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<meta name="author" content="Ethan Heinzen" />
<title>The write2 function</title>
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<body>
<h1 class="title toc-ignore">The write2 function</h1>
<h4 class="author">Ethan Heinzen</h4>
<div id="TOC">
<ul>
<li><a href="#introduction">Introduction</a></li>
<li><a href="#a-note-on-piping">A note on piping</a></li>
<li><a href="#examples-using-arsenal-objects">Examples Using <code>arsenal</code> Objects</a>
<ul>
<li><a href="#tableby"><code>tableby</code></a></li>
<li><a href="#modelsum"><code>modelsum</code></a></li>
<li><a href="#freqlist"><code>freqlist</code></a></li>
<li><a href="#comparedf"><code>comparedf</code></a></li>
</ul></li>
<li><a href="#examples-using-other-objects">Examples Using Other Objects</a>
<ul>
<li><a href="#knitrkable"><code>knitr::kable()</code></a></li>
<li><a href="#xtablextable"><code>xtable::xtable()</code></a></li>
<li><a href="#panderpander_return"><code>pander::pander_return()</code></a></li>
</ul></li>
<li><a href="#output-multiple-tables-to-one-document">Output Multiple Tables to One Document</a></li>
<li><a href="#output-other-objects-monospaced-as-if-in-a-terminal">Output Other Objects Monospaced (as if in a terminal)</a></li>
<li><a href="#add-a-yaml-header-to-the-output">Add a YAML Header to the Output</a></li>
<li><a href="#add-a-code-chunk-to-the-output">Add a Code Chunk to the Output</a></li>
<li><a href="#faqs">FAQs</a>
<ul>
<li><a href="#how-do-i-suppress-the-note-about-my-document-getting-rendered">How do I suppress the note about my document getting rendered?</a></li>
<li><a href="#how-do-i-look-at-the-temporary-.rmd-file">How do I look at the temporary <code>.Rmd</code> file?</a></li>
<li><a href="#how-do-i-prevent-my-document-from-being-rendered">How do I prevent my document from being rendered?</a></li>
<li><a href="#how-do-i-output-headers-raw-htmllatex-paragraphs-etc.">How do I output headers, raw HTML/LaTeX, paragraphs, etc.?</a></li>
<li><a href="#how-do-i-tweak-the-default-format-from-write2word-write2html-or-write2pdf">How do I tweak the default format from <code>write2word()</code>, <code>write2html()</code>, or <code>write2pdf()</code>?</a></li>
<li><a href="#how-do-i-output-to-a-file-format-other-than-word-html-and-pdf">How do I output to a file format other than word, HTML, and PDF?</a></li>
<li><a href="#how-do-i-avoid-prefixes-on-my-table-captions-in-pdf">How do I avoid prefixes on my table captions in PDF?</a></li>
<li><a href="#how-do-i-output-multiple-tables-with-different-titles">How do I output multiple tables with different titles?</a></li>
<li><a href="#why-is-write2-not-working-in-r-markdownr-studio">Why is <code>write2()</code> not working in R Markdown/R Studio?</a></li>
</ul></li>
</ul>
</div>
<div id="introduction" class="section level1">
<h1>Introduction</h1>
<p>The <code>write2*()</code> functions were designed as an alternative to SAS’s <code>ODS</code> procedure for useRs who want to save R Markdown tables to separate Word, HTML, or PDF files without needing separate R Markdown programs.</p>
<p>There are three shortcut functions for the most common output types: HTML, PDF, and Word. Each of these three functions calls <code>write2()</code>, an S3 function which accepts many file output types (see the help pages for <code>rmarkdown::render()</code>). Methods have been implemented for <code>tableby()</code>, <code>modelsum()</code>, and <code>freqlist()</code>, but also <code>knitr::kable()</code>, <code>xtable::xtable()</code>, and <code>pander::pander_return()</code>.</p>
<p>The two most important things to recognize with <code>write2()</code> are the following:</p>
<ol style="list-style-type: decimal">
<li><p>Which function is being used to output the object. Sometimes the <code>write2</code> functions use <code>summary()</code>, while other times they will use <code>print()</code>. The details for each object specifically are described below.</p></li>
<li><p>How the <code>...</code> arguments are passed. To change the options for the summary-like or print-like function, you can pass named arguments which will in turn get passed to the appropriate function. Details for each object specifically are described below.</p></li>
</ol>
</div>
<div id="a-note-on-piping" class="section level1">
<h1>A note on piping</h1>
<p><code>arsenal</code> is piping-compatible!</p>
<p>The <code>write2*()</code> functions are probably the most useful place to take advantage of the <code>magrittr</code> package’s piping framework, since commands are often nested several functions deep in the context of <code>write2*()</code>. Piping also allows the <code>arsenal</code> package to become a part of more standard analysis pipelines; instead of needing to write separate R Markdown programs, intermediate analysis tables and output can be easily incorporated into piped statements.</p>
