aboutsummaryrefslogtreecommitdiff
path: root/docs/reference/hierarchical_kinetics.html
diff options
context:
space:
mode:
authorJohannes Ranke <jranke@uni-bremen.de>2023-04-20 20:17:12 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2023-04-20 20:17:12 +0200
commit7b7c4bf493ba15824ea43bed764661678b4aca03 (patch)
tree48de1e32327c36ee49fc476dc76ece8397ab55c6 /docs/reference/hierarchical_kinetics.html
parent842998b688037c007d8876d7e1110c929fe2374c (diff)
parent9ae42bd20bc2543a94cf1581ba9820c2f9e3afbd (diff)
Merge branch 'v1.2.3_pkgdown'
Diffstat (limited to 'docs/reference/hierarchical_kinetics.html')
-rw-r--r--docs/reference/hierarchical_kinetics.html197
1 files changed, 197 insertions, 0 deletions
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 class="container template-reference-topic">
+ <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">mkin</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.3</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav"><li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu"><li>
+ <a href="../articles/mkin.html">Introduction to mkin</a>
+ </li>
+ <li class="divider">
+ <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li>
+ <li>
+ <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li class="divider">
+ <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li>
+ <li>
+ <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a>
+ </li>
+ <li>
+ <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a>
+ </li>
+ <li>
+ <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
+ </li>
+ <li class="divider">
+ <li class="dropdown-header">Performance</li>
+ <li>
+ <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
+ </li>
+ <li class="divider">
+ <li class="dropdown-header">Miscellaneous</li>
+ <li>
+ <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+ </li>
+ </ul></li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul><ul class="nav navbar-nav navbar-right"><li>
+ <a href="https://github.com/jranke/mkin/" class="external-link">
+ <span class="fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul></div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header><div class="row">
+ <div class="col-md-9 contents">
+ <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>
+ <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>
+

Contact - Imprint