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authorJohannes Ranke <johannes.ranke@jrwb.de>2025-02-14 09:15:20 +0100
committerJohannes Ranke <johannes.ranke@jrwb.de>2025-02-14 09:15:20 +0100
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+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 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"></head><body>
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+
+ <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="d-none name"><code>parplot.Rd</code></div>
+ </div>
+
+ <div class="ref-description section level2">
+ <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 class="section level2">
+ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+ <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 class '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> llquant <span class="op">=</span> <span class="cn">NA</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 class="section level2">
+ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
+<dd><p>The <a href="multistart.html">multistart</a> object</p></dd>
+
+
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dd><p>Passed to <a href="https://rdrr.io/r/graphics/boxplot.html" class="external-link">boxplot</a></p></dd>
+
+
+<dt id="arg-llmin">llmin<a class="anchor" aria-label="anchor" href="#arg-llmin"></a></dt>
+<dd><p>The minimum likelihood of objects to be shown</p></dd>
+
+
+<dt id="arg-llquant">llquant<a class="anchor" aria-label="anchor" href="#arg-llquant"></a></dt>
+<dd><p>Fractional value for selecting only the fits with higher
+likelihoods. Overrides 'llmin'.</p></dd>
+
+
+<dt id="arg-scale">scale<a class="anchor" aria-label="anchor" href="#arg-scale"></a></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 id="arg-lpos">lpos<a class="anchor" aria-label="anchor" href="#arg-lpos"></a></dt>
+<dd><p>Positioning of the legend.</p></dd>
+
+
+<dt id="arg-main">main<a class="anchor" aria-label="anchor" href="#arg-main"></a></dt>
+<dd><p>Title of the plot</p></dd>
+
+</dl></div>
+ <div class="section level2">
+ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+ <p>Starting values of degradation model parameters and error model parameters
+are shown as green circles. The results obtained in the original run
+are shown as red circles.</p>
+ </div>
+ <div class="section level2">
+ <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></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 class="section level2">
+ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+ <div class="dont-index"><p><a href="multistart.html">multistart</a></p></div>
+ </div>
+
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