<p>This vignette will sprinkle the foward pipe (<code>%>%</code>) throughout as a hint at the power and flexibility of <code>arsenal</code> and piping.</p>
</div>
<div id="examples-using-arsenal-objects" class="section level1">
<h1>Examples Using <code>arsenal</code> Objects</h1>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(arsenal)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(magrittr)</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="fu">data</span>(mockstudy)</span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a>tmpdir <span class="ot"><-</span> <span class="fu">tempdir</span>()</span></code></pre></div>
<div id="tableby" class="section level2">
<h2><code>tableby</code></h2>
<p>For <code>tableby</code> objects, the output function in <code>write2()</code> is <code>summary()</code>. For <code>summary.tableby</code> objects, the output function is <code>print()</code>. For available arguments, see the help pages for <code>summary.tableby()</code>. Don’t use the option <code>text = TRUE</code> with the <code>write2</code> functions.</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>mylabels <span class="ot"><-</span> <span class="fu">list</span>(<span class="at">sex =</span> <span class="st">"SEX"</span>, <span class="at">age =</span><span class="st">"Age, yrs"</span>)</span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>tab1 <span class="ot"><-</span> <span class="fu">tableby</span>(arm <span class="sc">~</span> sex <span class="sc">+</span> age, <span class="at">data=</span>mockstudy)</span>
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a><span class="fu">write2html</span>(</span>
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a> tab1, <span class="fu">paste0</span>(tmpdir, <span class="st">"/test.tableby.html"</span>), <span class="at">quiet =</span> <span class="cn">TRUE</span>,</span>
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a> <span class="at">title =</span> <span class="st">"My test table"</span>, <span class="co"># passed to summary.tableby</span></span>
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a> <span class="at">labelTranslations =</span> mylabels, <span class="co"># passed to summary.tableby</span></span>
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a> <span class="at">total =</span> <span class="cn">FALSE</span> <span class="co"># passed to summary.tableby</span></span>
<span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a>)</span></code></pre></div>
</div>
<div id="modelsum" class="section level2">
<h2><code>modelsum</code></h2>
<p>For <code>modelsum</code> objects, the output function in <code>write2()</code> is <code>summary()</code>. For <code>summary.modelsum</code> objects, the output function is <code>print()</code>. For available arguments, see the help pages for <code>summary.modelsum()</code>. Don’t use the option <code>text = TRUE</code> with the <code>write2</code> functions.</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>tab2 <span class="ot"><-</span> <span class="fu">modelsum</span>(alk.phos <span class="sc">~</span> arm <span class="sc">+</span> ps <span class="sc">+</span> hgb, <span class="at">adjust=</span> <span class="sc">~</span> age <span class="sc">+</span> sex, <span class="at">family =</span> <span class="st">"gaussian"</span>, <span class="at">data =</span> mockstudy)</span>
<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a><span class="fu">write2pdf</span>(</span>
<span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a> tab2, <span class="fu">paste0</span>(tmpdir, <span class="st">"/test.modelsum.pdf"</span>), <span class="at">quiet =</span> <span class="cn">TRUE</span>,</span>
<span id="cb3-5"><a href="#cb3-5" aria-hidden="true" tabindex="-1"></a> <span class="at">title =</span> <span class="st">"My test table"</span>, <span class="co"># passed to summary.modelsum</span></span>
<span id="cb3-6"><a href="#cb3-6" aria-hidden="true" tabindex="-1"></a> <span class="at">show.intercept =</span> <span class="cn">FALSE</span>, <span class="co"># passed to summary.modelsum</span></span>
<span id="cb3-7"><a href="#cb3-7" aria-hidden="true" tabindex="-1"></a> <span class="at">digits =</span> <span class="dv">5</span> <span class="co"># passed to summary.modelsum</span></span>
<span id="cb3-8"><a href="#cb3-8" aria-hidden="true" tabindex="-1"></a>)</span></code></pre></div>
</div>
<div id="freqlist" class="section level2">
<h2><code>freqlist</code></h2>
