diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2022-03-02 18:03:54 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2022-03-02 18:03:54 +0100 |
| commit | 2bb59c88d49b193f278916ad9cc4de83c0de9604 (patch) | |
| tree | f286bba254d7c5f2d32eeb2b11f6148938b0e1e1 /docs/reference/nlme.mmkin.html | |
| parent | 351248d07f810ccb6c497633a02cd48ee35526e6 (diff) | |
Make tests more platform independent, update docs
Diffstat (limited to 'docs/reference/nlme.mmkin.html')
| -rw-r--r-- | docs/reference/nlme.mmkin.html | 694 |
1 files changed, 305 insertions, 389 deletions
diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html index b3052605..56770856 100644 --- a/docs/reference/nlme.mmkin.html +++ b/docs/reference/nlme.mmkin.html @@ -1,69 +1,14 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <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>Create an nlme model for an mmkin row object — nlme.mmkin • 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="Create an nlme model for an mmkin row object — nlme.mmkin" /> -<meta property="og: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=1.0"><title>Create an nlme model for an mmkin row object — nlme.mmkin • 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="Create an nlme model for an mmkin row object — nlme.mmkin"><meta property="og:description" content="This functions sets up a nonlinear mixed effects model for an mmkin row object. 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]> +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]--> - +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - </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"> + <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"> @@ -74,13 +19,12 @@ have been obtained by fitting the same model to a list of datasets." /> </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">1.0.5</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> @@ -89,8 +33,7 @@ have been obtained by fitting the same model to a list of datasets." /> <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -100,6 +43,9 @@ have been obtained by fitting the same model to a list of datasets." /> <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/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> @@ -114,34 +60,27 @@ have been obtained by fitting the same model to a list of datasets." /> <li> <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> </li> - </ul> -</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/"> + </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 --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Create an nlme model for an mmkin row object</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/nlme.mmkin.R'><code>R/nlme.mmkin.R</code></a></small> + <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="hidden name"><code>nlme.mmkin.Rd</code></div> </div> @@ -151,339 +90,316 @@ object. 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.</p> </div> - <pre class="usage"><span class='co'># S3 method for mmkin</span> -<span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span> - <span class='va'>model</span>, - data <span class='op'>=</span> <span class='st'>"auto"</span>, - fixed <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>as.list</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='fu'><a href='nlme_function.html'>mean_degparms</a></span><span class='op'>(</span><span class='va'>model</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>el</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/eval.html'>eval</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/parse.html'>parse</a></span><span class='op'>(</span>text <span class='op'>=</span> - <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='va'>el</span>, <span class='fl'>1</span>, sep <span class='op'>=</span> <span class='st'>"~"</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>, - random <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/pdDiag.html'>pdDiag</a></span><span class='op'>(</span><span class='va'>fixed</span><span class='op'>)</span>, - <span class='va'>groups</span>, - start <span class='op'>=</span> <span class='fu'><a href='nlme_function.html'>mean_degparms</a></span><span class='op'>(</span><span class='va'>model</span>, random <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>, - correlation <span class='op'>=</span> <span class='cn'>NULL</span>, - weights <span class='op'>=</span> <span class='cn'>NULL</span>, - <span class='va'>subset</span>, - method <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"ML"</span>, <span class='st'>"REML"</span><span class='op'>)</span>, - na.action <span class='op'>=</span> <span class='va'>na.fail</span>, - <span class='va'>naPattern</span>, - control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='op'>)</span>, - verbose <span class='op'>=</span> <span class='cn'>FALSE</span> -<span class='op'>)</span> - -<span class='co'># S3 method for nlme.mmkin</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>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'>max</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>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 class='co'># S3 method for nlme.mmkin</span> -<span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>model</th> - <td><p>An <a href='mmkin.html'>mmkin</a> row object.