If it reports words you want to ignore, just put these words in a text file <code>inst/WORDLIST</code> (with one word per line).</p>
 </div>
 <div id="pkgdown" class="section level3 hasAnchor" number="6.5.3">
 <h3><span class="header-section-number">6.5.3</span> Pkgdown<a href="packages.html#pkgdown" class="anchor-section" aria-label="Anchor link to header"></a></h3>
@@ -413,7 +413,7 @@ <h3><span class="header-section-number">6.5.3</span> Pkgdown<a href="packages.ht
 <li><p>Run <code>pkgdown:::build_site()</code>.</p></li>
 <li><p>On GitHub, go to the settings of your repo, and enable GitHub Pages from the <code>/docs</code> folder.
 <img src="images/github-pages.jpg" width="70%" style="display: block; margin: auto;" /></p></li>
-<li><p>Push the new files. This will render everything that you have in this folder as a website (after 0-2 minutes).</p></li>
+<li><p>Push the new files. This will render everything that you have in this folder as a website (after 0-2 minutes). You will find your package’s website at <code>https://&lt;github-username&gt;.github.io/minidplyr/</code>.</p></li>
 </ol>
 <p>To get more information and especially to configure the website, see <a href="http://pkgdown.r-lib.org/articles/pkgdown.html">the documentation</a>, as a {pkgdown} website, of course.
 For an example, see <a href="https://privefl.github.io/bigstatsr/">the website of my package {bigstatsr}</a> and <a href="https://github.com/privefl/bigstatsr/blob/master/_pkgdown.yml">the corresponding YAML file</a>.</p>
@@ -424,19 +424,19 @@ <h3><span class="header-section-number">6.5.3</span> Pkgdown<a href="packages.ht
 <h2><span class="header-section-number">6.6</span> More<a href="packages.html#more" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <div id="rcpp" class="section level3 hasAnchor" number="6.6.1">
 <h3><span class="header-section-number">6.6.1</span> Rcpp<a href="packages.html#rcpp" class="anchor-section" aria-label="Anchor link to header"></a></h3>
-<p>We learned about Rcpp in section <a href="performance.html#Rcpp">5.4</a>. To use Rcpp code in your package, just use <code>usethis::use_rcpp()</code> and put the 2 roxygen tags e.g. in the file <code>R/&lt;package&gt;-package.R</code>. Then, create .cpp files with RStudio and save them the <code>src/</code> directory.</p>
+<p>We learned about Rcpp in section <a href="performance.html#Rcpp">5.4</a>. To use Rcpp code in your package, just run <code>usethis::use_rcpp()</code>. Then, create .cpp files with RStudio and save them the <code>src/</code> directory.</p>
 <p>Note that the <code>// [[Rcpp::export]]</code> makes the C++ function available to R, it doesn’t export the function as part of your package (though you could access it with <code>&lt;package&gt;:::&lt;rcpp-fun&gt;()</code>). If you want your package to explicitly provides an Rcpp function (as an R function), you also need roxygen comments (beginning with <code>//'</code> instead of <code>#'</code>, including <code>//' @export</code>) on top of your Rcpp function.</p>
 <p>If you need some C++ code from another package (e.g. from package {RcppArmadillo}), normally you would use</p>
-<div class="sourceCode" id="cb456"><pre class="sourceCode cpp"><code class="sourceCode cpp"><span id="cb456-1"><a href="packages.html#cb456-1" tabindex="-1"></a><span class="co">// [[Rcpp::depends(RcppArmadillo)]]</span></span>
-<span id="cb456-2"><a href="packages.html#cb456-2" tabindex="-1"></a><span class="pp">#include </span><span class="im">&lt;RcppArmadillo.h&gt;</span></span></code></pre></div>
-<p>In an R package, you don’t need the first line but instead you need to add the package to the <code>LinkingTo</code> field of the <em>DESCRIPTION</em> file (e.g. with <code>usethis::use_package("RcppArmadillo", "LinkingTo")</code>).</p>
+<div class="sourceCode" id="cb4"><pre class="sourceCode cpp"><code class="sourceCode cpp"><span id="cb4-1"><a href="packages.html#cb4-1" tabindex="-1"></a><span class="co">// [[Rcpp::depends(RcppArmadillo)]]</span></span>
+<span id="cb4-2"><a href="packages.html#cb4-2" tabindex="-1"></a><span class="pp">#include </span><span class="im">&lt;RcppArmadillo.h&gt;</span></span></code></pre></div>
+<p>In an R package, you don’t need the first line <code>// [[Rcpp::depends(RcppArmadillo)]]</code>, but instead you need to add the package to the <code>LinkingTo</code> field of the <em>DESCRIPTION</em> file (e.g. with <code>usethis::use_package("RcppArmadillo", "LinkingTo")</code>).</p>
 </div>
 <div id="ignore-files" class="section level3 hasAnchor" number="6.6.2">
 <h3><span class="header-section-number">6.6.2</span> Ignore files<a href="packages.html#ignore-files" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <p>There are two types of ignore:</p>
