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<section>
<h1 class="title">Write your Dynamic Documents</h1>
<h2 class="author">Sau-Chin Chen, Tobias Heycke</h2>
<h3 class="date">2019/2/7</h3>
</section>
<section id="before-we-start" class="slide level2">
<h2>Before we start</h2>
<ul>
<li class="fragment"><a href="https://www.r-project.org/">R</a></li>
<li class="fragment"><a href="https://www.rstudio.com/">Rstudio</a></li>
<li class="fragment">(Optional) <a href="https://git-scm.com/">Git</a>,<a href="https://pandoc.org/installing.html">pandoc</a>,<a href="https://www.zotero.org/download/">Zotero</a></li>
<li class="fragment">Download the <a href="https://github.com/SCgeeker/WS_dynamic_doc/archive/master.zip">example files</a></li>
</ul>
</section>
<section id="overview" class="slide level2">
<h2>Overview</h2>
<table>
<colgroup>
<col style="width: 10%" />
<col style="width: 32%" />
<col style="width: 35%" />
<col style="width: 21%" />
</colgroup>
<thead>
<tr class="header">
<th>Input<br>Format</th>
<th>Content</th>
<th>Render</th>
<th>Output<br>Format</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>.md</td>
<td>text<br>markdown tags<br>latex codes<br>citation key</td>
<td>pandoc<br>pandoc-citeproc</td>
<td>.html<br>.pdf<br>.docx</td>
</tr>
<tr class="even">
<td>.Rmd</td>
<td>code chunks<br>inline codes</td>
<td>rmarkdown</td>
<td>.html<br>.pdf<br>.docx</td>
</tr>
<tr class="odd">
<td>Templates<br>(e.g., APA)</td>
<td>footnote<br>appendix doc</td>
<td>papaja</td>
<td>.pdf</td>
</tr>
</tbody>
</table>
</section>
<section id="resource" class="slide level2">
<h2>Resource</h2>
<p><a href="https://bookdown.org/yihui/rmarkdown/">R Markdown: The Definitive Guide</a></p>
<p><a href="https://crsh.github.io/papaja_man/">papaja: Reproducible APA manuscripts with R Markdown</a></p>
</section>
<section><section id="markdown" class="title-slide slide level1"><h1>Markdown</h1></section><section id="section" class="slide level2">
<h2></h2>
<p><strong>Example Materials</strong>:<br> <code>markdown_demo.md</code><br><code>markdown_demo.bib</code><br><code>Workshop-Open-Science1.png</code></p>
</section><section id="preparation" class="slide level2">
<h2>Preparation</h2>
<ul>
<li class="fragment"><p><a href="https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet">markdown cheatsheet</a></p></li>
<li class="fragment">off-line editor
<ul>
<li class="fragment">any text editor</li>
<li class="fragment">Rstudio</li>
</ul></li>
<li class="fragment">render: <a href="http://pandoc.org/">pandoc</a>, <a href="https://pandoc.org/installing.html">installation guide</a></li>
<li class="fragment"><p>(Optional)Version Control tool: <a href="https://git-scm.com/">Git</a></p></li>
</ul>
</section><section id="tips" class="slide level2">
<h2>Tips</h2>
<ul>
<li class="fragment">Keep your text as ‘clean’ as you can.</li>
<li class="fragment">Leave typesetting to <em>markdown tags</em>, <em>Latex codes</em></li>
<li class="fragment">Organize the bibliography in <a href="http://zotero.org/">Zotero</a></li>
</ul>
</section></section>
<section><section id="rmarkdown" class="title-slide slide level1"><h1>Rmarkdown</h1></section><section id="section-1" class="slide level2">
<h2></h2>
<p><strong>Example Materials</strong>:<br> <code>Rmd_demo.md</code><br><code>Orientation Cross Languages.bib</code><br><code>Lab-summary.csv</code></p>
</section><section id="preparation-1" class="slide level2">
<h2>Preparation</h2>
<ul>
<li class="fragment"><a href="https://www.r-project.org/">R</a></li>