</p></td> - </tr> - <tr> - <th>data</th> - <td><p>Ignored, data are taken from the mmkin model</p></td> - </tr> - <tr> - <th>fixed</th> - <td><p>Ignored, all degradation parameters fitted in the -mmkin model are used as fixed parameters</p></td> - </tr> - <tr> - <th>random</th> - <td><p>If not specified, correlated random effects are set up -for all optimised degradation model parameters using the log-Cholesky -parameterization <a href='https://rdrr.io/pkg/nlme/man/pdLogChol.html'>nlme::pdLogChol</a> that is also the default of -the generic <a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a> method.</p></td> - </tr> - <tr> - <th>groups</th> - <td><p>See the documentation of nlme</p></td> - </tr> - <tr> - <th>start</th> - <td><p>If not specified, mean values of the fitted degradation -parameters taken from the mmkin object are used</p></td> - </tr> - <tr> - <th>correlation</th> - <td><p>See the documentation of nlme</p></td> - </tr> - <tr> - <th>weights</th> - <td><p>passed to nlme</p></td> - </tr> - <tr> - <th>subset</th> - <td><p>passed to nlme</p></td> - </tr> - <tr> - <th>method</th> - <td><p>passed to nlme</p></td> - </tr> - <tr> - <th>na.action</th> - <td><p>passed to nlme</p></td> - </tr> - <tr> - <th>naPattern</th> - <td><p>passed to nlme</p></td> - </tr> - <tr> - <th>control</th> - <td><p>passed to nlme</p></td> - </tr> - <tr> - <th>verbose</th> - <td><p>passed to nlme</p></td> - </tr> - <tr> - <th>x</th> - <td><p>An nlme.mmkin object to print</p></td> - </tr> - <tr> - <th>digits</th> - <td><p>Number of digits to use for printing</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Update specifications passed to update.nlme</p></td> - </tr> - <tr> - <th>object</th> - <td><p>An nlme.mmkin object to update</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for mmkin</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 class="va">model</span>, + data <span class="op">=</span> <span class="st">"auto"</span>, + fixed <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="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">as.list</a></span><span class="op">(</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="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">model</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>, <span class="kw">function</span><span class="op">(</span><span class="va">el</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/eval.html" class="external-link">eval</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/parse.html" class="external-link">parse</a></span><span class="op">(</span>text <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="va">el</span>, <span class="fl">1</span>, sep <span class="op">=</span> <span class="st">"~"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>, + random <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/pdDiag.html" class="external-link">pdDiag</a></span><span class="op">(</span><span class="va">fixed</span><span class="op">)</span>, + <span class="va">groups</span>, + start <span class="op">=</span> <span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">model</span>, random <span class="op">=</span> <span class="cn">TRUE</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, + correlation <span class="op">=</span> <span class="cn">NULL</span>, + weights <span class="op">=</span> <span class="cn">NULL</span>, + <span class="va">subset</span>, + method <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">"ML"</span>, <span class="st">"REML"</span><span class="op">)</span>, + na.action <span class="op">=</span> <span class="va">na.fail</span>, + <span class="va">naPattern</span>, + control <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="op">)</span>, + verbose <span class="op">=</span> <span class="cn">FALSE</span> +<span class="op">)</span> + +<span class="co"># S3 method for nlme.mmkin</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 class="co"># S3 method for nlme.mmkin</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></code></pre></div> + </div> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>model</dt> +<dd><p>An <a href="mmkin.html">mmkin</a> row object.</p></dd> +<dt>data</dt> +<dd><p>Ignored, data are taken from the mmkin model</p></dd> +<dt>fixed</dt> +<dd><p>Ignored, all degradation parameters fitted in the +mmkin model are used as fixed parameters</p></dd> +<dt>random</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> +<dd><p>See the documentation of nlme</p></dd> +<dt>start</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> +<dd><p>See the documentation of nlme</p></dd> +<dt>weights</dt> +<dd><p>passed to nlme</p></dd> +<dt>subset</dt> +<dd><p>passed to nlme</p></dd> +<dt>method</dt> +<dd><p>passed to nlme</p></dd> +<dt>na.action</dt> +<dd><p>passed to nlme</p></dd> +<dt>naPattern</dt> +<dd><p>passed to nlme</p></dd> +<dt>control</dt> +<dd><p>passed to nlme</p></dd> +<dt>verbose</dt> +<dd><p>passed to nlme</p></dd> +<dt>x</dt> +<dd><p>An nlme.mmkin object to print</p></dd> +<dt>digits</dt> +<dd><p>Number of digits to use for printing</p></dd> +<dt>...