<!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>Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models — mhmkin • 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="Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models — mhmkin"><meta property="og:description" content="The name of the methods expresses that (multiple) hierarchichal (also known as multilevel) multicompartment kinetic models are fitted. Our kinetic models are nonlinear, so we can use various nonlinear mixed-effects model fitting functions."><!-- 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-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</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> <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/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </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/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </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> <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> </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>Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mhmkin.R" class="external-link"><code>R/mhmkin.R</code></a></small> <div class="hidden name"><code>mhmkin.Rd</code></div> </div> <div class="ref-description"> <p>The name of the methods expresses that (<strong>m</strong>ultiple) <strong>h</strong>ierarchichal (also known as multilevel) <strong>m</strong>ulticompartment <strong>kin</strong>etic models are fitted. Our kinetic models are nonlinear, so we can use various nonlinear mixed-effects model fitting functions.</p> </div> <div id="ref-usage"> <div class="sourceCode"><pre><code>mhmkin(objects, ...) # S3 method for mmkin mhmkin(objects, ...) # S3 method for list mhmkin( objects, backend = "saemix", algorithm = "saem", no_random_effect = NULL, auto_ranef_threshold = 3, ..., cores = if (Sys.info()["sysname"] == "Windows") 1 else parallel::detectCores(), cluster = NULL ) # S3 method for mhmkin [(x, i, j, ..., drop = FALSE) # S3 method for mhmkin print(x, ...)</code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>objects</dt> <dd><p>A list of <a href="mmkin.html">mmkin</a> objects containing fits of the same degradation models to the same data, but using different error models. Alternatively, a single <a href="mmkin.html">mmkin</a> object containing fits of several degradation models to the same data</p></dd> <dt>...</dt> <dd><p>Further arguments that will be passed to the nonlinear mixed-effects model fitting function.</p></dd> <dt>backend</dt> <dd><p>The backend to be used for fitting. Currently, only saemix is supported</p></dd> <dt>algorithm</dt> <dd><p>The algorithm to be used for fitting (currently not used)</p></dd> <dt>no_random_effect</dt> <dd><p>Default is NULL and will be passed to <a href="saem.html">saem</a>. If you specify "auto", random effects are only included if the number of datasets in which the parameter passed the t-test is at least 'auto_ranef_threshold'. Beware that while this may make for convenient model reduction or even numerical stability of the algorithm, it will likely lead to underparameterised models.</p></dd> <dt>auto_ranef_threshold</dt> <dd><p>See 'no_random_effect.</p></dd> <dt>cores</dt> <dd><p>The number of cores to be used for multicore processing. This is only used when the <code>cluster</code> argument is <code>NULL</code>. On Windows machines, cores > 1 is not supported, you need to use the <code>cluster</code> argument to use multiple logical processors. Per default, all cores detected by <code><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">parallel::detectCores()</a></code> are used, except on Windows where the default is 1.</p></dd> <dt>cluster</dt> <dd><p>A cluster as returned by makeCluster to be used for parallel execution.</p></dd> <dt>x</dt> <dd><p>An mhmkin object.</p></dd> <dt>i</dt> <dd><p>Row index selecting the fits for specific models</p></dd> <dt>j</dt> <dd><p>Column index selecting the fits to specific datasets</p></dd> <dt>drop</dt> <dd><p>If FALSE, the method always returns an mhmkin object, otherwise either a list of fit objects or a single fit object.</p></dd> </dl></div> <div id="value"> <h2>Value</h2> <p>A two-dimensional <a href="https://rdrr.io/r/base/array.html" class="external-link">array</a> of fit objects and/or try-errors that can be indexed using the degradation model names for the first index (row index) and the error model names for the second index (column index), with class attribute 'mhmkin'.</p> <p>An object of class <code>mhmkin</code>.</p> </div> <div id="see-also"> <h2>See also</h2> <div class="dont-index"><p><code>[.mhmkin</code> for subsetting mhmkin objects</p></div> </div> <div id="author"> <h2>Author</h2> <p>Johannes Ranke</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> </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> 2.0.6.</p> </div> </footer></div> </body></html>