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CONTRIBUTING.html
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<li>
<a href="index.html">Home</a>
</li>
<li>
<a href="00-before-we-start.html">Before we start</a>
</li>
<li>
<a href="01-intro-to-R.html">Intro to R</a>
</li>
<li>
<a href="02-starting-with-data.html">Starting with data</a>
</li>
<li>
<a href="03-data-frames.html">Data frames</a>
</li>
<li>
<a href="04-dplyr.html">The dplyr package</a>
</li>
<li>
<a href="05-data-visualization.html">Data visualization</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
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<a href="https://github.com/data-lessons/R-genomics">
<span class="fa fa-github fa-lg"></span>
</a>
</li>
</ul>
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<div id="contributing" class="section level1">
<h1>Contributing</h1>
<p><a href="http://datacarpentry.org">Data Carpentry</a> in an open source project, and we welcome contributions of all kinds: new lessons, fixes to existing material, bug reports, and reviews of proposed changes are all welcome.</p>
<div id="contributor-agreement" class="section level2">
<h2>Contributor Agreement</h2>
<p>By contributing, you agree that we may redistribute your work under <a href="http://www.datacarpentry.org/R-genomics/LICENSE.html">our license</a>. In exchange, we will address your issues and/or assess your change proposal as promptly as we can, and help you become a member of our community. Everyone involved in <a href="https://software-carpentry.org">Software Carpentry</a> and <a href="http://datacarpentry.org">Data Carpentry</a> agrees to abide by our <a href="http://www.datacarpentry.org/R-genomics/CONDUCT.html">code of conduct</a>.</p>
</div>
<div id="working-with-github" class="section level2">
<h2>Working With GitHub</h2>
<p><strong>NOTE: this repository uses <code>gh-pages</code> as our default branch.</strong></p>
<ol style="list-style-type: decimal">
<li><p>Fork the <code>datacarpentry/R-genomics</code> repository on GitHub. <em>See the “Fork” button in the top-right corner of the screen on the GitHub website.</em></p></li>
<li><p>Clone that repository to your own machine. (It is also possible to make minor edits right on GitHub.) <em>At your terminal:</em></p>
<div class="sourceCode" id="cb1"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="fu">git</span> clone https://github.com/your_username/R-genomics.git R-genomics</a>
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="bu">cd</span> R-genomics</a>
<a class="sourceLine" id="cb1-3" data-line-number="3"><span class="fu">git</span> remote add upstream https://github.com/datacarpentry/R-genomics.git</a></code></pre></div></li>
<li><p>Create a branch from <code>gh-pages</code> for your changes. Give your branch a meaningful name, such as <code>fix-typos-dplyr-lesson</code> or <code>add-tutorial-on-visualization</code>. <em>At your terminal:</em></p>
<div class="sourceCode" id="cb2"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="fu">git</span> checkout -b fix-typos-dplyr-lesson</a></code></pre></div></li>
<li><p>Make your changes to the Rmd file. If you’d like to check the rendered version of your changes, you can do one of three things:</p>
<ul>
<li>if you have <code>GNU Make</code> installed on your system, type <code>make</code> at your shell terminal.</li>
<li>if you use RStudio, click on the “Knit” button in the top-right corner of your editor pane.</li>
<li>in other cases, you can type: <code>rmarkdown::render_site("01-intro-to-r.Rmd")</code> in your R terminal (make sure your working directory is at the root of the lesson) to generate the corresponding html file.</li>
</ul></li>
<li><p>Commit the Rmd file you edited (<code>git add file-you-changed.Rmd</code>, followed by <code>git commit -m "fix typos in dplyr lesson"</code>), and push your changes to your repository on GitHub (<code>git push origin fix-typos-dplyr-lesson</code>). If your change affects a lesson, <strong>please only commit and push the <code>Rmd</code> files</strong>. The rendered versions will be generated by the lesson maintainers to avoid merge conflicts.</p></li>
<li><p>Send a pull request (PR) to the <code>gh-pages</code> branch of the <code>datacarpentry/R-genomics</code> repository for this lesson at <a href="http://github.com/datacarpentry/R-genomics" class="uri">http://github.com/datacarpentry/R-genomics</a></p></li>
</ol>