</dt> +<dd><p>Update specifications passed to update.nlme</p></dd> +<dt>object</dt> +<dd><p>An nlme.mmkin object to update</p></dd> +</dl></div> + <div id="value"> + <h2>Value</h2> <p>Upon success, a fitted 'nlme.mmkin' object, which is an nlme object with additional elements. It also inherits from 'mixed.mmkin'.</p> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - + </div> + <div id="details"> + <h2>Details</h2> <p>Note that the convergence of the nlme algorithms depends on the quality of the data. In degradation kinetics, we often only have few datasets (e.g. data for few soils) and complicated degradation models, which may make it impossible to obtain convergence with nlme.</p> - <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> - - <p>As the object inherits from <a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme::nlme</a>, there is a wealth of + </div> + <div id="note"> + <h2>Note</h2> + <p>As the object inherits from <a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme::nlme</a>, there is a wealth of methods that will automatically work on 'nlme.mmkin' objects, such as -<code><a href='https://rdrr.io/pkg/nlme/man/intervals.html'>nlme::intervals()</a></code>, <code><a href='https://rdrr.io/pkg/nlme/man/anova.lme.html'>nlme::anova.lme()</a></code> and <code><a href='https://rdrr.io/pkg/nlme/man/coef.lme.html'>nlme::coef.lme()</a></code>.</p> - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <div class='dont-index'><p><code><a href='nlme_function.html'>nlme_function()</a></code>, <a href='plot.mixed.mmkin.html'>plot.mixed.mmkin</a>, <a href='summary.nlme.mmkin.html'>summary.nlme.mmkin</a></p></div> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='va'>ds</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>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 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'>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'>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='va'>name</span> <span class='op'>==</span> <span class='st'>"parent"</span><span class='op'>)</span><span class='op'>)</span> -<span class='va'>f</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'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</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 class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://svn.r-project.org/R-packages/trunk/nlme/'>nlme</a></span><span class='op'>)</span> -<span class='va'>f_nlme_sfo</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span> - -<span class='co'># \dontrun{</span> - - <span class='va'>f_nlme_dfop</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span> - <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo</span>, <span class='va'>f_nlme_dfop</span><span class='op'>)</span> -</div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio p-value -#> f_nlme_sfo 1 5 625.0539 637.5529 -307.5269 -#> f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9269 <.0001</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span> -</div><div class='output co'>#> Kinetic nonlinear mixed-effects model fit by maximum likelihood -#> -#> Structural model: -#> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * -#> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) -#> * parent -#> -#> Data: -#> 90 observations of 1 variable(s) grouped in 5 datasets -#> -#> Log-likelihood: -238.6 -#> -#> Fixed effects: -#> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) -#> parent_0 log_k1 log_k2 g_qlogis -#> 94.1702 -1.8002 -4.1474 0.0324 -#> -#> Random effects: -#> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) -#> Level: ds -#> Structure: Diagonal -#> parent_0 log_k1 log_k2 g_qlogis Residual -#> StdDev: 2.488 0.8447 1.33 0.4652 2.321 -#> </div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span> -</div><div class='img'><img src='nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span> -</div><div class='output co'>#> $distimes -#> DT50 DT90 DT50back DT50_k1 DT50_k2 -#> parent 10.79857 100.7937 30.34193 4.193938 43.85443 -#> </div><div class='input'> - <span class='va'>ds_2</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>, - <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>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='va'>m_sfo_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"A1"</span><span class='op'>)</span>, - A1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"min"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> - <span class='va'>m_sfo_sfo_ff</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"A1"</span><span class='op'>)</span>, - A1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> - <span