<p>For <code>freqlist</code> objects, the output function in <code>write2()</code> is <code>summary()</code>. For <code>summary.freqlist</code> objects, the output function is <code>print()</code>. For available arguments, see the help pages for <code>summary.freqlist()</code>.</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a>mockstudy[, <span class="fu">c</span>(<span class="st">"arm"</span>, <span class="st">"sex"</span>, <span class="st">"mdquality.s"</span>)] <span class="sc">%>%</span> </span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">table</span>(<span class="at">useNA =</span> <span class="st">"ifany"</span>) <span class="sc">%>%</span> </span>
<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">freqlist</span>(<span class="at">groupBy =</span> <span class="fu">c</span>(<span class="st">"arm"</span>, <span class="st">"sex"</span>)) <span class="sc">%>%</span> </span>
<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">write2word</span>(</span>
<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">paste0</span>(tmpdir, <span class="st">"/test.freqlist.doc"</span>), <span class="at">quiet =</span> <span class="cn">TRUE</span>,</span>
<span id="cb4-6"><a href="#cb4-6" aria-hidden="true" tabindex="-1"></a> <span class="at">single =</span> <span class="cn">FALSE</span>, <span class="co"># passed to summary.freqlist</span></span>
<span id="cb4-7"><a href="#cb4-7" aria-hidden="true" tabindex="-1"></a> <span class="at">title =</span> <span class="st">"My cool title"</span> <span class="co"># passed to summary.freqlist</span></span>
<span id="cb4-8"><a href="#cb4-8" aria-hidden="true" tabindex="-1"></a> )</span></code></pre></div>
</div>
<div id="comparedf" class="section level2">
<h2><code>comparedf</code></h2>
<p>For <code>comparedf</code> objects, the output function in <code>write2()</code> is <code>summary()</code>. For <code>summary.comparedf</code> objects, the output function is <code>print()</code>.</p>
</div>
</div>
<div id="examples-using-other-objects" class="section level1">
<h1>Examples Using Other Objects</h1>
<div id="knitrkable" class="section level2">
<h2><code>knitr::kable()</code></h2>
<p>For objects resulting from a call to <code>kable()</code>, the output function in <code>write2()</code> is <code>print()</code>. There aren’t any arguments to the <code>print.knitr_kable()</code> function.</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>mockstudy <span class="sc">%>%</span> </span>
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">head</span>() <span class="sc">%>%</span> </span>
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a> knitr<span class="sc">::</span><span class="fu">kable</span>() <span class="sc">%>%</span> </span>
<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">write2html</span>(<span class="fu">paste0</span>(tmpdir, <span class="st">"/test.kable.html"</span>), <span class="at">quiet =</span> <span class="cn">TRUE</span>)</span></code></pre></div>
</div>
<div id="xtablextable" class="section level2">
<h2><code>xtable::xtable()</code></h2>
<p>For <code>xtable</code> objects, the output function in <code>write2()</code> is <code>print()</code>. For available arguments, see the help pages for <code>print.xtable()</code>.</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a>mockstudy <span class="sc">%>%</span> </span>
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">head</span>() <span class="sc">%>%</span> </span>
<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a> xtable<span class="sc">::</span><span class="fu">xtable</span>(<span class="at">caption =</span> <span class="st">"My xtable"</span>) <span class="sc">%>%</span> </span>
<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">write2pdf</span>(</span>
<span id="cb6-5"><a href="#cb6-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">paste0</span>(tmpdir, <span class="st">"/test.xtable.pdf"</span>), <span class="at">quiet =</span> <span class="cn">TRUE</span>,</span>
<span id="cb6-6"><a href="#cb6-6" aria-hidden="true" tabindex="-1"></a> <span class="at">comment =</span> <span class="cn">FALSE</span>, <span class="co"># passed to print.xtable to turn off the default message about xtable version</span></span>
<span id="cb6-7"><a href="#cb6-7" aria-hidden="true" tabindex="-1"></a> <span class="at">include.rownames =</span> <span class="cn">FALSE</span>, <span class="co"># passed to print.xtable</span></span>
<span id="cb6-8"><a href="#cb6-8" aria-hidden="true" tabindex="-1"></a> <span class="at">caption.placement =</span> <span class="st">"top"</span> <span class="co"># passed to print.xtable</span></span>
<span id="cb6-9"><a href="#cb6-9" aria-hidden="true" tabindex="-1"></a> )</span></code></pre></div>
<p>To make an HTML document, use the <code>print.xtable()</code> option <code>type = "html"</code>.</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a>mockstudy <span class="sc">%>%</span> </span>
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">head</span>() <span class="sc">%>%</span> </span>
<span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a> xtable<span class="sc">::</span><span class="fu">xtable</span>(<span class="at">caption =</span> <span class="st">"My xtable"</span>) <span class="sc">%>%</span> </span>