 <ul>
 <li><p>Files ignored by Git, specified in the <em>.gitignore</em> file. For example, you don’t want to track changes for some large data files or some binaries often changing. You can ignore files by using <code>usethis::use_git_ignore()</code>.</p></li>
-<li><p>Files ignored during the build of your package, specified in the <em>.Rbuildignore</em> file. For example, in my packages, I generally have two directories called <code>tmp-tests</code> and <code>tmp-save</code> where I just put some random code that I used once during development. Checks will tell you if your package contains non-standard files or directories. Moreover, I generally ignore vignettes; they are still built as part of the {pkgdown} website.
+<li><p>Files ignored during the build of your package, specified in the <em>.Rbuildignore</em> file. For example, in my packages, I generally have directories called <code>tmp-tests</code> and <code>tmp-data</code> where I put code and data that I used during development, but that should not be part of the final package. Checks will tell you if your package contains non-standard files or directories. Moreover, I generally ignore vignettes; they are still built as part of the {pkgdown} website.
 There is also a {usethis} function for this: <code>usethis::use_build_ignore()</code>.</p></li>
 </ul>
 </div>
@@ -521,20 +521,6 @@ <h2><span class="header-section-number">6.7</span> Release on CRAN<a href="packa
 });
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diff --git a/docs/reference-keys.txt b/docs/reference-keys.txt
index d24fbb8..c2bb51b 100644
--- a/docs/reference-keys.txt
+++ b/docs/reference-keys.txt
@@ -94,3 +94,4 @@ visualize-the-data
 compilation-of-tweets
 example-1
 presentation
+package-exercise
diff --git a/docs/search_index.json b/docs/search_index.json
index 5b550bc..7f56d5e 100644
--- a/docs/search_index.json
+++ b/docs/search_index.json
@@ -1 +1 @@
-[["project.html", "Chapter 8 Project 8.1 What is Tidy Tuesday? 8.2 Tidy Thursday", " Chapter 8 Project Either have some idea about new functions you want to create and share, and make it as a new R package, explore, visualize, and analyze some data (cf. hereinafter). 8.1 What is Tidy Tuesday? A weekly data project from the R4DS community. The aim is to understand how to summarize and arrange data to make meaningful charts with ggplot2, tidyr, dplyr, and other tools in the tidyverse ecosystem. Safe and supportive space for individuals to practice their wrangling and data visualization skills independent of drawing conclusions. How it works: The dataset comes from a source article and it is made available on Mondays. People then play with the data set using the tidyverse, explore things that they think are interesting, and/or try to recreate the source article plots/results. And share their own version on Twitter (with the hashtag #TidyTuesday). 8.2 Tidy Thursday Our own mini-version of Tidy Tuesday! Join in teams of 2 (or 3). Choose a dataset from the ones provided. Come up with an interesting topic to visualize (or recreate an existing one). Apply things you have learned in this course, and try to learn new things with our help and Google’s help. Share the resulting plot(s) and the code with the rest on Friday with a short presentation talking about challenges and conclusions from the plot. 8.2.1 Choose a dataset Install the {tidytuesdayR} package: install.packages(&quot;tidytuesdayR&quot;) Some interesting datasets: Olympic medals data &lt;- tidytuesdayR::tt_load(&#39;2021-07-27&#39;)[[&quot;olympics&quot;]] Netflix titles data &lt;- tidytuesdayR::tt_load(&#39;2021-04-20&#39;)[[&quot;netflix_titles&quot;]] Spotify songs data &lt;- tidytuesdayR::tt_load(&#39;2020-01-21&#39;)[[&quot;spotify_songs&quot;]] If you do not like any of these, you can also choose from all the previous tidy Tuesday datasets here. 8.2.2 Visualize the data Come up with a question, or an interesting thing to learn from the data. You can get inspired by looking at other participants on Twitter: Shiny app with a compilation of tweets ordered by likes TidyTuesdayRocks Search for #TidyTuesday + dataset_name on Twitter. Remember that the code is always available at the author’s github page. 8.2.3 Compilation of tweets 8.2.4 Example Someone tried the recreate a plot using the Netflix dataset: In today&#39;s #TidyTuesday I looked at Netflix movies, specifically checking out movie duration over time. #Rstats https://t.co/PeVIhpAsSy pic.twitter.com/2TOZ9nFKQP&mdash; Marieke (@marieke_k_jones) April 20, 2021 Clara’s (quick) version: library(tidyverse) netflix_titles &lt;- tidytuesdayR::tt_load(&#39;2021-04-20&#39;)[[&quot;netflix_titles&quot;]] ## ## Downloading file 1 of 1: `netflix_titles.csv` netflix_titles %&gt;% filter(type == &quot;Movie&quot;) %&gt;% mutate(duration = as.numeric(str_extract(duration, &quot;(\\\\d)+&quot;)), cat = map_chr(listed_in, ~str_split(.x, &quot;, &quot;)[[1]][1]), cat = case_when( cat %in% c(&quot;Horror Movies&quot;, &quot;Thrillers&quot;) ~ &quot;Horror Movies &amp; Thrillers&quot;, TRUE ~ cat)) %&gt;% group_by(release_year, cat) %&gt;% summarise(mean_duration = mean(duration)) %&gt;% filter(cat %in% c(&quot;Action &amp; Adventure&quot;, &quot;Children &amp; Family Movies&quot;, &quot;Comedies&quot;, &quot;Documentaries&quot;, &quot;Dramas&quot;, &quot;Horror Movies &amp; Thrillers&quot;)) %&gt;% ggplot(aes(x = release_year, y = mean_duration, color = cat)) + geom_line() + scale_x_continuous(limits = c(1980, 2020)) + scale_y_continuous(limits = c(50, 160), breaks = seq(50,150, 25)) + facet_wrap(~cat) + theme_minimal() + theme(text = element_text(size = 14), legend.position = &quot;none&quot;, axis.title.x = element_blank()) + labs(title = &quot;Children&#39;s movies and Dramas decrease in duration over time&quot;, y = &quot;Average movie duration (min)&quot;) 8.2.5 Presentation Make a short (5-10 min) presentation; you can simply make an HTML from RMarkdown, push to GitHub and we can preview it on http://htmlpreview.github.io/. What you can present: Introduce the data set and the variables you have chosen to visualize. Show the resulting plot and discuss the trends/patterns in the data. If you chose to recreate a visualization from Twitter, comment on the quality of the plot or potential problems. Show the generative code and comment on the steps and transformations you have applied to the data. Did you find a set of tidyverse functions particularly useful? Did you discover another useful package? Some examples from students in 2022-2023: alcohol consumption lego sets F1 winners baby names UFO sightings tornados wealth inequalities in the USA Eurovision horror movies a package for clinical data a package to read BAM files "],["404.html", "Page not found", " Page not found The page you requested cannot be found (perhaps it was moved or renamed). You may want to try searching to find the page's new location, or use the table of contents to find the page you are looking for. "]]
+[["packages.html", "Chapter 6 Packages 6.1 Resources 6.2 Package exercise 6.3 Quick start 6.4 Basic stuff 6.5 Good practices 6.6 More 6.7 Release on CRAN", " Chapter 6 Packages 6.1 Resources R Packages book (read it!) Writing R extensions, the official CRAN guide (easier to read as a bookdown) Look at popular R packages on GitHub Customizing Package Build Options Mastering Software Development in R How to develop good R packages (for open science) How to decide when to trust an R package? 6.2 Package exercise Just to experiment with making an R package, we’ll try to make a small package that implements some of the features of package {dplyr} that we learned in chapter 4. We can call this package {minidplyr}. After having read the following two sections (6.3 and 6.4), create a first function that helps you select variables of a data frame by using a character vector of variable names or an integer vector of variable positions. Which accessor could you use? Document this function and use it. Check your package with Ctrl/Cmd + Shift + E and fix all problems. At this point, there should be no ERROR or WARNING, unless you did not document the previous function properly. However, you should still update the DESCRIPTION file with proper information. Do it, fix any problem, and run checks again. You could almost submit this package to CRAN in its current form; congratulations on your new R package! Commit everything and push to GitHub. Try to install the package from someone else using remotes::install_github(\"&lt;github-username&gt;/minidplyr\"). Learn how to make unit tests in section 6.5.1 and do that for your new function select2. Which silly cases you should test? Here, you can use usethis::use_package(\"dplyr\", type = \"Suggests\") to add package {dplyr} to the suggested packages (because you will use this package in tests only). You can see the unit tests I came up with for this function. Make a function filter2 that enables to filter rows of a data frame. Add some documentation and tests for this function as well. Learn about continuous checking of your package in section 6.5.2. Follow the instructions to set it up. Check your package locally, then commit and push your changes. Go check your new badges on GitHub! Learn how to make a website out of your package in section 6.5.3 and build one for this package (or another of your packages). Implement more functions if you find this project interesting. For example, make a function mutate2 with the help of base R function transform (or within). Try to make the previous functions more general by taking many arguments at once (in ...). Make sure to keep your existing code as internal functions in order to break your code in manageable parts. 