|
|
<!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>Extract model parameters — parms • 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="Extract model parameters — parms"><meta property="og:description" content="This function returns degradation model parameters as well as error
model parameters per default, in order to avoid working with a fitted model
without considering the error structure that was assumed for the fit."><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">1.2.5</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav"><li>
<a 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/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>
</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>Extract model parameters</h1>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parms.R" class="external-link"><code>R/parms.R</code></a>, <a href="https://github.com/jranke/mkin/blob/HEAD/R/saem.R" class="external-link"><code>R/saem.R</code></a></small>
<div class="hidden name"><code>parms.Rd</code></div>
</div>
<div class="ref-description">
<p>This function returns degradation model parameters as well as error
model parameters per default, in order to avoid working with a fitted model
without considering the error structure that was assumed for the fit.</p>
</div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">parms</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 mkinfit</span></span>
<span><span class="fu">parms</span><span class="op">(</span><span class="va">object</span>, transformed <span class="op">=</span> <span class="cn">FALSE</span>, errparms <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for mmkin</span></span>
<span><span class="fu">parms</span><span class="op">(</span><span class="va">object</span>, transformed <span class="op">=</span> <span class="cn">FALSE</span>, errparms <span class="op">=</span> <span class="cn">TRUE</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">parms</span><span class="op">(</span><span class="va">object</span>, exclude_failed <span class="op">=</span> <span class="cn">TRUE</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">parms</span><span class="op">(</span><span class="va">object</span>, ci <span class="op">=</span> <span class="cn">FALSE</span>, covariates <span class="op">=</span> <span class="cn">NULL</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>A fitted model object.</p></dd>
<dt>...</dt>
<dd><p>Not used</p></dd>
<dt>transformed</dt>
<dd><p>Should the parameters be returned as used internally
during the optimisation?</p></dd>
<dt>errparms</dt>
<dd><p>Should the error model parameters be returned
in addition to the degradation parameters?</p></dd>
<dt>exclude_failed</dt>
<dd><p>For <a href="multistart.html">multistart</a> objects, should rows for failed fits
be removed from the returned parameter matrix?</p></dd>
<dt>ci</dt>
<dd><p>Should a matrix with estimates and confidence interval boundaries
be returned? If FALSE (default), a vector of estimates is returned if no
covariates are given, otherwise a matrix of estimates is returned, with
each column corresponding to a row of the data frame holding the covariates</p></dd>
<dt>covariates</dt>
<dd><p>A data frame holding covariate values for which to
return parameter values. Only has an effect if 'ci' is FALSE.</p></dd>
</dl></div>
<div id="value">
<h2>Value</h2>
<p>Depending on the object, a numeric vector of fitted model parameters,
a matrix (e.g. for mmkin row objects), or a list of matrices (e.g. for
mmkin objects with more than one row).</p>
</div>
<div id="see-also">
<h2>See also</h2>
<div class="dont-index"><p><a href="saem.html">saem</a>, <a href="multistart.html">multistart</a></p></div>
</div>
<div id="ref-examples">
<h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># mkinfit objects</span></span></span>
<span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> parent_0 k_parent sigma </span>
<span class="r-out co"><span class="r-pr">#></span> 82.4921598 0.3060633 4.6730124 </span>
<span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fit</span>, transformed <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent sigma </span>
<span class="r-out co"><span class="r-pr">#></span> 82.492160 -1.183963 4.673012 </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># mmkin objects</span></span></span>
<span class="r-in"><span><span class="va">ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
<span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">data</span><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">"name"</span>, <span class="st">"time"</span>, <span class="st">"value"</span><span class="op">)</span><span class="op">]</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
<span class="r-in"><span><span class="va">fits</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><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">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span>
<span class="r-out co"><span class="r-pr">#></span> parent_0 88.52275400 82.666781678 86.8547308 91.7779306 82.14809450</span>
<span class="r-out co"><span class="r-pr">#></span> k_parent 0.05794659 0.009647805 0.2102974 0.1232258 0.00720421</span>
<span class="r-out co"><span class="r-pr">#></span> sigma 5.15274487 7.040168584 3.6769645 6.4669234 6.50457673</span>