<span id="cb7-4"><a href="#cb7-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">write2html</span>(</span>
<span id="cb7-5"><a href="#cb7-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">paste0</span>(tmpdir, <span class="st">"/test.xtable.html"</span>), <span class="at">quiet =</span> <span class="cn">TRUE</span>,</span>
<span id="cb7-6"><a href="#cb7-6" aria-hidden="true" tabindex="-1"></a> <span class="at">type =</span> <span class="st">"html"</span>, <span class="co"># passed to print.xtable</span></span>
<span id="cb7-7"><a href="#cb7-7" aria-hidden="true" tabindex="-1"></a> <span class="at">comment =</span> <span class="cn">FALSE</span>, <span class="co"># passed to print.xtable to turn off the default message about xtable version</span></span>
<span id="cb7-8"><a href="#cb7-8" aria-hidden="true" tabindex="-1"></a> <span class="at">include.rownames =</span> <span class="cn">FALSE</span>, <span class="co"># passed to print.xtable</span></span>
<span id="cb7-9"><a href="#cb7-9" aria-hidden="true" tabindex="-1"></a> <span class="at">caption.placement =</span> <span class="st">"top"</span> <span class="co"># passed to print.xtable</span></span>
<span id="cb7-10"><a href="#cb7-10" aria-hidden="true" tabindex="-1"></a> )</span></code></pre></div>
<p>User beware! <code>xtable()</code> is not compatible with <code>write2word()</code>.</p>
</div>
<div id="panderpander_return" class="section level2">
<h2><code>pander::pander_return()</code></h2>
<p>Pander is a little bit more tricky. Since <code>pander::pander()</code> doesn’t return an object, the useR should instead use <code>pander::pander_return()</code>. For this (and for all character vectors), the the output function in <code>write2()</code> is <code>cat(sep = '\n')</code>.</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="fu">write2word</span>(pander<span class="sc">::</span><span class="fu">pander_return</span>(<span class="fu">head</span>(mockstudy)), <span class="at">file =</span> <span class="fu">paste0</span>(tmpdir, <span class="st">"/test.pander.doc"</span>), <span class="at">quiet =</span> <span class="cn">TRUE</span>)</span></code></pre></div>
</div>
</div>
<div id="output-multiple-tables-to-one-document" class="section level1">
<h1>Output Multiple Tables to One Document</h1>
<p>To output multiple tables into a document, simply make a list of them and call the same function as before.</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a>mylist <span class="ot"><-</span> <span class="fu">list</span>(</span>
<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">tableby</span>(sex <span class="sc">~</span> age, <span class="at">data =</span> mockstudy),</span>
<span id="cb9-3"><a href="#cb9-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">freqlist</span>(<span class="fu">table</span>(mockstudy[, <span class="fu">c</span>(<span class="st">"sex"</span>, <span class="st">"arm"</span>)])),</span>
<span id="cb9-4"><a href="#cb9-4" aria-hidden="true" tabindex="-1"></a> knitr<span class="sc">::</span><span class="fu">kable</span>(<span class="fu">head</span>(mockstudy))</span>
<span id="cb9-5"><a href="#cb9-5" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb9-6"><a href="#cb9-6" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb9-7"><a href="#cb9-7" aria-hidden="true" tabindex="-1"></a><span class="fu">write2pdf</span>(mylist, <span class="fu">paste0</span>(tmpdir, <span class="st">"/test.mylist.pdf"</span>), <span class="at">quiet =</span> <span class="cn">TRUE</span>)</span></code></pre></div>
<p>One neat side-effect of this function is that you can output text and headers, etc. The possibilities are endless!</p>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a>mylist2 <span class="ot"><-</span> <span class="fu">list</span>(</span>
<span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a> <span class="st">"# Header 1"</span>,</span>
<span id="cb10-3"><a href="#cb10-3" aria-hidden="true" tabindex="-1"></a> <span class="st">"This is a small paragraph introducing tableby."</span>,</span>
<span id="cb10-4"><a href="#cb10-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">tableby</span>(sex <span class="sc">~</span> age, <span class="at">data =</span> mockstudy),</span>
<span id="cb10-5"><a href="#cb10-5" aria-hidden="true" tabindex="-1"></a> <span class="st">"<hr>"</span>,</span>
<span id="cb10-6"><a href="#cb10-6" aria-hidden="true" tabindex="-1"></a> <span class="st">"# Header 2"</span>,</span>
<span id="cb10-7"><a href="#cb10-7" aria-hidden="true" tabindex="-1"></a> <span class="st">"<font color='red'>I can change color of my text!</font>"</span></span>