6.3 Quick start In my first package, I just put some functions I used again and again in my work. To quickly start your package, just follow these steps: Create a new RStudio project (not a package). Here, I advise you to create a new project on GitHub (with a README) and then clone it as an RStudio project. It is a good practice to put all your (public) stuff on GitHub (as we learned in section 2.3). Run the following lines of R code. usethis::use_description(list(License = &quot;GPL-3&quot;)) usethis::use_namespace() dir.create(&quot;R&quot;) usethis::use_package_doc() usethis::use_roxygen_md() Restart RStudio and change the following options. You should see a new “Build” panel next to the “Git” panel. Then use Ctrl/Cmd + Shift + B to build and reload your package. Create a simple function and put it in an .R file in the R/ directory. Inside the function, use Code -&gt; Insert Roxygen Skeleton. Build and reload your package and check the documentation of your new function and that you can use it. 6.4 Basic stuff 6.4.1 DESCRIPTION file See this chapter on the DESCRIPTION file. 6.4.2 R code Put your R code in the R/ directory. Basically it would be mostly functions. Don’t use random lines of code like in R scripts. Never explicitly load a package with library() or require(). Use usethis::use_package() to add one package to your DESCRIPTION file. Then, refer to some function with &lt;package&gt;::&lt;function&gt;() in your code, or by using the @import &lt;package&gt; or @importFrom &lt;package&gt; &lt;function&gt; roxygen tags. If one R function need another function in another R file, use the @import &lt;basename&gt;.R to make sure it is built and documented before; it is for example useful if you define new generics and methods in different files. If you modify global options() or graphics par() in a function of your package (try to avoid it), save the old values and reset when you are done: old &lt;- options(stringsAsFactors = FALSE) on.exit(options(old), add = TRUE) 6.4.3 Documentation Documentation is super useful for other people (including future-you, in 6 months when you won’t remember what you implemented in your package). Make sure to document your code as soon as you write it, otherwise you will never do it. Forget about the man/ (manual) directory, files in this directory will be automatically generated thanks to the roxygen comments you use on top of your R functions. Learn more with this chapter. Note that you can now use the Markdown syntax in the documentation. For example, instead of having to use \\code{foo}, you can directly use `foo` in the roxygen comments. To use (and export) functions already implemented in other packages, for example the pipe from package {magrittr}, you can use usethis::use_package(\"magrittr\") and put the following code somewhere in an R file of your package. #&#39; @importFrom magrittr %&gt;% #&#39; @export magrittr::`%&gt;%` Fun: [How to] Include a dancing banana in your R package documentation. 6.4.4 NAMESPACE file You can also forget about this for now because it should be automatically generated by {roxygen}. If you want to understand what’s going on, read this chapter. 6.5 Good practices 6.5.1 Testing You are probably already testing your code, you’re only doing it informally. The problem with this approach is that when you come back to this code in 3 months time to add a new feature, you’ve probably forgotten some of the informal tests you ran the first time around. This makes it very easy to break existing code that used to work (which you should avoid as much as you can). A very good practice is to use unit tests. Read this chapter. To make your first unit tests, use usethis::use_test() while having open the R file you want to test. Write some unit tests, then you can run tests of your package with Ctrl/Cmd + Shift + T. 6.5.2 Continuous checking I would rarely trust a package that doesn’t use these continuous integration services. It’s good practice to check your package regularly and on different Operating Systems (OS). Learn more about the different checks there. An easy way to regularly check your package on GitHub is to use GitHub