<span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span><span class="op">[</span>, <span class="fl">2</span><span class="op">]</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> $SFO</span>
<span class="r-out co"><span class="r-pr">#></span> Dataset 7</span>
<span class="r-out co"><span class="r-pr">#></span> parent_0 82.666781678</span>
<span class="r-out co"><span class="r-pr">#></span> k_parent 0.009647805</span>
<span class="r-out co"><span class="r-pr">#></span> sigma 7.040168584</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> $FOMC</span>
<span class="r-out co"><span class="r-pr">#></span> Dataset 7</span>
<span class="r-out co"><span class="r-pr">#></span> parent_0 92.6837649</span>
<span class="r-out co"><span class="r-pr">#></span> alpha 0.4967832</span>
<span class="r-out co"><span class="r-pr">#></span> beta 14.1451255</span>
<span class="r-out co"><span class="r-pr">#></span> sigma 1.9167519</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> $DFOP</span>
<span class="r-out co"><span class="r-pr">#></span> Dataset 7</span>
<span class="r-out co"><span class="r-pr">#></span> parent_0 91.058971589</span>
<span class="r-out co"><span class="r-pr">#></span> k1 0.044946770</span>
<span class="r-out co"><span class="r-pr">#></span> k2 0.002868336</span>
<span class="r-out co"><span class="r-pr">#></span> g 0.526942415</span>
<span class="r-out co"><span class="r-pr">#></span> sigma 2.221302196</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> $SFO</span>
<span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span>
<span class="r-out co"><span class="r-pr">#></span> parent_0 88.52275400 82.666781678 86.8547308 91.7779306 82.14809450</span>
<span class="r-out co"><span class="r-pr">#></span> k_parent 0.05794659 0.009647805 0.2102974 0.1232258 0.00720421</span>
<span class="r-out co"><span class="r-pr">#></span> sigma 5.15274487 7.040168584 3.6769645 6.4669234 6.50457673</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> $FOMC</span>
<span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span>
<span class="r-out co"><span class="r-pr">#></span> parent_0 95.558575 92.6837649 90.719787 98.383939 94.8481459</span>
<span class="r-out co"><span class="r-pr">#></span> alpha 1.338667 0.4967832 1.639099 1.074460 0.2805272</span>
<span class="r-out co"><span class="r-pr">#></span> beta 13.033315 14.1451255 5.007077 4.397126 6.9052224</span>
<span class="r-out co"><span class="r-pr">#></span> sigma 1.847671 1.9167519 1.066063 3.146056 1.6222778</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> $DFOP</span>
<span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span>
<span class="r-out co"><span class="r-pr">#></span> parent_0 96.55213663 91.058971589 90.34509493 98.14858820 94.311323734</span>
<span class="r-out co"><span class="r-pr">#></span> k1 0.21954588 0.044946770 0.41232288 0.31697588 0.080663857</span>
<span class="r-out co"><span class="r-pr">#></span> k2 0.02957934 0.002868336 0.07581766 0.03260384 0.003425417</span>
<span class="r-out co"><span class="r-pr">#></span> g 0.44845068 0.526942415 0.66091967 0.65322767 0.342652880</span>
<span class="r-out co"><span class="r-pr">#></span> sigma 1.35690468 2.221302196 1.34169076 2.87159846 1.942067831</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span>, transformed <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> $SFO</span>
<span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span>
<span class="r-out co"><span class="r-pr">#></span> parent_0 88.522754 82.666782 86.854731 91.777931 82.148094</span>
<span class="r-out co"><span class="r-pr">#></span> log_k_parent -2.848234 -4.641025 -1.559232 -2.093737 -4.933090</span>
<span class="r-out co"><span class="r-pr">#></span> sigma 5.152745 7.040169 3.676964 6.466923 6.504577</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> $FOMC</span>
<span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span>
<span class="r-out co"><span class="r-pr">#></span> parent_0 95.5585751 92.6837649 90.7197870 98.38393897 94.848146</span>
<span class="r-out co"><span class="r-pr">#></span> log_alpha 0.2916741 -0.6996015 0.4941466 0.07181816 -1.271085</span>
<span class="r-out co"><span class="r-pr">#></span> log_beta 2.5675088 2.6493701 1.6108523 1.48095106 1.932278</span>
<span class="r-out co"><span class="r-pr">#></span> sigma 1.8476712 1.9167519 1.0660627 3.14605557 1.622278</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> $DFOP</span>
<span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span>
<span class="r-out co"><span class="r-pr">#></span> parent_0 96.5521366 91.0589716 90.3450949 98.1485882 94.3113237</span>
<span class="r-out co"><span class="r-pr">#></span> log_k1 -1.5161940 -3.1022764 -0.8859486 -1.1489296 -2.5174647</span>
<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.5206791 -5.8540232 -2.5794240 -3.4233253 -5.6765322</span>
<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.2069326 0.1078741 0.6673953 0.6332573 -0.6514943</span>
<span class="r-out co"><span class="r-pr">#></span> sigma 1.3569047 2.2213022 1.3416908 2.8715985 1.9420678</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></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> 2.0.7.</p>
</div>
</footer></div>
</body></html>
|