<li class="fragment"><a href="https://www.rstudio.com/">Rstudio</a></li>
<li class="fragment"><a href="https://cran.r-project.org/web/packages/knitr/index.html">knitr package</a></li>
<li class="fragment">bibtext file(s)</li>
<li class="fragment"><a href="https://github.com/crsh/citr">Rstudio addin: citr</a></li>
</ul>
</section><section id="setup-of-sweave" class="slide level2">
<h2>Setup of sweave</h2>
<figure>
<img data-src="https://i2.wp.com/gforge.se/wp-content/uploads/2012/06/Sweave-to-knitr-options.jpg" alt="Source: G-Force, 2012/8/6" /><figcaption>Source: G-Force, 2012/8/6</figcaption>
</figure>
</section><section id="tips-1" class="slide level2">
<h2>Tips</h2>
<ul>
<li class="fragment">in text -&gt; in table -&gt; in figure</li>
<li class="fragment">Import the analytical data at beginning.</li>
<li class="fragment">If statistical models take time, it is better to summarize them prior to organize them in chunks.</li>
<li class="fragment">If it is workable, making of tables and figures by codes is better than the external files.</li>
</ul>
</section></section>
<section><section id="papaja" class="title-slide slide level1"><h1>papaja</h1></section><section id="section-2" class="slide level2">
<h2></h2>
<p><strong>Example Materials</strong>:<br> <code>papaja_appendix_test.zip</code></p>
</section><section id="preparation-2" class="slide level2">
<h2>Preparation</h2>
<ul>
<li class="fragment">TeX distribution
<ul>
<li class="fragment"><a href="https://yihui.name/tinytex/">TinyTex</a></li>
<li class="fragment"><a href="http://miktex.org/">MikTeX</a> for Windows (<a href="(https://tobiasheycke.github.io/pages/fullmiktex)">installation guide</a> by Tobias)</li>
<li class="fragment"><a href="https://tug.org/mactex/">MacTeX</a> for Mac</li>
<li class="fragment"><a href="http://www.tug.org/texlive/">TeX Live</a> for Linux</li>
</ul></li>
<li class="fragment">papaja package
<ul>
<li class="fragment"><a href="https://crsh.github.io/papaja_man/introduction.html#installing-papaja">installing commands</a></li>
</ul></li>
</ul>
</section><section id="tips-2" class="slide level2">
<h2>Tips</h2>
<ul>
<li class="fragment">Full TeX distribution installation before your first <code>papaja</code> article.</li>
<li class="fragment">Manage “Title page” and “Abstract” in YAML.</li>
<li class="fragment">Prepare your bibliography file and citation style while writing paper. Set them up in YAML(<a href="https://crsh.github.io/papaja_man/writing.html#citations">Guide by Frederik</a> ).</li>
<li class="fragment">Check .tex file(s) when you don’t get what you want.</li>
<li class="fragment"><code>papaja</code> is under development. Search the solutions and submit your questions at <a href="https://github.com/crsh/papaja/issues">Github</a>.</li>
</ul>
</section><section id="append-appendices-to-manuscript" class="slide level2">
<h2>Append appendices to manuscript</h2>
<figure>
<img data-src="https://user-images.githubusercontent.com/1747068/43012188-b6bff12c-8c13-11e8-9277-f4ce36f859e9.png" alt="in YAML" /><figcaption>in YAML</figcaption>
</figure>
</section><section id="append-appendices-to-manuscript-1" class="slide level2">
<h2>Append appendices to manuscript</h2>
<figure>
<img data-src="https://user-images.githubusercontent.com/1747068/43012230-daf80188-8c13-11e8-894d-d750cb03c6ae.png" alt="end of main Rmd" /><figcaption>end of main Rmd</figcaption>
</figure>
</section></section>
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