class='va'>m_dfop_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='st'>"A1"</span><span class='op'>)</span>, - A1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> - - <span class='va'>f_2</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/list.html'>list</a></span><span class='op'>(</span><span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>m_sfo_sfo</span>, - <span class='st'>"SFO-SFO-ff"</span> <span class='op'>=</span> <span class='va'>m_sfo_sfo_ff</span>, - <span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>m_dfop_sfo</span><span class='op'>)</span>, - <span class='va'>ds_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> - - <span class='va'>f_nlme_sfo_sfo</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> - <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span> -</div><div class='img'><img src='nlme.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'> - <span class='co'># With formation fractions this does not coverge with defaults</span> - <span class='co'># f_nlme_sfo_sfo_ff <- nlme(f_2["SFO-SFO-ff", ])</span> - <span class='co'>#plot(f_nlme_sfo_sfo_ff)</span> - - <span class='co'># For the following, we need to increase pnlsMaxIter and the tolerance</span> - <span class='co'># to get convergence</span> - <span class='va'>f_nlme_dfop_sfo</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>, - control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>5e-4</span><span class='op'>)</span><span class='op'>)</span> - - <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span><span class='op'>)</span> -</div><div class='img'><img src='nlme.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'> - <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span> -</div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio p-value -#> f_nlme_dfop_sfo 1 13 843.8548 884.6201 -408.9274 -#> f_nlme_sfo_sfo 2 9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3273 <.0001</div><div class='input'> - <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span> -</div><div class='output co'>#> $ff -#> parent_sink parent_A1 A1_sink -#> 0.5912432 0.4087568 1.0000000 -#> -#> $distimes -#> DT50 DT90 -#> parent 19.13518 63.5657 -#> A1 66.02155 219.3189 -#> </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span><span class='op'>)</span> -</div><div class='output co'>#> $ff -#> parent_A1 parent_sink -#> 0.2768575 0.7231425 -#> -#> $distimes -#> DT50 DT90 DT50back DT50_k1 DT50_k2 -#> parent 11.07091 104.6320 31.49737 4.462384 46.20825 -#> A1 162.30492 539.1653 NA NA NA -#> </div><div class='input'> - <span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='fu'>findFunction</span><span class='op'>(</span><span class='st'>"varConstProp"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>></span> <span class='fl'>0</span><span class='op'>)</span> <span class='op'>{</span> <span class='co'># tc error model for nlme available</span> - <span class='co'># Attempts to fit metabolite kinetics with the tc error model are possible,</span> - <span class='co'># but need tweeking of control values and sometimes do not converge</span> - - <span class='va'>f_tc</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'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</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>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> - <span class='va'>f_nlme_sfo_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_tc</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span> - <span class='va'>f_nlme_dfop_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_tc</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span> - <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo</span>, <span class='va'>f_nlme_sfo_tc</span>, <span class='va'>f_nlme_dfop</span>, <span class='va'>f_nlme_dfop_tc</span><span class='op'>)</span> - <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_tc</span><span class='op'>)</span> - <span class='op'>}</span> -</div><div class='output co'>#> Kinetic nonlinear mixed-effects model fit by maximum likelihood -#> -#> Structural model: -#> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * -#> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) -#> * parent -#> -#> Data: -#> 90 observations of 1 variable(s) grouped in 5 datasets -#> -#> Log-likelihood: -238.4 -#> -#> Fixed effects: -#> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) -#> parent_0 log_k1 log_k2 g_qlogis -#> 94.04774 -1.82340 -4.16716 0.05686 -#> -#> Random effects: -#> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) -#> Level: ds -#> Structure: Diagonal -#> parent_0 log_k1 log_k2 g_qlogis Residual -#> StdDev: 2.474 0.85 1.337 0.4659 1 -#> -#> Variance function: -#> Structure: Constant plus proportion of variance covariate -#> Formula: ~fitted(.) -#> Parameter estimates: -#> const prop -#> 2.23223147 0.01262395 </div><div class='input'> - <span class='va'>f_2_obs</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_2</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span><span