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diff --git a/docs/reference/hierarchical_kinetics.html b/docs/reference/hierarchical_kinetics.html new file mode 100644 index 00000000..98764bf0 --- /dev/null +++ b/docs/reference/hierarchical_kinetics.html @@ -0,0 +1,197 @@ +<!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]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + + + <div 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<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> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> +</div> + + </footer></div> + + + + + + + </body></html> + |