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authorJohannes Ranke <jranke@uni-bremen.de>2022-09-16 10:51:48 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2022-09-16 10:51:48 +0200
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+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>
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