<span id="cb10-8"><a href="#cb10-8" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb10-9"><a href="#cb10-9" aria-hidden="true" tabindex="-1"></a><span class="fu">write2html</span>(mylist2, <span class="fu">paste0</span>(tmpdir, <span class="st">"/test.mylist2.html"</span>), <span class="at">quiet =</span> <span class="cn">TRUE</span>)</span></code></pre></div>
<p>In fact, you can even recurse on the lists!</p>
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="fu">write2pdf</span>(<span class="fu">list</span>(mylist2, mylist), <span class="fu">paste0</span>(tmpdir, <span class="st">"/test.mylists.pdf"</span>), <span class="at">quiet =</span> <span class="cn">TRUE</span>)</span></code></pre></div>
</div>
<div id="output-other-objects-monospaced-as-if-in-a-terminal" class="section level1">
<h1>Output Other Objects Monospaced (as if in a terminal)</h1>
<p>It may be useful at times to write output that would normally be copied from the terminal. The default method for <code>write2()</code> does this automatically. To output the results of <code>summary.lm()</code>, for example:</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="fu">lm</span>(age <span class="sc">~</span> sex, <span class="at">data =</span> mockstudy) <span class="sc">%>%</span> </span>
<span id="cb12-2"><a href="#cb12-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">summary</span>() <span class="sc">%>%</span> </span>
<span id="cb12-3"><a href="#cb12-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">write2pdf</span>(<span class="fu">paste0</span>(tmpdir, <span class="st">"/test.lm.pdf"</span>), <span class="at">quiet =</span> <span class="cn">TRUE</span>)</span></code></pre></div>
<p>The <code>verbatim()</code> function is another option to explicitly alert <code>write2()</code> to do this. This becomes particularly helpful to overrule existing S3 methods.</p>
<p>For example, suppose you wanted to just print a tableby object (as if it were to print in the terminal):</p>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a>tab4 <span class="ot"><-</span> <span class="fu">tableby</span>(arm <span class="sc">~</span> sex <span class="sc">+</span> age, <span class="at">data=</span>mockstudy)</span>
<span id="cb13-2"><a href="#cb13-2" aria-hidden="true" tabindex="-1"></a><span class="fu">write2html</span>(<span class="fu">verbatim</span>(tab4), <span class="fu">paste0</span>(tmpdir, <span class="st">"/test.print.tableby.html"</span>), <span class="at">quiet =</span> <span class="cn">TRUE</span>)</span></code></pre></div>
<p>Or suppose you wanted to print a character vector (as if it were to print in the terminal):</p>
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb14-1"><a href="#cb14-1" aria-hidden="true" tabindex="-1"></a>chr <span class="ot"><-</span> <span class="fu">paste0</span>(<span class="st">"MyVector"</span>, <span class="dv">1</span><span class="sc">:</span><span class="dv">10</span>)</span>
<span id="cb14-2"><a href="#cb14-2" aria-hidden="true" tabindex="-1"></a><span class="fu">write2pdf</span>(<span class="fu">verbatim</span>(chr), <span class="fu">paste0</span>(tmpdir, <span class="st">"/test.character.pdf"</span>), <span class="at">quiet =</span> <span class="cn">TRUE</span>)</span></code></pre></div>
<p>Note that you can combine multiple objects in one call:</p>
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb15-1"><a href="#cb15-1" aria-hidden="true" tabindex="-1"></a><span class="fu">write2pdf</span>(<span class="fu">verbatim</span>(tab4, chr), <span class="fu">paste0</span>(tmpdir, <span class="st">"/test.verbatim.pdf"</span>), <span class="at">quiet =</span> <span class="cn">TRUE</span>)</span></code></pre></div>
</div>
<div id="add-a-yaml-header-to-the-output" class="section level1">
<h1>Add a YAML Header to the Output</h1>
<p>You can add a YAML header to <code>write2()</code> output using the <code>yaml()</code> function.</p>
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb16-1"><a href="#cb16-1" aria-hidden="true" tabindex="-1"></a>mylist3 <span class="ot"><-</span> <span class="fu">list</span>(</span>
<span id="cb16-2"><a href="#cb16-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">yaml</span>(<span class="at">title =</span> <span class="st">"Test YAML Title"</span>, <span class="at">author =</span> <span class="st">"My cool author name"</span>),</span>
<span id="cb16-3"><a href="#cb16-3" aria-hidden="true" tabindex="-1"></a> <span class="st">"# Header 1"</span>,</span>
<span id="cb16-4"><a href="#cb16-4" aria-hidden="true" tabindex="-1"></a> <span class="st">"This is a small paragraph introducing tableby."</span>,</span>
<span id="cb16-5"><a href="#cb16-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">tableby</span>(sex <span class="sc">~</span> age, <span class="at">data =</span> mockstudy)</span>
