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diff --git a/docs/reference/hierarchical_kinetics.html b/docs/reference/hierarchical_kinetics.html
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+++ b/docs/reference/hierarchical_kinetics.html
@@ -1,88 +1,75 @@
<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content='R markdown format for setting up hierarchical kinetics based on a template
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provided with the mkin package. This format is based on rmarkdown::pdf_document.
Chunk options are adapted. Echoing R code from code chunks and caching are
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+includes them.'><meta property="og:description" content='R markdown format for setting up hierarchical kinetics based on a template
provided with the mkin package. This format is based on rmarkdown::pdf_document.
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
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+ <li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a></li>
+ <li><a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li>
+ <li><a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></li>
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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>
+
+ <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>
@@ -105,22 +92,24 @@ includes them.</p>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
- <dl><dt>...</dt>
+
+
+<dl><dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></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>
+<dt id="arg-keep-tex">keep_tex<a class="anchor" aria-label="anchor" href="#arg-keep-tex"></a></dt>
+<dd><p>Keep the intermediate tex file used in the conversion to PDF.
+Note that this argument does not control whether to keep the auxiliary
+files (e.g., <code class="file">.aux</code>) generated by LaTeX when compiling <code class="file">.tex</code> to
+<code class="file">.pdf</code>. To keep these files, you may set <code>options(tinytex.clean =
+FALSE)</code>.</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
+ <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>
@@ -147,23 +136,23 @@ and then to run 'tinytex::tlmgr_install(c("float", "listing"))'.</p>
<span class="r-in"><span></span></span>
</code></pre></div>
</div>
- </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+ </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
</nav></aside></div>
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+ <p>Developed by Johannes Ranke.</p>
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+ <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
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