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<main id="main" class="col-md-9"><div class="page-header">
<img src="" class="logo" alt=""><h1>Hierarchical kinetics template</h1>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/hierarchical_kinetics.R" class="external-link"><code>R/hierarchical_kinetics.R</code></a></small>
<div class="d-none name"><code>hierarchical_kinetics.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>R markdown format for setting up hierarchical kinetics based on a template
provided with the mkin package. This format is based on <a href="https://pkgs.rstudio.com/rmarkdown/reference/pdf_document.html" class="external-link">rmarkdown::pdf_document</a>.
Chunk options are adapted. Echoing R code from code chunks and caching are
turned on per default. character for prepending output from code chunks is
set to the empty string, code tidying is off, figure alignment defaults to
centering, and positioning of figures is set to "H", which means that
figures will not move around in the document, but stay where the user
includes them.</p>
</div>
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">hierarchical_kinetics</span><span class="op">(</span><span class="va">...</span>, keep_tex <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>...</dt>
<dd><p>Arguments to <code><a href="https://pkgs.rstudio.com/rmarkdown/reference/pdf_document.html" class="external-link">rmarkdown::pdf_document</a></code></p></dd>
<dt>keep_tex</dt>
<dd><p>Keep the intermediate tex file used in the conversion to PDF</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>R Markdown output format to pass to
<code><a href="https://pkgs.rstudio.com/rmarkdown/reference/render.html" class="external-link">render</a></code></p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>The latter feature (positioning the figures with "H") depends on the LaTeX
package 'float'. In addition, the LaTeX package 'listing' is used in the
template for showing model fit summaries in the Appendix. This means that
the LaTeX packages 'float' and 'listing' need to be installed in the TeX
distribution used.</p>
<p>On Windows, the easiest way to achieve this (if no TeX distribution
is present before) is to install the 'tinytex' R package, to run
'tinytex::install_tinytex()' to get the basic tiny Tex distribution,
and then to run 'tinytex::tlmgr_install(c("float", "listing"))'.</p>
</div>
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/rstudio/rmarkdown" class="external-link">rmarkdown</a></span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="co"># The following is now commented out after the relase of v1.2.3 for the generation</span></span></span>
<span class="r-in"><span><span class="co"># of online docs, as the command creates a directory and opens an editor</span></span></span>
<span class="r-in"><span><span class="co">#draft("example_analysis.rmd", template = "hierarchical_kinetics", package = "mkin")</span></span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
<span class="r-in"><span></span></span>
</code></pre></div>
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