<span id="cb16-6"><a href="#cb16-6" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb16-7"><a href="#cb16-7" aria-hidden="true" tabindex="-1"></a><span class="fu">write2html</span>(mylist3, <span class="fu">paste0</span>(tmpdir, <span class="st">"/test.yaml.html"</span>), <span class="at">quiet =</span> <span class="cn">TRUE</span>)</span></code></pre></div>
<p>In fact, all detected YAML pieces will be moved as the first output, so that the above code chunk gives the same output as this one:</p>
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb17-1"><a href="#cb17-1" aria-hidden="true" tabindex="-1"></a>mylist4 <span class="ot"><-</span> <span class="fu">list</span>(</span>
<span id="cb17-2"><a href="#cb17-2" aria-hidden="true" tabindex="-1"></a> <span class="st">"# Header 1"</span>,</span>
<span id="cb17-3"><a href="#cb17-3" aria-hidden="true" tabindex="-1"></a> <span class="st">"This is a small paragraph introducing tableby."</span>,</span>
<span id="cb17-4"><a href="#cb17-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">yaml</span>(<span class="at">title =</span> <span class="st">"Test YAML Title"</span>),</span>
<span id="cb17-5"><a href="#cb17-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">tableby</span>(sex <span class="sc">~</span> age, <span class="at">data =</span> mockstudy),</span>
<span id="cb17-6"><a href="#cb17-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">yaml</span>(<span class="at">author =</span> <span class="st">"My cool author name"</span>)</span>
<span id="cb17-7"><a href="#cb17-7" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb17-8"><a href="#cb17-8" aria-hidden="true" tabindex="-1"></a><span class="fu">write2html</span>(mylist4, <span class="fu">paste0</span>(tmpdir, <span class="st">"/test.yaml2.html"</span>), <span class="at">quiet =</span> <span class="cn">TRUE</span>)</span></code></pre></div>
</div>
<div id="add-a-code-chunk-to-the-output" class="section level1">
<h1>Add a Code Chunk to the Output</h1>
<p>It is now possible to add code chunks to the output <code>.Rmd</code>:</p>
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb18-1"><a href="#cb18-1" aria-hidden="true" tabindex="-1"></a>mylist5 <span class="ot"><-</span> <span class="fu">list</span>(</span>
<span id="cb18-2"><a href="#cb18-2" aria-hidden="true" tabindex="-1"></a> <span class="st">"# What is 1 + 2?"</span>,</span>
<span id="cb18-3"><a href="#cb18-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">code.chunk</span>(a <span class="ot"><-</span> <span class="dv">1</span>, b <span class="ot"><-</span> <span class="dv">2</span>),</span>
<span id="cb18-4"><a href="#cb18-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">code.chunk</span>(a <span class="sc">+</span> b, <span class="at">chunk.opts =</span> <span class="st">"r echo=FALSE, eval=TRUE"</span>)</span>
<span id="cb18-5"><a href="#cb18-5" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb18-6"><a href="#cb18-6" aria-hidden="true" tabindex="-1"></a><span class="fu">write2html</span>(mylist5, <span class="fu">paste0</span>(tmpdir, <span class="st">"/test.code.chunk.html"</span>), <span class="at">quiet =</span> <span class="cn">TRUE</span>)</span></code></pre></div>
<p>This allow flexibility to create objects on-the-fly, to read in saved objects to the temporary <code>.Rmd</code>, etc. The possibilities are endless!</p>
</div>
<div id="faqs" class="section level1">
<h1>FAQs</h1>
<div id="how-do-i-suppress-the-note-about-my-document-getting-rendered" class="section level2">
<h2>How do I suppress the note about my document getting rendered?</h2>
<p>This is easily accomplished by using the argument <code>quiet = TRUE</code> (passed to the <code>rmarkdown::render()</code> function).</p>
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb19-1"><a href="#cb19-1" aria-hidden="true" tabindex="-1"></a><span class="fu">write2html</span>(</span>
<span id="cb19-2"><a href="#cb19-2" aria-hidden="true" tabindex="-1"></a> knitr<span class="sc">::</span><span class="fu">kable</span>(<span class="fu">head</span>(mockstudy)), <span class="fu">paste0</span>(tmpdir, <span class="st">"/test.kable.quiet.html"</span>),</span>
<span id="cb19-3"><a href="#cb19-3" aria-hidden="true" tabindex="-1"></a> <span class="at">quiet =</span> <span class="cn">TRUE</span> <span class="co"># passed to rmarkdown::render</span></span>
<span id="cb19-4"><a href="#cb19-4" aria-hidden="true" tabindex="-1"></a>)</span></code></pre></div>
</div>
<div id="how-do-i-look-at-the-temporary-.rmd-file" class="section level2">
<h2>How do I look at the temporary <code>.Rmd</code> file?</h2>
<p>This is easily accomplished by using the option <code>keep.rmd = TRUE</code>.</p>
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb20-1"><a href="#cb20-1" aria-hidden="true" tabindex="-1"></a><span class="fu">write2html</span>(</span>
<span id="cb20-2"><a href="#cb20-2" aria-hidden="true" tabindex="-1"></a> knitr<span class="sc">::</span><span class="fu">kable</span>(<span class="fu">head</span>(mockstudy)), <span class="fu">paste0</span>(tmpdir, <span class="st">"/test.kable.keep.rmd.html"</span>),</span>
