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diff --git a/docs/dev/reference/mhmkin.html b/docs/dev/reference/mhmkin.html deleted file mode 100644 index b41c11df..00000000 --- a/docs/dev/reference/mhmkin.html +++ /dev/null @@ -1,336 +0,0 @@ -<!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."><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"> - 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<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, - ..., - 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 a -character vector is supplied, it will be passed to all calls to <a href="saem.html">saem</a>, -which will exclude random effects for all matching parameters. Alternatively, -a list of character vectors or an object of class <a href="illparms.html">illparms.mhmkin</a> can be -specified. They have to have the same dimensions that the return object of -the current call will have, i.e. the number of rows must match the number -of degradation models in the mmkin object(s), and the number of columns must -match the number of error models used in the mmkin object(s).</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 inheriting from <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 id="ref-examples"> - <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> -<span class="r-in"><span><span class="co"># We start with separate evaluations of all the first six datasets with two</span></span></span> -<span class="r-in"><span><span class="co"># degradation models and two error models</span></span></span> -<span class="r-in"><span><span class="va">f_sep_const</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="op">)</span>, <span class="va">ds_fomc</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">6</span><span class="op">]</span>, cores <span class="op">=</span> <span class="fl">2</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="va">f_sep_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_sep_const</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="co"># The mhmkin function sets up hierarchical degradation models aka</span></span></span> -<span class="r-in"><span><span class="co"># nonlinear mixed-effects models for all four combinations, specifying</span></span></span> -<span class="r-in"><span><span class="co"># uncorrelated random effects for all degradation parameters</span></span></span> -<span class="r-in"><span><span class="va">f_saem_1</span> <span class="op"><-</span> <span class="fu">mhmkin</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">f_sep_const</span>, <span class="va">f_sep_tc</span><span class="op">)</span>, cores <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="fu"><a href="status.html">status</a></span><span class="op">(</span><span class="va">f_saem_1</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> error</span> -<span class="r-out co"><span class="r-pr">#></span> degradation const tc</span> -<span class="r-out co"><span class="r-pr">#></span> SFO OK OK</span> -<span class="r-out co"><span class="r-pr">#></span> FOMC OK OK</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> OK: Fit terminated successfully</span> -<span class="r-in"><span><span class="co"># The 'illparms' function shows that in all hierarchical fits, at least</span></span></span> -<span class="r-in"><span><span class="co"># one random effect is ill-defined (the confidence interval for the</span></span></span> -<span class="r-in"><span><span class="co"># random effect expressed as standard deviation includes zero)</span></span></span> -<span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_1</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> error</span> -<span class="r-out co"><span class="r-pr">#></span> degradation const tc </span> -<span class="r-out co"><span class="r-pr">#></span> SFO sd(parent_0) sd(parent_0) </span> -<span class="r-out co"><span class="r-pr">#></span> FOMC sd(log_beta) sd(parent_0), sd(log_beta)</span> -<span class="r-in"><span><span class="co"># Therefore we repeat the fits, excluding the ill-defined random effects</span></span></span> -<span class="r-in"><span><span class="va">f_saem_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_1</span>, no_random_effect <span class="op">=</span> <span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_1</span><span class="op">)</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="fu"><a href="status.html">status</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> error</span> -<span class="r-out co"><span class="r-pr">#></span> degradation const tc</span> -<span class="r-out co"><span class="r-pr">#></span> SFO OK OK</span> -<span class="r-out co"><span class="r-pr">#></span> FOMC OK OK</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> OK: Fit terminated successfully</span> -<span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> error</span> -<span class="r-out co"><span class="r-pr">#></span> degradation const tc</span> -<span class="r-out co"><span class="r-pr">#></span> SFO </span> -<span class="r-out co"><span class="r-pr">#></span> FOMC </span> -<span class="r-in"><span><span class="co"># Model comparisons show that FOMC with two-component error is preferable,</span></span></span> -<span class="r-in"><span><span class="co"># and confirms our reduction of the default parameter model</span></span></span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_1</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> Data: 95 observations of 1 variable(s) grouped in 6 datasets</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik</span> -<span class="r-out co"><span class="r-pr">#></span> SFO const 5 574.40 573.35 -282.20</span> -<span class="r-out co"><span class="r-pr">#></span> SFO tc 6 543.72 542.47 -265.86</span> -<span class="r-out co"><span class="r-pr">#></span> FOMC const 7 489.67 488.22 -237.84</span> -<span class="r-out co"><span class="r-pr">#></span> FOMC tc 8 406.11 404.44 -195.05</span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> Data: 95 observations of 1 variable(s) grouped in 6 datasets</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik</span> -<span class="r-out co"><span class="r-pr">#></span> SFO const 4 572.22 571.39 -282.11</span> -<span class="r-out co"><span class="r-pr">#></span> SFO tc 5 541.63 540.59 -265.81</span> -<span class="r-out co"><span class="r-pr">#></span> FOMC const 6 487.38 486.13 -237.69</span> -<span class="r-out co"><span class="r-pr">#></span> FOMC tc 6 402.12 400.88 -195.06</span> -<span class="r-in"><span><span class="co"># The convergence plot for the selected model looks fine</span></span></span> -<span class="r-in"><span><span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></span> -<span class="r-plt img"><img src="mhmkin-1.png" alt="" width="700" height="433"></span> -<span class="r-in"><span><span class="co"># The plot of predictions versus data shows that we have a pretty data-rich</span></span></span> -<span class="r-in"><span><span class="co"># situation with homogeneous distribution of residuals, because we used the</span></span></span> -<span class="r-in"><span><span class="co"># same degradation model, error model and parameter distribution model that</span></span></span> -<span class="r-in"><span><span class="co"># was used in the data generation.</span></span></span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></span> -<span class="r-plt img"><img src="mhmkin-2.png" alt="" width="700" height="433"></span> -<span class="r-in"><span><span class="co"># We can specify the same parameter model reductions manually</span></span></span> -<span class="r-in"><span><span class="va">no_ranef</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"parent_0"</span>, <span class="st">"log_beta"</span>, <span class="st">"parent_0"</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">"parent_0"</span>, <span class="st">"log_beta"</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/dim.html" class="external-link">dim</a></span><span class="op">(</span><span class="va">no_ranef</span><span class="op">)</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="fl">2</span>, <span class="fl">2</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="va">f_saem_2m</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_1</span>, no_random_effect <span class="op">=</span> <span class="va">no_ranef</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_2m</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> Data: 95 observations of 1 variable(s) grouped in 6 datasets</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik</span> -<span class="r-out co"><span class="r-pr">#></span> SFO const 4 572.22 571.39 -282.11</span> -<span class="r-out co"><span class="r-pr">#></span> SFO tc 5 541.63 540.59 -265.81</span> -<span class="r-out co"><span class="r-pr">#></span> FOMC const 6 487.38 486.13 -237.69</span> -<span class="r-out co"><span class="r-pr">#></span> FOMC tc 6 402.12 400.88 -195.06</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> - |