Actions. Indeed, each time you push to your GitHub repository, checks are run on different OS. To use this service, you can run usethis::use_github_action(\"check-standard\"). To get the coverage of your tests, use Codecov by running usethis::use_coverage() and usethis::use_github_action(\"test-coverage\"). Finally, to prevent typos in your package and especially for non-native English speakers, it can be useful to check the spelling in your package. If you think that the word “programmation” exists and that “prefered” has only one ‘r’ at the end (I did!), you should definitely use package {spelling}. Just run spelling::spell_check_setup(); this will check spelling in your package at the end of checks. If it reports words you want to ignore, just put these words in a text file inst/WORDLIST (with one word per line). 6.5.3 Pkgdown Run usethis::use_pkgdown(). If added, remove docs from the .gitignore file. Run pkgdown:::build_site(). On GitHub, go to the settings of your repo, and enable GitHub Pages from the /docs folder. Push the new files. This will render everything that you have in this folder as a website (after 0-2 minutes). You will find your package’s website at https://&lt;github-username&gt;.github.io/minidplyr/. To get more information and especially to configure the website, see the documentation, as a {pkgdown} website, of course. For an example, see the website of my package {bigstatsr} and the corresponding YAML file. If you want to make a personal website, check this quick tutorial. 6.6 More 6.6.1 Rcpp We learned about Rcpp in section 5.4. To use Rcpp code in your package, just run usethis::use_rcpp(). Then, create .cpp files with RStudio and save them the src/ directory. Note that the // [[Rcpp::export]] makes the C++ function available to R, it doesn’t export the function as part of your package (though you could access it with &lt;package&gt;:::&lt;rcpp-fun&gt;()). If you want your package to explicitly provides an Rcpp function (as an R function), you also need roxygen comments (beginning with //' instead of #', including //' @export) on top of your Rcpp function. If you need some C++ code from another package (e.g. from package {RcppArmadillo}), normally you would use // [[Rcpp::depends(RcppArmadillo)]] #include &lt;RcppArmadillo.h&gt; In an R package, you don’t need the first line // [[Rcpp::depends(RcppArmadillo)]], but instead you need to add the package to the LinkingTo field of the DESCRIPTION file (e.g. with usethis::use_package(\"RcppArmadillo\", \"LinkingTo\")). 6.6.2 Ignore files There are two types of ignore: Files ignored by Git, specified in the .gitignore file. For example, you don’t want to track changes for some large data files or some binaries often changing. You can ignore files by using usethis::use_git_ignore(). Files ignored during the build of your package, specified in the .Rbuildignore file. For example, in my packages, I generally have directories called tmp-tests and tmp-data where I put code and data that I used during development, but that should not be part of the final package. Checks will tell you if your package contains non-standard files or directories. Moreover, I generally ignore vignettes; they are still built as part of the {pkgdown} website. There is also a {usethis} function for this: usethis::use_build_ignore(). 6.6.3 The inst/ directory When a package is installed, everything in inst/ is copied into the top-level package directory. For example, you can have: inst/extdata/: additional external data for examples and vignettes. See section 6.6.4 for more detail. You can also use inst/testdata/ for data you need in tests. To access one file in this directory, use system.file(). For example, if you have a file inst/extdata/mydata.csv in your package, an user can find it using system.file(\"extdata\", \"mydata.csv\", package = \"&lt;package&gt;\"). inst/include: some C++ code that others can use by LinkingTo your package. For example, when you use #include &lt;Rcpp.h&gt; at the top of your Rcpp code, you’re using the code in there. inst/CITATION: how to cite the package. Learn more there. 6.6.4 External data Learn more with this book chapter. 6.7 Release on CRAN If you want your package to be on CRAN, read this chapter. "],["404.html", "Page not found", " Page not found The page you requested cannot be found (perhaps it was moved or renamed). You may want to try searching to find the page's new location, or use the table of contents to find the page you are looking for. "]]
diff --git a/packages.Rmd b/packages.Rmd
index e89c004..334157b 100644
--- a/packages.Rmd
+++ b/packages.Rmd
@@ -22,13 +22,13 @@ source("spelling-check.R")
 