<span id="cb20-3"><a href="#cb20-3" aria-hidden="true" tabindex="-1"></a> <span class="at">quiet =</span> <span class="cn">TRUE</span>, <span class="co"># passed to rmarkdown::render</span></span>
<span id="cb20-4"><a href="#cb20-4" aria-hidden="true" tabindex="-1"></a> <span class="at">keep.rmd =</span> <span class="cn">TRUE</span></span>
<span id="cb20-5"><a href="#cb20-5" aria-hidden="true" tabindex="-1"></a>)</span></code></pre></div>
</div>
<div id="how-do-i-prevent-my-document-from-being-rendered" class="section level2">
<h2>How do I prevent my document from being rendered?</h2>
<p>This is easily accomplished by using the option <code>render. = FALSE</code>. Note that this will then default to <code>keep.rmd = TRUE</code>.</p>
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb21-1"><a href="#cb21-1" aria-hidden="true" tabindex="-1"></a><span class="fu">write2html</span>(</span>
<span id="cb21-2"><a href="#cb21-2" aria-hidden="true" tabindex="-1"></a> knitr<span class="sc">::</span><span class="fu">kable</span>(<span class="fu">head</span>(mockstudy)), <span class="fu">paste0</span>(tmpdir, <span class="st">"/test.kable.dont.render.html"</span>),</span>
<span id="cb21-3"><a href="#cb21-3" aria-hidden="true" tabindex="-1"></a> <span class="at">render. =</span> <span class="cn">FALSE</span></span>
<span id="cb21-4"><a href="#cb21-4" aria-hidden="true" tabindex="-1"></a>)</span></code></pre></div>
</div>
<div id="how-do-i-output-headers-raw-htmllatex-paragraphs-etc." class="section level2">
<h2>How do I output headers, raw HTML/LaTeX, paragraphs, etc.?</h2>
<p>One can simply abuse the list S3 method for <code>write2()</code>!</p>
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb22-1"><a href="#cb22-1" aria-hidden="true" tabindex="-1"></a>mylist2 <span class="ot"><-</span> <span class="fu">list</span>(</span>
<span id="cb22-2"><a href="#cb22-2" aria-hidden="true" tabindex="-1"></a> <span class="st">"# Header 1"</span>,</span>
<span id="cb22-3"><a href="#cb22-3" aria-hidden="true" tabindex="-1"></a> <span class="st">"This is a small paragraph introducing tableby."</span>,</span>
<span id="cb22-4"><a href="#cb22-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">tableby</span>(sex <span class="sc">~</span> age, <span class="at">data =</span> mockstudy),</span>
<span id="cb22-5"><a href="#cb22-5" aria-hidden="true" tabindex="-1"></a> <span class="st">"<hr>"</span>,</span>
<span id="cb22-6"><a href="#cb22-6" aria-hidden="true" tabindex="-1"></a> <span class="st">"# Header 2"</span>,</span>
<span id="cb22-7"><a href="#cb22-7" aria-hidden="true" tabindex="-1"></a> <span class="st">"<font color='red'>I can change color of my text!</font>"</span></span>
<span id="cb22-8"><a href="#cb22-8" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb22-9"><a href="#cb22-9" aria-hidden="true" tabindex="-1"></a><span class="fu">write2html</span>(mylist2, <span class="fu">paste0</span>(tmpdir, <span class="st">"/test.mylist2.html"</span>), <span class="at">quiet =</span> <span class="cn">TRUE</span>)</span></code></pre></div>
</div>
<div id="how-do-i-tweak-the-default-format-from-write2word-write2html-or-write2pdf" class="section level2">
<h2>How do I tweak the default format from <code>write2word()</code>, <code>write2html()</code>, or <code>write2pdf()</code>?</h2>
<p>You can pass arguments to the format functions used behind the scenes.</p>
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb23-1"><a href="#cb23-1" aria-hidden="true" tabindex="-1"></a><span class="fu">write2html</span>(</span>
<span id="cb23-2"><a href="#cb23-2" aria-hidden="true" tabindex="-1"></a> knitr<span class="sc">::</span><span class="fu">kable</span>(<span class="fu">head</span>(mockstudy)), <span class="fu">paste0</span>(tmpdir, <span class="st">"/test.kable.theme.html"</span>),</span>
<span id="cb23-3"><a href="#cb23-3" aria-hidden="true" tabindex="-1"></a> <span class="at">quiet =</span> <span class="cn">TRUE</span>, <span class="co"># passed to rmarkdown::render</span></span>
<span id="cb23-4"><a href="#cb23-4" aria-hidden="true" tabindex="-1"></a> <span class="at">theme =</span> <span class="st">"yeti"</span> <span class="co"># passed to rmarkdown::html_document</span></span>
<span id="cb23-5"><a href="#cb23-5" aria-hidden="true" tabindex="-1"></a>)</span></code></pre></div>
<p>See the help pages for <code>rmarkdown::word_document()</code>, <code>rmarkdown::html_document()</code>, and <code>rmarkdown::pdf_document()</code>.</p>
</div>
<div id="how-do-i-output-to-a-file-format-other-than-word-html-and-pdf" class="section level2">
<h2>How do I output to a file format other than word, HTML, and PDF?</h2>