<p>If it is easier for you to send edits to us some other way, please mail us at <a href="mailto:[email protected]">[email protected]</a>. Given a choice between you creating content or wrestling with Git, we’d rather have you doing the former.</p>
</div>
<div id="file-locations-and-formats" class="section level2">
<h2>File Locations and Formats</h2>
<p>Each lesson is composed of files such as <code>00-before-we-start.Rmd</code>, <code>01-intro-to-r.Rmd</code> and so on. (We use two digits followed by a topic key to ensure files appear in the right order when listed.)</p>
<p>For the R material, lessons must be written in RMarkdown (ending in <code>Rmd</code>). A Makefile converts the Rmd files into HTML that are processed by Jekyll (the tool GitHub uses to create websites) as explained in <a href="https://github.com/datacarpentry/R-genomics#readme">the README file</a>.</p>
<p><em>Important Note:</em> We use the <code>purl()</code> function from <code>knitr</code> to generate a skeleton file that contains code to be distributed to the workshop participants. This strategy is useful in particular for error-prone pieces of code (e.g., if it contains long URLs). To take full advantage, every line of code that should be included in the handout <strong>must</strong> be enclosed in an <code>R</code> code chunk with <code>purl=TRUE</code> in the chunk options. Further, to aid students’ use of the handout code, consider including explanatory comments. When writing Challenges in particular, you may need to include redundant comments and used the chunk option <code>echo=FALSE</code>. In doubt consult the <code>Rmd</code> files for examples.</p>
<p>Images (e.g., screenshots) go into the <code>img/</code> folder. Graphics generated by some R code also go into this folder and get the prefix <code>R-ecology-</code>. This latter case is handled automatically with some knitr options in the <code>setup.R</code> file.</p>
<p>Raw data go into <code>data/</code>. However, at this stage, this folder is created programmatically and only contain dataset downloaded directly from the figshare repository. In other words, it can be safely be deleted (e.g. using <code>make clean-data</code> or <code>make clean</code>.)</p>
<p>The <code>data_output/</code> folder only contains data generated/exported by R code.</p>
<p>The <code>site_libs</code> folder is generated by the <strong>rmarkdown</strong> package and holds the javascript, css, and fonts used by the website.</p>
</div>
<div id="datasets" class="section level2">
<h2>Datasets</h2>
<p>We don’t store data for lessons inside the lesson repositories. For completed lessons the data should be publicly available in a data repository appropriate to the data type. For lesson development the data may be provided in any way that is convenient including posting to a website, on <a href="http://figshare.com/">figshare</a>, a public Dropbox link, a <a href="https://gist.github.com">GitHub gist</a>, or even included in the pull request (PR). Once the PR is ready to merge the data should be placed in the <a href="https://dx.doi.org/10.6084/m9.figshare.1314459.v5">official data repository</a> and all links to the data updated.</p>
</div>
<div id="formatting-of-the-material" class="section level2">
<h2>Formatting of the material</h2>
<p>To ensure a consistent formatting of the lessons, we recommend the following guidelines:</p>
<ul>
<li>No trailing white space</li>
<li>Wrap lines at 80 characters (unless it breaks URLs)</li>
<li>Use consistent capitalization (e.g., R not r, RStudio not rstudio or Rstudio)</li>
<li>Function names are written as <code>function()</code> while variables packages are written as <code>variable</code>, and package names as <strong><code>package</code></strong>.</li>
<li>Use unclosed atx style headers (see below):</li>
</ul>
<pre><code>## Use this format for headers
And not this format
-------------------</code></pre>
</div>
<div id="faq" class="section level2">
<h2>FAQ</h2>
<ul>
<li><em>Where can I get help?</em> <br/> Mail us at <a href="mailto:[email protected]">[email protected]</a> or come chat with us on <a href="https://gitter.im/data-carpentry/Lobby">our Gitter chat</a>.</li>
</ul>
</div>
</div>
<hr/>
<p><a href="http://datacarpentry.org/">Data Carpentry</a>,
2017-2018. <a href="LICENSE.html">License</a>. <a href="CONTRIBUTING.html">Contributing</a>. <br/>
Questions? Feedback?
Please <a href="https://github.com/datacarpentry/R-genomics/issues/new">file
an issue on GitHub</a>. <br/> On
Twitter: <a href="https://twitter.com/datacarpentry">@datacarpentry</a></p>
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