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1 files changed, 121 insertions, 191 deletions
diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html index 6821bacf..5eebecaa 100644 --- a/docs/reference/nlme.html +++ b/docs/reference/nlme.html @@ -1,70 +1,15 @@ -<!-- 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>Helper functions to create nlme models from mmkin row objects — nlme_function • 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="Helper functions to create nlme models from mmkin row objects — nlme_function" /> -<meta property="og:description" content="These functions facilitate setting up a nonlinear mixed effects model for +<!-- 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>Helper functions to create nlme models from mmkin row objects — nlme_function • 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="Helper functions to create nlme models from mmkin row objects — nlme_function"><meta property="og:description" content="These functions facilitate setting 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. They are used internally by the nlme.mmkin() method." /> - - - - -<!-- 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]> +datasets. They are used internally by the nlme.mmkin() method."><!-- 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"> @@ -75,13 +20,12 @@ datasets. They are used internally by the nlme.mmkin() method." /> </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"> @@ -90,8 +34,7 @@ datasets. They are used internally by the nlme.mmkin() method." /> <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> @@ -101,6 +44,9 @@ datasets. They are used internally by the nlme.mmkin() method." /> <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> @@ -115,34 +61,27 @@ datasets. They are used internally by the nlme.mmkin() method." /> <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>Helper functions to create nlme models from mmkin row objects</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/nlme.R'><code>R/nlme.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/nlme.R" class="external-link"><code>R/nlme.R</code></a></small> <div class="hidden name"><code>nlme.Rd</code></div> </div> @@ -150,137 +89,128 @@ datasets. They are used internally by the nlme.mmkin() method." /> <p>These functions facilitate setting 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. They are used internally by the <code><a href='nlme.mmkin.html'>nlme.mmkin()</a></code> method.</p> +datasets. They are used internally by the <code><a href="nlme.mmkin.html">nlme.mmkin()</a></code> method.</p> </div> - <pre class="usage"><span class='fu'>nlme_function</span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span> - -<span class='fu'>mean_degparms</span><span class='op'>(</span><span class='va'>object</span>, random <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> - -<span class='fu'>nlme_data</span><span class='op'>(</span><span class='va'>object</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>object</th> - <td><p>An mmkin row object containing several fits of the same model to different datasets</p></td> - </tr> - <tr> - <th>random</th> - <td><p>Should a list with fixed and random effects be returned?</p></td> - </tr> - </table> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">nlme_function</span><span class="op">(</span><span class="va">object</span><span class="op">)</span> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>A function that can be used with nlme</p> -<p>If random is FALSE (default), a named vector containing mean values -of the fitted degradation model parameters. If random is TRUE, a list with -fixed and random effects, in the format required by the start argument of -nlme for the case of a single grouping variable ds.</p> -<p>A <code><a href='https://rdrr.io/pkg/nlme/man/groupedData.html'>groupedData</a></code> object</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.mmkin.html'>nlme.mmkin</a></code></p></div> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='va'>sampling_times</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='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span> -<span class='va'>m_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='op'>)</span><span class='op'>)</span> -<span class='va'>d_SFO_1</span> <span class='op'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>m_SFO</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>98</span><span class='op'>)</span>, <span class='va'>sampling_times</span><span class='op'>)</span> -<span class='va'>d_SFO_1_long</span> <span class='op'><-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span><span class='op'>(</span><span class='va'>d_SFO_1</span>, time <span class='op'>=</span> <span class='st'>"time"</span><span class='op'>)</span> -<span class='va'>d_SFO_2</span> <span class='op'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>m_SFO</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.05</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>102</span><span class='op'>)</span>, <span class='va'>sampling_times</span><span class='op'>)</span> -<span class='va'>d_SFO_2_long</span> <span class='op'><-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span><span class='op'>(</span><span class='va'>d_SFO_2</span>, time <span class='op'>=</span> <span class='st'>"time"</span><span class='op'>)</span> -<span class='va'>d_SFO_3</span> <span class='op'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>m_SFO</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.02</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>103</span><span class='op'>)</span>, <span class='va'>sampling_times</span><span class='op'>)</span> -<span class='va'>d_SFO_3_long</span> <span class='op'><-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span><span class='op'>(</span><span class='va'>d_SFO_3</span>, time <span class='op'>=</span> <span class='st'>"time"</span><span class='op'>)</span> - -<span class='va'>d1</span> <span class='op'><-</span> <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>d_SFO_1</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fl'>3</span>, n <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> -<span class='va'>d2</span> <span class='op'><-</span> <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>d_SFO_2</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fl'>2</span>, n <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> -<span class='va'>d3</span> <span class='op'><-</span> <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>d_SFO_3</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fl'>4</span>, n <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> -<span class='va'>ds</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>d1 <span class='op'>=</span> <span class='va'>d1</span>, d2 <span class='op'>=</span> <span class='va'>d2</span>, d3 <span class='op'>=</span> <span class='va'>d3</span><span class='op'>)</span> +<span class="fu">nlme_data</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></code></pre></div> + </div> -<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='st'>"SFO"</span>, <span class='va'>ds</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>mean_dp</span> <span class='op'><-</span> <span class='fu'>mean_degparms</span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span> -<span class='va'>grouped_data</span> <span class='op'><-</span> <span class='fu'>nlme_data</span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span> -<span class='va'>nlme_f</span> <span class='op'><-</span> <span class='fu'>nlme_function</span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span> -<span class='co'># These assignments are necessary for these objects to be</span> -<span class='co'># visible to nlme and augPred when evaluation is done by</span> -<span class='co'># pkgdown to generated the html docs.