<p>This can be done using the generic <code>write2()</code> function. The last argument in the function can be another format specification. For details on the acceptable inputs, see the help page for <code>write2()</code>.</p>
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb24-1"><a href="#cb24-1" aria-hidden="true" tabindex="-1"></a><span class="fu">write2</span>(</span>
<span id="cb24-2"><a href="#cb24-2" aria-hidden="true" tabindex="-1"></a> knitr<span class="sc">::</span><span class="fu">kable</span>(<span class="fu">head</span>(mockstudy[, <span class="dv">1</span><span class="sc">:</span><span class="dv">4</span>])), <span class="fu">paste0</span>(tmpdir, <span class="st">"/test.kable.rtf"</span>),</span>
<span id="cb24-3"><a href="#cb24-3" aria-hidden="true" tabindex="-1"></a> <span class="at">quiet =</span> <span class="cn">TRUE</span>, <span class="co"># passed to rmarkdown::render</span></span>
<span id="cb24-4"><a href="#cb24-4" aria-hidden="true" tabindex="-1"></a> <span class="at">output_format =</span> rmarkdown<span class="sc">::</span>rtf_document</span>
<span id="cb24-5"><a href="#cb24-5" aria-hidden="true" tabindex="-1"></a>)</span></code></pre></div>
</div>
<div id="how-do-i-avoid-prefixes-on-my-table-captions-in-pdf" class="section level2">
<h2>How do I avoid prefixes on my table captions in PDF?</h2>
<p>You can do this pretty easily with the <code>yaml()</code> function:</p>
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb25-1"><a href="#cb25-1" aria-hidden="true" tabindex="-1"></a>mylist5 <span class="ot"><-</span> <span class="fu">list</span>(</span>
<span id="cb25-2"><a href="#cb25-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">yaml</span>(<span class="st">"header-includes"</span> <span class="ot">=</span> <span class="fu">list</span>(<span class="st">"</span><span class="sc">\\</span><span class="st">usepackage[labelformat=empty]{caption}"</span>)),</span>
<span id="cb25-3"><a href="#cb25-3" aria-hidden="true" tabindex="-1"></a> <span class="st">"# Header 1"</span>,</span>
<span id="cb25-4"><a href="#cb25-4" aria-hidden="true" tabindex="-1"></a> <span class="st">"This is a small paragraph introducing tableby."</span>,</span>
<span id="cb25-5"><a href="#cb25-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">tableby</span>(sex <span class="sc">~</span> age, <span class="at">data =</span> mockstudy)</span>
<span id="cb25-6"><a href="#cb25-6" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb25-7"><a href="#cb25-7" aria-hidden="true" tabindex="-1"></a><span class="fu">write2pdf</span>(mylist5, <span class="fu">paste0</span>(tmpdir, <span class="st">"/test.noprefixes.pdf"</span>), <span class="at">title =</span> <span class="st">"My tableby"</span>)</span></code></pre></div>
</div>
<div id="how-do-i-output-multiple-tables-with-different-titles" class="section level2">
<h2>How do I output multiple tables with different titles?</h2>
<p>There are now <code>write2()</code> methods for the summary objects of <code>arsenal</code> functions. This allows you to specify a title for each table:</p>
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb26-1"><a href="#cb26-1" aria-hidden="true" tabindex="-1"></a>mylist6 <span class="ot"><-</span> <span class="fu">list</span>(</span>
<span id="cb26-2"><a href="#cb26-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">summary</span>(<span class="fu">tableby</span>(sex <span class="sc">~</span> age, <span class="at">data =</span> mockstudy), <span class="at">title =</span> <span class="st">"A Title for tableby"</span>),</span>
<span id="cb26-3"><a href="#cb26-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">summary</span>(<span class="fu">modelsum</span>(age <span class="sc">~</span> sex, <span class="at">data =</span> mockstudy), <span class="at">title =</span> <span class="st">"A Title for modelsum"</span>),</span>
<span id="cb26-4"><a href="#cb26-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">summary</span>(<span class="fu">freqlist</span>(<span class="sc">~</span> sex, <span class="at">data =</span> mockstudy), <span class="at">title =</span> <span class="st">"A Title for freqlist"</span>)</span>
<span id="cb26-5"><a href="#cb26-5" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb26-6"><a href="#cb26-6" aria-hidden="true" tabindex="-1"></a><span class="fu">write2pdf</span>(mylist6, <span class="fu">paste0</span>(tmpdir, <span class="st">"/test.multiple.titles.pdf"</span>))</span></code></pre></div>
</div>
<div id="why-is-write2-not-working-in-r-markdownr-studio" class="section level2">
<h2>Why is <code>write2()</code> not working in R Markdown/R Studio?</h2>
<p>It’s possible that a global option in R Studio is preventing the tables from rendering. Consider turning off (i.e., unchecking) the option Tools > Global Options > R Markdown > Show output inline for all R Markdown documents.</p>
</div>
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