 - [How to decide when to trust an R package?](https://github.com/jtleek/simplystats_posts_sisbid/blob/master/posts/2015-11-06-how-i-decide-when-to-trust-an-r-package.md)
 
-## Project exercise
+## Package exercise
 
 Just to experiment with making an R package, we'll try to make a small package that implements some of the features of package {dplyr} that we learned in chapter \@ref(tidyverse). We can call this package {minidplyr}.
 
-1. After having read the following two sections (\@ref(pkg-start) and \@ref(pkg-basics)), create a first function that helps you `select` variables of a data frame by using a character vector of variable names or an integer vector of variable positions. Which accessor could you use? Document this function and use it. Bonus (for later): can you use base R function `subset` to use variables names without quoting them?
+1. After having read the following two sections (\@ref(pkg-start) and \@ref(pkg-basics)), create a first function that helps you `select` variables of a data frame by using a character vector of variable names or an integer vector of variable positions. Which accessor could you use? Document this function and use it.
 
-1. Check your package with `Ctrl/Cmd + Shift + E` and fix all problems. At this point, there should be no ERROR or WARNING, unless you did not document the previous function properly. However, you should still update the *DESCRIPTION* file with proper information. Do it, fix any problem, and run checks again. You could submit this package to CRAN in its present form; congratulations on your new R package!
+1. Check your package with `Ctrl/Cmd + Shift + E` and fix all problems. At this point, there should be no ERROR or WARNING, unless you did not document the previous function properly. However, you should still update the *DESCRIPTION* file with proper information. Do it, fix any problem, and run checks again. You could almost submit this package to CRAN in its current form; congratulations on your new R package!
 
 1. Commit everything and push to GitHub. Try to install the package from someone else using `remotes::install_github("<github-username>/minidplyr")`.
 
@@ -36,7 +36,7 @@ Just to experiment with making an R package, we'll try to make a small package t
 
 1. Make a function `filter2` that enables to filter rows of a data frame. Add some documentation and tests for this function as well.
 
-1. Learn about continuous checking of your package in section \@ref(pkg-ci). Follow the instructions, commit and push your changes. Go check your new badges on GitHub!
+1. Learn about continuous checking of your package in section \@ref(pkg-ci). Follow the instructions to set it up. Check your package locally, then commit and push your changes. Go check your new badges on GitHub!
 
 1. Learn how to make a website out of your package in section \@ref(pkgdown) and build one for this package (or another of your packages).
 
@@ -133,11 +133,11 @@ To make your first unit tests, use `usethis::use_test()` while having open the R
 I would rarely trust a package that doesn't use these continuous integration services.
 It's good practice to check your package regularly and on different Operating Systems (OS). Learn more about the different checks [there](http://r-pkgs.had.co.nz/check.html).
 
-An easy way to regularly check your package on GitHub is to use [GitHub Actions](https://github.com/features/actions). Indeed, each time you push to your GitHub repository, checks are run on different OS. To use this service, you can run `usethis::use_github_action_check_standard()`. 
+An easy way to regularly check your package on GitHub is to use [GitHub Actions](https://github.com/features/actions). Indeed, each time you push to your GitHub repository, checks are run on different OS. To use this service, you can run `usethis::use_github_action("check-standard")`. 
 
 To get the coverage of your tests, use [Codecov](https://codecov.io/) by running `usethis::use_coverage()` and `usethis::use_github_action("test-coverage")`.
 
