aboutsummaryrefslogtreecommitdiff
path: root/docs/reference/parplot.html
diff options
context:
space:
mode:
authorJohannes Ranke <jranke@uni-bremen.de>2023-11-16 06:02:05 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2023-11-16 06:02:05 +0100
commit8b7edd4eaf0d196e674a085f744d1a69260a6c91 (patch)
tree96d79f504b775d2626ab2a9f700732bd142d66d9 /docs/reference/parplot.html
parent6ae6b5230efd2e3d25b68600bd988ded60d3db77 (diff)
Update pkgdown docs to bootstrap 5 with search
Diffstat (limited to 'docs/reference/parplot.html')
-rw-r--r--docs/reference/parplot.html196
1 files changed, 80 insertions, 116 deletions
diff --git a/docs/reference/parplot.html b/docs/reference/parplot.html
index 2ae8d39f..5a4bada1 100644
--- a/docs/reference/parplot.html
+++ b/docs/reference/parplot.html
@@ -1,122 +1,90 @@
<!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
+<!-- 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, shrink-to-fit=no"><meta name="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)."><title>Plot parameter variability of multistart objects — parplot • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><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)."><!-- 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">
+<![endif]--></head><body>
+ <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
- <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">1.2.6</span>
- </span>
- </div>
+ <nav class="navbar fixed-top navbar-default navbar-expand-lg bg-light"><div class="container">
+
+ <a class="navbar-brand me-2" href="../index.html">mkin</a>
- <div id="navbar" class="navbar-collapse collapse">
- <ul class="nav navbar-nav"><li>
- <a href="../reference/index.html">Reference</a>
+ <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.6</small>
+
+
+ <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+ <span class="navbar-toggler-icon"></span>
+ </button>
+
+ <div id="navbar" class="collapse navbar-collapse ms-3">
+ <ul class="navbar-nav me-auto"><li class="active nav-item">
+ <a class="nav-link" 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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</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 class="nav-item dropdown">
+ <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+ <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+ <a class="dropdown-item" href="../articles/mkin.html">Introduction to mkin</a>
+ <div class="dropdown-divider"></div>
+ <h6 class="dropdown-header" data-toc-skip>Example evaluations with (generalised) nonlinear least squares</h6>
+ <a class="dropdown-item" href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+ <a class="dropdown-item" href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+ <a class="dropdown-item" href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ <div class="dropdown-divider"></div>
+ <h6 class="dropdown-header" data-toc-skip>Example evaluations with hierarchical models (nonlinear mixed-effects models)</h6>
+ <a class="dropdown-item" href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a>
+ <a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a>
+ <a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a>
+ <a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a>
+ <a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a>
+ <a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
+ <div class="dropdown-divider"></div>
+ <h6 class="dropdown-header" data-toc-skip>Performance</h6>
+ <a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+ <a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+ <a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
+ <div class="dropdown-divider"></div>
+ <h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6>
+ <a class="dropdown-item" href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+ <a class="dropdown-item" href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+ </div>
</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>
+<li class="nav-item">
+ <a class="nav-link" href="../news/index.html">News</a>
+</li>
+ </ul><form class="form-inline my-2 my-lg-0" role="search">
+ <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
+
+ <ul class="navbar-nav"><li class="nav-item">
+ <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github">
+ <span class="fab fa 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>
+ </ul></div>
+
+
+ </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+ <main id="main" class="col-md-9"><div class="page-header">
+ <img src="" class="logo" alt=""><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">
+ <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 id="ref-usage">
+ <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 multistart.saem.mmkin</span></span>
@@ -131,8 +99,8 @@ or by their medians as proposed in the paper by Duchesne et al. (2021).</p>
<span><span class="op">)</span></span></code></pre></div>
</div>
- <div id="arguments">
- <h2>Arguments</h2>
+ <div class="section level2">
+ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>object</dt>
<dd><p>The <a href="multistart.html">multistart</a> object</p></dd>
@@ -164,44 +132,40 @@ If 'median', parameters are scaled using the median parameters from all fits.</p
<dd><p>Title of the plot</p></dd>
</dl></div>
- <div id="details">
- <h2>Details</h2>
+ <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 id="references">
- <h2>References</h2>
+ <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 id="see-also">
- <h2>See also</h2>
+ <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>
- </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>
+ </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+ </nav></aside></div>
- <footer><div class="copyright">
+ <footer><div class="pkgdown-footer-left">
<p></p><p>Developed by Johannes Ranke.</p>
</div>
-<div class="pkgdown">
+<div class="pkgdown-footer-right">
<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>
+ </footer></div>
-
</body></html>

Contact - Imprint