class='op'>)</span> - <span class='va'>f_nlme_sfo_sfo_obs</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2_obs</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> - <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo_obs</span><span class='op'>)</span> -</div><div class='output co'>#> Kinetic nonlinear mixed-effects model fit by maximum likelihood -#> -#> Structural model: -#> d_parent/dt = - k_parent_sink * parent - k_parent_A1 * parent -#> d_A1/dt = + k_parent_A1 * parent - k_A1_sink * A1 -#> -#> Data: -#> 170 observations of 2 variable(s) grouped in 5 datasets -#> -#> Log-likelihood: -473 -#> -#> Fixed effects: -#> list(parent_0 ~ 1, log_k_parent_sink ~ 1, log_k_parent_A1 ~ 1, log_k_A1_sink ~ 1) -#> parent_0 log_k_parent_sink log_k_parent_A1 log_k_A1_sink -#> 87.976 -3.670 -4.164 -4.645 -#> -#> Random effects: -#> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1, log_k_parent_A1 ~ 1, log_k_A1_sink ~ 1) -#> Level: ds -#> Structure: Diagonal -#> parent_0 log_k_parent_sink log_k_parent_A1 log_k_A1_sink Residual -#> StdDev: 3.992 1.777 1.055 0.4821 6.483 -#> -#> Variance function: -#> Structure: Different standard deviations per stratum -#> Formula: ~1 | name -#> Parameter estimates: -#> parent A1 -#> 1.0000000 0.2049995 </div><div class='input'> <span class='va'>f_nlme_dfop_sfo_obs</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2_obs</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>, - control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>5e-4</span><span class='op'>)</span><span class='op'>)</span> - - <span class='va'>f_2_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_2</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> - <span class='co'># f_nlme_sfo_sfo_tc <- nlme(f_2_tc["SFO-SFO", ]) # No convergence with 50 iterations</span> - <span class='co'># f_nlme_dfop_sfo_tc <- nlme(f_2_tc["DFOP-SFO", ],</span> - <span class='co'># control = list(pnlsMaxIter = 120, tolerance = 5e-4)) # Error in X[, fmap[[nm]]] <- gradnm</span> +<code><a href="https://rdrr.io/pkg/nlme/man/intervals.html" class="external-link">nlme::intervals()</a></code>, <code><a href="https://rdrr.io/pkg/nlme/man/anova.lme.html" class="external-link">nlme::anova.lme()</a></code> and <code><a href="https://rdrr.io/pkg/nlme/man/coef.lme.html" class="external-link">nlme::coef.lme()</a></code>.</p> + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><code><a href="nlme.html">nlme_function()</a></code>, <a href="plot.mixed.mmkin.html">plot.mixed.mmkin</a>, <a href="summary.nlme.mmkin.html">summary.nlme.mmkin</a></p></div> + </div> - <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='va'>f_nlme_dfop_sfo_obs</span><span class='op'>)</span> -</div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio -#> f_nlme_dfop_sfo 1 13 843.8548 884.6201 -408.9274 -#> f_nlme_dfop_sfo_obs 2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32093 -#> p-value -#> f_nlme_dfop_sfo -#> f_nlme_dfop_sfo_obs <.0001</div><div class='input'> -<span class='co'># }</span> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><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 class="r-in"> <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="va">name</span> <span class="op">==</span> <span class="st">"parent"</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span class="va">f</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">"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 class="r-in"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span> +<span class="r-in"><span class="va">f_nlme_sfo</span> <span class="op"><-</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 class="va">f</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span></span> +<span class="r-in"></span> +<span class="r-in"><span class="co"># \dontrun{</span></span> +<span class="r-in"></span> +<span class="r-in"> <span class="va">f_nlme_dfop</span> <span class="op"><-</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 class="va">f</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span></span> +<span class="r-in"> <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_nlme_sfo</span>, <span class="va">f_nlme_dfop</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> Model df AIC BIC logLik Test L.Ratio p-value</span> +<span class="r-out co"><span class="r-pr">#></span> f_nlme_sfo 1 5 625.0539 637.5529 -307.5269 </span> +<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9269 <.0001</span> +<span class="r-in"> <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">f_nlme_dfop</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> Kinetic nonlinear mixed-effects model fit by maximum likelihood</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Structural model:</span> +<span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> +<span class="r-out co"><span class="r-pr">#></span> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))</span> +<span class="r-out co"><span class="r-pr">#></span> * parent</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Data:</span> +<span