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authorJohannes Ranke <jranke@uni-bremen.de>2023-04-20 19:53:28 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2023-04-20 20:03:32 +0200
commit9ae42bd20bc2543a94cf1581ba9820c2f9e3afbd (patch)
treeb3539a9689f5930b8444a5fc459781b825e00fa4 /docs/reference/hierarchical_kinetics.html
parentad0efc2d16a84c674307ad2df9d44153b44a9cf8 (diff)
Fix and rebuild documentation, see NEWS
I had to fix the two pathway vignettes, as they did not work with the released version any more. So they and the multistart vignette which got some small fixes as well were rebuilt. Complete rebuild of the online docs with the released version. The documentation of the 'hierarchial_kinetics' format had to be fixed as well.
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+<!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=1.0"><title>Hierarchical kinetics template — hierarchical_kinetics • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Hierarchical kinetics template — hierarchical_kinetics"><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
+includes them.'><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+ <div class="page-header">
+ <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="hidden name"><code>hierarchical_kinetics.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <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 id="ref-usage">
+ <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 id="arguments">
+ <h2>Arguments</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 id="value">
+ <h2>Value</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 id="details">
+ <h2>Details</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 id="ref-examples">
+ <h2>Examples</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>
+ </div>
+ </div>
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+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
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