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diff --git a/docs/reference/mhmkin.html b/docs/reference/mhmkin.html index 36003f7c..26bfd34b 100644 --- a/docs/reference/mhmkin.html +++ b/docs/reference/mhmkin.html @@ -1,83 +1,67 @@ <!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="The name of the methods expresses that (multiple) hierarchichal +<!-- 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>Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models — mhmkin • 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="Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models — mhmkin"><meta name="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."><title>Fit nonlinear mixed-effects models built from one or more kinetic -degradation models and one or more error models — mhmkin • 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="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 +mixed-effects model fitting functions."><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> +mixed-effects model fitting functions."></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>Fit nonlinear mixed-effects models built from one or more kinetic -degradation models and one or more error models</h1> + + <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="d-none name"><code>mhmkin.Rd</code></div> </div> @@ -91,53 +75,55 @@ mixed-effects model fitting functions.</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><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 class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mhmkin</span><span class="op">(</span><span class="va">objects</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for class 'mmkin'</span></span> +<span><span class="fu">mhmkin</span><span class="op">(</span><span class="va">objects</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for class 'list'</span></span> +<span><span class="fu">mhmkin</span><span class="op">(</span></span> +<span> <span class="va">objects</span>,</span> +<span> backend <span class="op">=</span> <span class="st">"saemix"</span>,</span> +<span> algorithm <span class="op">=</span> <span class="st">"saem"</span>,</span> +<span> no_random_effect <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> <span class="va">...</span>,</span> +<span> cores <span class="op">=</span> <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.info.html" class="external-link">Sys.info</a></span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="st">"sysname"</span><span class="op">]</span> <span class="op">==</span> <span class="st">"Windows"</span><span class="op">)</span> <span class="fl">1</span> <span class="kw">else</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span>,</span> +<span> cluster <span class="op">=</span> <span class="cn">NULL</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for class 'mhmkin'</span></span> +<span><span class="va">x</span><span class="op">[</span><span class="va">i</span>, <span class="va">j</span>, <span class="va">...</span>, drop <span class="op">=</span> <span class="cn">FALSE</span><span class="op">]</span></span> +<span></span> +<span><span class="co"># S3 method for class 'mhmkin'</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>, <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>objects</dt> + + +<dl><dt id="arg-objects">objects<a class="anchor" aria-label="anchor" href="#arg-objects"></a></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> +<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt> <dd><p>Further arguments that will be passed to the nonlinear mixed-effects model fitting function.</p></dd> -<dt>backend</dt> +<dt id="arg-backend">backend<a class="anchor" aria-label="anchor" href="#arg-backend"></a></dt> <dd><p>The backend to be used for fitting. Currently, only saemix is supported</p></dd> -<dt>algorithm</dt> +<dt id="arg-algorithm">algorithm<a class="anchor" aria-label="anchor" href="#arg-algorithm"></a></dt> <dd><p>The algorithm to be used for fitting (currently not used)</p></dd> -<dt>no_random_effect</dt> +<dt id="arg-no-random-effect">no_random_effect<a class="anchor" aria-label="anchor" href="#arg-no-random-effect"></a></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, @@ -148,7 +134,7 @@ 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> +<dt id="arg-cores">cores<a class="anchor" aria-label="anchor" href="#arg-cores"></a></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> @@ -157,38 +143,34 @@ by <code><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-l is 1.</p></dd> -<dt>cluster</dt> +<dt id="arg-cluster">cluster<a class="anchor" aria-label="anchor" href="#arg-cluster"></a></dt> <dd><p>A cluster as returned by makeCluster to be used for parallel execution.</p></dd> -<dt>x</dt> +<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt> <dd><p>An mhmkin object.</p></dd> -<dt>i</dt> +<dt id="arg-i">i<a class="anchor" aria-label="anchor" href="#arg-i"></a></dt> <dd><p>Row index selecting the fits for specific models</p></dd> -<dt>j</dt> +<dt id="arg-j">j<a class="anchor" aria-label="anchor" href="#arg-j"></a></dt> <dd><p>Column index selecting the fits to specific datasets</p></dd> -<dt>drop</dt> +<dt id="arg-drop">drop<a class="anchor" aria-label="anchor" href="#arg-drop"></a></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 class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></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 + <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 class="section level2"> @@ -282,23 +264,23 @@ attribute 'mhmkin'.</p> <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> |