class="r-out co"><span class="r-pr">#></span> 90 observations of 1 variable(s) grouped in 5 datasets</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Log-likelihood: -238.6</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Fixed effects:</span> +<span class="r-out co"><span class="r-pr">#></span> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) </span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k1 log_k2 g_qlogis </span> +<span class="r-out co"><span class="r-pr">#></span> 94.1702 -1.8002 -4.1474 0.0324 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Random effects:</span> +<span class="r-out co"><span class="r-pr">#></span> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)</span> +<span class="r-out co"><span class="r-pr">#></span> Level: ds</span> +<span class="r-out co"><span class="r-pr">#></span> Structure: Diagonal</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k1 log_k2 g_qlogis Residual</span> +<span class="r-out co"><span class="r-pr">#></span> StdDev: 2.488 0.8447 1.33 0.4652 2.321</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"> <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_nlme_dfop</span><span class="op">)</span></span> +<span class="r-plt img"><img src="nlme.mmkin-1.png" alt="" width="700" height="433"></span> +<span class="r-in"> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">f_nlme_dfop</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> $distimes</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back DT50_k1 DT50_k2</span> +<span class="r-out co"><span class="r-pr">#></span> parent 10.79857 100.7937 30.34193 4.193938 43.85443</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"></span> +<span class="r-in"> <span class="va">ds_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span> +<span class="r-in"> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="va">x</span><span class="op">$</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> +<span class="r-in"> <span class="va">m_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span> +<span class="r-in"> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"min"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"> <span class="va">m_sfo_sfo_ff</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span> +<span class="r-in"> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"> <span class="va">m_dfop_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span> +<span class="r-in"> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"></span> +<span class="r-in"> <span class="va">f_2</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/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"SFO-SFO"</span> <span class="op">=</span> <span class="va">m_sfo_sfo</span>,</span> +<span class="r-in"> <span class="st">"SFO-SFO-ff"</span> <span class="op">=</span> <span class="va">m_sfo_sfo_ff</span>,</span> +<span class="r-in"> <span class="st">"DFOP-SFO"</span> <span class="op">=</span> <span class="va">m_dfop_sfo</span><span class="op">)</span>,</span> +<span class="r-in"> <span class="va">ds_2</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"></span> +<span class="r-in"> <span class="va">f_nlme_sfo_sfo</span> <span class="op"><-</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 class="va">f_2</span><span class="op">[</span><span class="st">"SFO-SFO"</span>, <span class="op">]</span><span class="op">)</span></span> +<span class="r-in"> <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_nlme_sfo_sfo</span><span class="op">)</span></span> +<span class="r-plt img"><img src="nlme.mmkin-2.png" alt="" width="700" height="433"></span> +<span class="r-in"></span> +<span class="r-in"> <span class="co"># With formation fractions this does not coverge with defaults</span></span> +<span class="r-in"> <span class="co"># f_nlme_sfo_sfo_ff <- nlme(f_2["SFO-SFO-ff", ])</span></span> +<span class="r-in"> <span class="co">#plot(f_nlme_sfo_sfo_ff)</span></span> +<span class="r-in"></span> +<span class="r-in"> <span class="co"># For the following, we need to increase pnlsMaxIter and the tolerance</span></span> +<span class="r-in"> <span class="co"># to get convergence</span></span> +<span class="r-in"> <span class="va">f_nlme_dfop_sfo</span> <span class="op"><-</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 class="va">f_2</span><span class="op">[</span><span class="st">"DFOP-SFO"</span>, <span class="op">]</span>,</span> +<span class="r-in"> control <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>pnlsMaxIter <span class="op">=</span> <span class="fl">120</span>, tolerance <span class="op">=</span> <span class="fl">5e-4</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"></span> +<span class="r-in"> <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_nlme_dfop_sfo</span><span class="op">)</span></span> +<span class="r-plt img"><img src="nlme.mmkin-3.png" alt="" width="700" height="433"></span> +<span class="r-in"></span> +<span class="r-in"> <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_nlme_dfop_sfo</span>, <span