Improve docs and update pkgdown

author: Johannes Ranke <jranke@uni-bremen.de> 2022-09-16 10:51:48 +0200
committer: Johannes Ranke <jranke@uni-bremen.de> 2022-09-16 10:51:48 +0200
commit: 2a521ab0a4b7d981a2042353e2c60b8a877489b8 (patch)
tree: 5198483a73f37335733cb78cb6507b3ffdbb9fe5 /docs/dev/reference/multistart.html
parent: 03e1598a3c79911a497758fe382461f288bf05e6 (diff)
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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>Perform a hierarchical model fit with multiple starting values — multistart • 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="Perform a hierarchical model fit with multiple starting values — multistart"><meta property="og:description" content="The purpose of this method is to check if a certain algorithm for fitting
+nonlinear hierarchical models (also known as nonlinear mixed-effects models)
+will reliably yield results that are sufficiently similar to each other, if
+started with a certain range of reasonable starting parameters. It is
+inspired by the article on practical identifiabiliy in the frame of nonlinear
+mixed-effects models 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]>
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+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Perform a hierarchical model fit with multiple starting values</h1>
+    <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/multistart.R" class="external-link"><code>R/multistart.R</code></a></small>
+    <div class="hidden name"><code>multistart.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>The purpose of this method is to check if a certain algorithm for fitting
+nonlinear hierarchical models (also known as nonlinear mixed-effects models)
+will reliably yield results that are sufficiently similar to each other, if
+started with a certain range of reasonable starting parameters. It is
+inspired by the article on practical identifiabiliy in the frame of nonlinear
+mixed-effects models by Duchesne et al (2021).</p>
+    </div>
+
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">multistart</span><span class="op">(</span><span class="va">object</span>, n <span class="op">=</span> <span class="fl">50</span>, cores <span class="op">=</span> <span class="fl">1</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for saem.mmkin</span></span>
+<span><span class="fu">multistart</span><span class="op">(</span><span class="va">object</span>, n <span class="op">=</span> <span class="fl">50</span>, cores <span class="op">=</span> <span class="fl">1</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for multistart</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for multistart</span></span>
+<span><span class="fu"><a href="parms.html">parms</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">parhist</span><span class="op">(</span><span class="va">object</span>, lpos <span class="op">=</span> <span class="st">"topleft"</span>, main <span class="op">=</span> <span class="st">""</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">llhist</span><span class="op">(</span><span class="va">object</span>, breaks <span class="op">=</span> <span class="st">"Sturges"</span>, lpos <span class="op">=</span> <span class="st">"topleft"</span>, main <span class="op">=</span> <span class="st">""</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>object</dt>
+<dd><p>The fit object to work with</p></dd>
+
+
+<dt>n</dt>
+<dd><p>How many different combinations of starting parameters should be
+used?</p></dd>
+
+
+<dt>cores</dt>
+<dd><p>How many fits should be run in parallel?</p></dd>
+
+
+<dt>...</dt>
+<dd><p>Passed to the update function, or to the basic plotting
+function in the case of the graphical functions.</p></dd>
+
+
+<dt>x</dt>
+<dd><p>The multistart object to print</p></dd>
+
+
+<dt>lpos</dt>
+<dd><p>Positioning of the legend.</p></dd>
+
+
+<dt>main</dt>
+<dd><p>title of the plot</p></dd>
+
+
+<dt>breaks</dt>
+<dd><p>Passed to <a href="https://rdrr.io/r/graphics/hist.html" class="external-link">hist</a></p></dd>
+
+</dl></div>
+    <div id="value">
+    <h2>Value</h2>
+    
+
+<p>A list of <a href="saem.html">saem.mmkin</a> objects, with class attributes
+'multistart.saem.mmkin' and 'multistart'.</p>
+    </div>
+    <div id="details">
+    <h2>Details</h2>
+    <p>Currently, parallel execution of the fits is only supported using
+<a href="https://rdrr.io/r/parallel/mclapply.html" class="external-link">parallel::mclapply</a>, i.e. not available on Windows.</p>
+    </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>
+  <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>
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author	Johannes Ranke <jranke@uni-bremen.de>	2022-09-16 10:51:48 +0200
committer	Johannes Ranke <jranke@uni-bremen.de>	2022-09-16 10:51:48 +0200
commit	2a521ab0a4b7d981a2042353e2c60b8a877489b8 (patch)
tree	5198483a73f37335733cb78cb6507b3ffdbb9fe5 /docs/dev/reference/multistart.html
parent	03e1598a3c79911a497758fe382461f288bf05e6 (diff)