blob: ffe93e6c2c730286184761d81921784c45318577 (
plain) (
tree)
|
|
<!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>Plot parameter variability of multistart objects — parplot • 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="Plot parameter variability of multistart objects — parplot"><meta property="og:description" content="Produces a boxplot with all parameters from the multiple runs, scaled
either by the parameters of the run with the highest likelihood,
or by their medians as proposed in the paper by Duchesne et al. (2021)."><meta name="robots" content="noindex"><!-- 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav"><li>
<a href="../reference/index.html">Functions and data</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>
<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/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
</li>
<li>
<a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
</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/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
</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>
<li>
<a href="../articles/web_only/benchmarks.html">Some benchmark timings</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>Plot parameter variability of multistart objects</h1>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parplot.R" class="external-link"><code>R/parplot.R</code></a></small>
<div class="hidden name"><code>parplot.Rd</code></div>
</div>
<div class="ref-description">
<p>Produces a boxplot with all parameters from the multiple runs, scaled
either by the parameters of the run with the highest likelihood,
or by their medians as proposed in the paper by Duchesne et al. (2021).</p>
</div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">parplot</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for multistart.saem.mmkin</span></span>
<span><span class="fu">parplot</span><span class="op">(</span></span>
<span> <span class="va">object</span>,</span>
<span> llmin <span class="op">=</span> <span class="op">-</span><span class="cn">Inf</span>,</span>
<span> scale <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"best"</span>, <span class="st">"median"</span><span class="op">)</span>,</span>
<span> lpos <span class="op">=</span> <span class="st">"bottomleft"</span>,</span>
<span> main <span class="op">=</span> <span class="st">""</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
<dl><dt>object</dt>
<dd><p>The <a href="multistart.html">multistart</a> object</p></dd>
<dt>...</dt>
<dd><p>Passed to <a href="https://rdrr.io/r/graphics/boxplot.html" class="external-link">boxplot</a></p></dd>
<dt>llmin</dt>
<dd><p>The minimum likelihood of objects to be shown</p></dd>
<dt>scale</dt>
<dd><p>By default, scale parameters using the best available fit.
If 'median', parameters are scaled using the median parameters from all fits.</p></dd>
<dt>lpos</dt>
<dd><p>Positioning of the legend.</p></dd>
<dt>main</dt>
<dd><p>Title of the plot</p></dd>
</dl></div>
<div id="references">
<h2>References</h2>
<p>Duchesne R, Guillemin A, Gandrillon O, Crauste F. Practical
identifiability in the frame of nonlinear mixed effects models: the example
of the in vitro erythropoiesis. BMC Bioinformatics. 2021 Oct 4;22(1):478.
doi: 10.1186/s12859-021-04373-4.</p>
</div>
<div id="see-also">
<h2>See also</h2>
<div class="dont-index"><p><a href="multistart.html">multistart</a></p></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> 2.0.6.</p>
</div>
</footer></div>
</body></html>
|