class="va">f_nlme_sfo_sfo</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> Model df AIC BIC logLik Test L.Ratio p-value</span> +<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 </span> +<span class="r-out co"><span class="r-pr">#></span> f_nlme_sfo_sfo 2 9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3274 <.0001</span> +<span class="r-in"></span> +<span class="r-in"> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">f_nlme_sfo_sfo</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> $ff</span> +<span class="r-out co"><span class="r-pr">#></span> parent_sink parent_A1 A1_sink </span> +<span class="r-out co"><span class="r-pr">#></span> 0.5912432 0.4087568 1.0000000 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $distimes</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> +<span class="r-out co"><span class="r-pr">#></span> parent 19.13518 63.5657</span> +<span class="r-out co"><span class="r-pr">#></span> A1 66.02155 219.3189</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">f_nlme_dfop_sfo</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> $ff</span> +<span class="r-out co"><span class="r-pr">#></span> parent_A1 parent_sink </span> +<span class="r-out co"><span class="r-pr">#></span> 0.2768574 0.7231426 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $distimes</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back DT50_k1 DT50_k2</span> +<span class="r-out co"><span class="r-pr">#></span> parent 11.07091 104.6320 31.49737 4.462383 46.20825</span> +<span class="r-out co"><span class="r-pr">#></span> A1 162.30519 539.1662 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"></span> +<span class="r-in"> <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="fu">findFunction</span><span class="op">(</span><span class="st">"varConstProp"</span><span class="op">)</span><span class="op">)</span> <span class="op">></span> <span class="fl">0</span><span class="op">)</span> <span class="op">{</span> <span class="co"># tc error model for nlme available</span></span> +<span class="r-in"> <span class="co"># Attempts to fit metabolite kinetics with the tc error model are possible,</span></span> +<span class="r-in"> <span class="co"># but need tweeking of control values and sometimes do not converge</span></span> +<span class="r-in"></span> +<span class="r-in"> <span class="va">f_tc</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">"DFOP"</span><span class="op">)</span>, <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> +<span class="r-in"> <span class="va">f_nlme_sfo_tc</span> <span class="op"><-</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 class="va">f_tc</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span></span> +<span class="r-in"> <span class="va">f_nlme_dfop_tc</span> <span class="op"><-</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 class="va">f_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span></span> +<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_nlme_sfo</span>, <span class="va">f_nlme_sfo_tc</span>, <span class="va">f_nlme_dfop</span>, <span class="va">f_nlme_dfop_tc</span><span class="op">)</span></span> +<span class="r-in"> <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">f_nlme_dfop_tc</span><span class="op">)</span></span> +<span class="r-in"> <span class="op">}</span></span> +<span class="r-out co"><span class="r-pr">#></span> Kinetic nonlinear mixed-effects model fit by maximum likelihood</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Structural model:</span> +<span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> +<span class="r-out co"><span class="r-pr">#></span> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))</span> +<span class="r-out co"><span class="r-pr">#></span> * parent</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Data:</span> +<span class="r-out co"><span class="r-pr">#></span> 90 observations of 1 variable(s) grouped in 5 datasets</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Log-likelihood: -238.4</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Fixed effects:</span> +<span class="r-out co"><span class="r-pr">#></span> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) </span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k1 log_k2 g_qlogis </span> +<span class="r-out co"><span class="r-pr">#></span> 94.04774 -1.82340 -4.16716 0.05686 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Random effects:</span> +<span class="r-out co"><span class="r-pr">#></span> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)</span> +<span class="r-out co"><span class="r-pr">#></span> Level: ds</span> +<span class="r-out co"><span class="r-pr">#></span> Structure: Diagonal</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k1 log_k2 g_qlogis Residual</span> +<span class="r-out co"><span class="r-pr">#></span> StdDev: 2.474 0.85 1.337 0.4659 1</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Variance function:</span> +<span class="r-out