-Finally, to prevent typos in your package and especially for non-native English speakers, it can be useful to check the spelling in your package. If you think that the word "programmation" exists and that "prefered" has only one 'r' at the end (I did!), you should definitely use package {spelling}. Just run `spelling::spell_check_setup()`; this will check spelling in your package at the end of checks. If it reports words you want to ignore, just put these words in a text file `inst/WORDLIST` (with one word by line).
+Finally, to prevent typos in your package and especially for non-native English speakers, it can be useful to check the spelling in your package. If you think that the word "programmation" exists and that "prefered" has only one 'r' at the end (I did!), you should definitely use package {spelling}. Just run `spelling::spell_check_setup()`; this will check spelling in your package at the end of checks. If it reports words you want to ignore, just put these words in a text file `inst/WORDLIST` (with one word per line).
 
 ### Pkgdown {#pkgdown}
 
@@ -150,7 +150,7 @@ Finally, to prevent typos in your package and especially for non-native English
 knitr::include_graphics("images/github-pages.jpg")
 ```
 
-1. Push the new files. This will render everything that you have in this folder as a website (after 0-2 minutes). 
+1. Push the new files. This will render everything that you have in this folder as a website (after 0-2 minutes). You will find your package's website at `https://<github-username>.github.io/minidplyr/`.
 
 To get more information and especially to configure the website, see [the documentation](http://pkgdown.r-lib.org/articles/pkgdown.html), as a {pkgdown} website, of course.
 For an example, see [the website of my package {bigstatsr}](https://privefl.github.io/bigstatsr/) and [the corresponding YAML file](https://github.com/privefl/bigstatsr/blob/master/_pkgdown.yml). 
@@ -162,7 +162,7 @@ If you want to make a personal website, check [this quick tutorial](https://gith
 
 ### Rcpp
 
-We learned about Rcpp in section \@ref(Rcpp). To use Rcpp code in your package, just use `usethis::use_rcpp()` and put the 2 roxygen tags e.g. in the file `R/<package>-package.R`. Then, create .cpp files with RStudio and save them the `src/` directory.
+We learned about Rcpp in section \@ref(Rcpp). To use Rcpp code in your package, just run `usethis::use_rcpp()`. Then, create .cpp files with RStudio and save them the `src/` directory.
 
 Note that the `// [[Rcpp::export]]` makes the C++ function available to R, it doesn't export the function as part of your package (though you could access it with `<package>:::<rcpp-fun>()`). If you want your package to explicitly provides an Rcpp function (as an R function), you also need roxygen comments (beginning with `//'` instead of `#'`, including `//' @export`) on top of your Rcpp function.
 
@@ -171,7 +171,7 @@ If you need some C++ code from another package (e.g. from package {RcppArmadillo
 // [[Rcpp::depends(RcppArmadillo)]]
 #include <RcppArmadillo.h>
 ```
-In an R package, you don't need the first line but instead you need to add the package to the `LinkingTo` field of the *DESCRIPTION* file (e.g. with `usethis::use_package("RcppArmadillo", "LinkingTo")`).
+In an R package, you don't need the first line `// [[Rcpp::depends(RcppArmadillo)]]`, but instead you need to add the package to the `LinkingTo` field of the *DESCRIPTION* file (e.g. with `usethis::use_package("RcppArmadillo", "LinkingTo")`).
 
 ### Ignore files
 
@@ -179,7 +179,7 @@ There are two types of ignore:
 
 - Files ignored by Git, specified in the *.gitignore* file. For example, you don't want to track changes for some large data files or some binaries often changing. You can ignore files by using `usethis::use_git_ignore()`.
 
-- Files ignored during the build of your package, specified in the *.Rbuildignore* file. For example, in my packages, I generally have two directories called `tmp-tests` and `tmp-save` where I just put some random code that I used once during development. Checks will tell you if your package contains non-standard files or directories. Moreover, I generally ignore vignettes; they are still built as part of the {pkgdown} website. 
+- Files ignored during the build of your package, specified in the *.Rbuildignore* file. For example, in my packages, I generally have directories called `tmp-tests` and `tmp-data` where I put code and data that I used during development, but that should not be part of the final package. Checks will tell you if your package contains non-standard files or directories. Moreover, I generally ignore vignettes; they are still built as part of the {pkgdown} website. 
 There is also a {usethis} function for this: `usethis::use_build_ignore()`.
 
 ### The `inst/` directory