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diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html index 0e0412c6..4f124b07 100644 --- a/docs/reference/nlme.mmkin.html +++ b/docs/reference/nlme.mmkin.html @@ -1,78 +1,65 @@ <!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, shrink-to-fit=no"><meta name="description" content="This functions sets up a nonlinear mixed effects model for an mmkin row +<!-- 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"><title>Create an nlme model for an mmkin row object — nlme.mmkin • 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-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create an nlme model for an mmkin row object — nlme.mmkin"><meta name="description" content="This functions sets up a nonlinear mixed effects model for an mmkin row object. 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An mmkin row object is essentially a list of mkinfit objects that -have been obtained by fitting the same model to a list of datasets."><!-- 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> +have been obtained by fitting the same model to a list of datasets."></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-default navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="default" aria-label="Site navigation"><div class="container"> + <a class="navbar-brand me-2" href="../index.html">mkin</a> - 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+ </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>Create an nlme model for an mmkin row object</h1> + + <h1>Create an nlme model for an mmkin row object</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/nlme.mmkin.R" class="external-link"><code>R/nlme.mmkin.R</code></a></small> <div class="d-none name"><code>nlme.mmkin.Rd</code></div> </div> @@ -85,7 +72,7 @@ have been obtained by fitting the same model to a list of datasets.</p> <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="co"># S3 method for mmkin</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for class 'mmkin'</span></span> <span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span></span> <span> <span class="va">model</span>,</span> <span> data <span class="op">=</span> <span class="st">"auto"</span>,</span> @@ -104,96 +91,96 @@ have been obtained by fitting the same model to a list of datasets.</p> <span> verbose <span class="op">=</span> <span class="cn">FALSE</span></span> <span><span class="op">)</span></span> <span></span> -<span><span class="co"># S3 method for nlme.mmkin</span></span> +<span><span class="co"># S3 method for class 'nlme.mmkin'</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> -<span><span class="co"># S3 method for nlme.mmkin</span></span> +<span><span class="co"># S3 method for class 'nlme.mmkin'</span></span> <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">object</span>, <span class="va">...</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>model</dt> + + +<dl><dt id="arg-model">model<a class="anchor" aria-label="anchor" href="#arg-model"></a></dt> <dd><p>An <a href="mmkin.html">mmkin</a> row object.</p></dd> -<dt>data</dt> +<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt> <dd><p>Ignored, data are taken from the mmkin model</p></dd> -<dt>fixed</dt> +<dt id="arg-fixed">fixed<a class="anchor" aria-label="anchor" href="#arg-fixed"></a></dt> <dd><p>Ignored, all degradation parameters fitted in the mmkin model are used as fixed parameters</p></dd> -<dt>random</dt> +<dt id="arg-random">random<a class="anchor" aria-label="anchor" href="#arg-random"></a></dt> <dd><p>If not specified, no correlations between random effects are set up for the optimised degradation model parameters. This is achieved by using the <a href="https://rdrr.io/pkg/nlme/man/pdDiag.html" class="external-link">nlme::pdDiag</a> method.</p></dd> -<dt>groups</dt> +<dt id="arg-groups">groups<a class="anchor" aria-label="anchor" href="#arg-groups"></a></dt> <dd><p>See the documentation of nlme</p></dd> -<dt>start</dt> +<dt id="arg-start">start<a class="anchor" aria-label="anchor" href="#arg-start"></a></dt> <dd><p>If not specified, mean values of the fitted degradation parameters taken from the mmkin object are used</p></dd> -<dt>correlation</dt> +<dt id="arg-correlation">correlation<a class="anchor" aria-label="anchor" href="#arg-correlation"></a></dt> <dd><p>See the documentation of nlme</p></dd> -<dt>weights</dt> +<dt id="arg-weights">weights<a class="anchor" aria-label="anchor" href="#arg-weights"></a></dt> <dd><p>passed to nlme</p></dd> -<dt>subset</dt> +<dt id="arg-subset">subset<a class="anchor" aria-label="anchor" href="#arg-subset"></a></dt> <dd><p>passed to nlme</p></dd> -<dt>method</dt> +<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt> <dd><p>passed to nlme</p></dd> -<dt>na.action</dt> +<dt id="arg-na-action">na.action<a class="anchor" aria-label="anchor" href="#arg-na-action"></a></dt> <dd><p>passed to nlme</p></dd> -<dt>naPattern</dt> +<dt id="arg-napattern">naPattern<a class="anchor" aria-label="anchor" href="#arg-napattern"></a></dt> <dd><p>passed to nlme</p></dd> -<dt>control</dt> +<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a></dt> <dd><p>passed to nlme</p></dd> -<dt>verbose</dt> +<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt> <dd><p>passed to nlme</p></dd> -<dt>x</dt> +<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt> <dd><p>An nlme.mmkin object to print</p></dd> -<dt>digits</dt> +<dt id="arg-digits">digits<a class="anchor" aria-label="anchor" href="#arg-digits"></a></dt> <dd><p>Number of digits to use for printing</p></dd> -<dt>...</dt> +<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt> <dd><p>Update specifications passed to update.nlme</p></dd> -<dt>object</dt> +<dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt> <dd><p>An nlme.mmkin object to update</p></dd> </dl></div> <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - - -<p>Upon success, a fitted 'nlme.mmkin' object, which is an nlme object + <p>Upon success, a fitted 'nlme.mmkin' object, which is an nlme object with additional elements. It also inherits from 'mixed.mmkin'.</p> </div> <div class="section level2"> @@ -406,23 +393,23 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <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> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> </div> </footer></div> - - + + </body></html> |