co"><span class="r-pr">#></span> Structure: Constant plus proportion of variance covariate</span> +<span class="r-out co"><span class="r-pr">#></span> Formula: ~fitted(.) </span> +<span class="r-out co"><span class="r-pr">#></span> Parameter estimates:</span> +<span class="r-out co"><span class="r-pr">#></span> const prop </span> +<span class="r-out co"><span class="r-pr">#></span> 2.23223147 0.01262395 </span> +<span class="r-in"></span> +<span class="r-in"> <span class="va">f_2_obs</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_2</span>, error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span></span> +<span class="r-in"> <span class="va">f_nlme_sfo_sfo_obs</span> <span class="op"><-</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 class="va">f_2_obs</span><span class="op">[</span><span class="st">"SFO-SFO"</span>, <span class="op">]</span><span class="op">)</span></span> +<span class="r-in"> <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">f_nlme_sfo_sfo_obs</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> Kinetic nonlinear mixed-effects model fit by maximum likelihood</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Structural model:</span> +<span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent_sink * parent - k_parent_A1 * parent</span> +<span class="r-out co"><span class="r-pr">#></span> d_A1/dt = + k_parent_A1 * parent - k_A1_sink * A1</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Data:</span> +<span class="r-out co"><span class="r-pr">#></span> 170 observations of 2 variable(s) grouped in 5 datasets</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Log-likelihood: -473</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Fixed effects:</span> +<span class="r-out co"><span class="r-pr">#></span> list(parent_0 ~ 1, log_k_parent_sink ~ 1, log_k_parent_A1 ~ 1, log_k_A1_sink ~ 1) </span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent_sink log_k_parent_A1 log_k_A1_sink </span> +<span class="r-out co"><span class="r-pr">#></span> 87.976 -3.670 -4.164 -4.645 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Random effects:</span> +<span class="r-out co"><span class="r-pr">#></span> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1, log_k_parent_A1 ~ 1, log_k_A1_sink ~ 1)</span> +<span class="r-out co"><span class="r-pr">#></span> Level: ds</span> +<span class="r-out co"><span class="r-pr">#></span> Structure: Diagonal</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent_sink log_k_parent_A1 log_k_A1_sink Residual</span> +<span class="r-out co"><span class="r-pr">#></span> StdDev: 3.992 1.777 1.055 0.4821 6.483</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Variance function:</span> +<span class="r-out co"><span class="r-pr">#></span> Structure: Different standard deviations per stratum</span> +<span class="r-out co"><span class="r-pr">#></span> Formula: ~1 | name </span> +<span class="r-out co"><span class="r-pr">#></span> Parameter estimates:</span> +<span class="r-out co"><span class="r-pr">#></span> parent A1 </span> +<span class="r-out co"><span class="r-pr">#></span> 1.0000000 0.2049995 </span> +<span class="r-in"> <span class="va">f_nlme_dfop_sfo_obs</span> <span class="op"><-</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 class="va">f_2_obs</span><span class="op">[</span><span class="st">"DFOP-SFO"</span>, <span class="op">]</span>,</span> +<span class="r-in"> control <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>pnlsMaxIter <span class="op">=</span> <span class="fl">120</span>, tolerance <span class="op">=</span> <span class="fl">5e-4</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"></span> +<span class="r-in"> <span class="va">f_2_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_2</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> +<span class="r-in"> <span class="co"># f_nlme_sfo_sfo_tc <- nlme(f_2_tc["SFO-SFO", ]) # No convergence with 50 iterations</span></span> +<span class="r-in"> <span class="co"># f_nlme_dfop_sfo_tc <- nlme(f_2_tc["DFOP-SFO", ],</span></span> +<span class="r-in"> <span class="co"># control = list(pnlsMaxIter = 120, tolerance = 5e-4)) # Error in X[, fmap[[nm]]] <- gradnm</span></span> +<span class="r-in"></span> +<span class="r-in"> <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_nlme_dfop_sfo</span>, <span class="va">f_nlme_dfop_sfo_obs</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> Model df AIC BIC logLik Test L.Ratio</span> +<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 </span> +<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo_obs 2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32091</span> +<span class="r-out co"><span class="r-pr">#></span> p-value</span> +<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo </span> +<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo_obs <.0001</span> +<span class="r-in"></span> +<span class="r-in"><span class="co"># }</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> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> |