</span> -<span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span><span class='op'>(</span><span class='st'>"nlme_f"</span>, <span class='va'>nlme_f</span>, <span class='fu'><a href='https://rdrr.io/r/base/environment.html'>globalenv</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span><span class='op'>(</span><span class='st'>"grouped_data"</span>, <span class='va'>grouped_data</span>, <span class='fu'><a href='https://rdrr.io/r/base/environment.html'>globalenv</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>An mmkin row object containing several fits of the same model to different datasets</p></dd> +</dl></div> + <div id="value"> + <h2>Value</h2> + <p>A function that can be used with nlme +A <code><a href="https://rdrr.io/pkg/nlme/man/groupedData.html" class="external-link">groupedData</a></code> object</p> + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><code><a href="nlme.mmkin.html">nlme.mmkin</a></code></p></div> + </div> -<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'>m_nlme</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'>value</span> <span class='op'>~</span> <span class='fu'>nlme_f</span><span class='op'>(</span><span class='va'>name</span>, <span class='va'>time</span>, <span class='va'>parent_0</span>, <span class='va'>log_k_parent_sink</span><span class='op'>)</span>, - data <span class='op'>=</span> <span class='va'>grouped_data</span>, - fixed <span class='op'>=</span> <span class='va'>parent_0</span> <span class='op'>+</span> <span class='va'>log_k_parent_sink</span> <span class='op'>~</span> <span class='fl'>1</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'>parent_0</span> <span class='op'>+</span> <span class='va'>log_k_parent_sink</span> <span class='op'>~</span> <span class='fl'>1</span><span class='op'>)</span>, - start <span class='op'>=</span> <span class='va'>mean_dp</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>m_nlme</span><span class='op'>)</span> -</div><div class='output co'>#> Nonlinear mixed-effects model fit by maximum likelihood -#> Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink) -#> Data: grouped_data -#> AIC BIC logLik -#> 300.6824 310.2426 -145.3412 -#> -#> Random effects: -#> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1) -#> Level: ds -#> Structure: Diagonal -#> parent_0 log_k_parent_sink Residual -#> StdDev: 1.697361 0.6801209 3.666073 -#> -#> Fixed effects: parent_0 + log_k_parent_sink ~ 1 -#> Value Std.Error DF t-value p-value -#> parent_0 100.99378 1.3890416 46 72.70753 0 -#> log_k_parent_sink -3.07521 0.4018589 46 -7.65246 0 -#> Correlation: -#> prnt_0 -#> log_k_parent_sink 0.027 -#> -#> Standardized Within-Group Residuals: -#> Min Q1 Med Q3 Max -#> -1.9942823 -0.5622565 0.1791579 0.7165038 2.0704781 -#> -#> Number of Observations: 50 -#> Number of Groups: 3 </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='fu'><a href='https://rdrr.io/pkg/nlme/man/augPred.html'>augPred</a></span><span class='op'>(</span><span class='va'>m_nlme</span>, level <span class='op'>=</span> <span class='fl'>0</span><span class='op'>:</span><span class='fl'>1</span><span class='op'>)</span>, layout <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='fl'>3</span>, <span class='fl'>1</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='img'><img src='nlme-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># augPred does not work on fits with more than one state</span> -<span class='co'># variable</span> -<span class='co'>#</span> -<span class='co'># The procedure is greatly simplified by the nlme.mmkin function</span> -<span class='va'>f_nlme</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='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme</span><span class='op'>)</span> -</div><div class='img'><img src='nlme-2.png' alt='' width='700' height='433' /></div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span> +<span class="r-in"><span class="va">m_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="op">)</span><span class="op">)</span></span> +<span class="r-in"><span class="va">d_SFO_1</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO</span>,</span> +<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span> +<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">98</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span> +<span class="r-in"><span class="va">d_SFO_1_long</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">d_SFO_1</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span> +<span class="r-in"><span class="va">d_SFO_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO</span>,</span> +<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span>,</span> +<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">102</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span> +<span class="r-in"><span class="va">d_SFO_2_long</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">d_SFO_2</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span> +<span class="r-in"><span class="va">d_SFO_3</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO</span>,</span> +<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.02</span><span class="op">)</span>,</span> +<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">103</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span> +<span class="r-in"><span class="va">d_SFO_3_long</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">d_SFO_3</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span> +<span class="r-in"></span> +<span class="r-in"><span class="va">d1</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_1</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">3</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> +<span class="r-in"><span class="va">d2</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_2</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">2</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> +<span class="r-in"><span class="va">d3</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_3</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">4</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> +<span class="r-in"><span class="va">ds</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>d1 <span class="op">=</span> <span class="va">d1</span>, d2 <span class="op">=</span> <span class="va">d2</span>, d3 <span class="op">=</span> <span class="va">d3</span><span class="op">)</span></span> +<span class="r-in"></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="st">"SFO"</span>, <span class="va">ds</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"><span class="va">mean_dp</span> <span class="op"><-</span> <span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span> +<span class="r-in"><span class="va">grouped_data</span> <span class="op"><-</span> <span class="fu">nlme_data</span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span> +<span class="r-in"><span class="va">nlme_f</span> <span class="op"><-</span> <span class="fu">nlme_function</span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span> +<span class="r-in"><span class="co"># These assignments are necessary for these objects to be</span></span> +<span class="r-in"><span class="co"># visible to nlme and augPred when evaluation is done by</span></span> +<span class="r-in"><span class="co"># pkgdown to generate the html docs.</span></span> +<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="st">"nlme_f"</span>, <span class="va">nlme_f</span>, <span class="fu"><a href="https://rdrr.io/r/base/environment.html" class="external-link">globalenv</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="st">"grouped_data"</span>, <span class="va">grouped_data</span>, <span class="fu"><a href="https://rdrr.io/r/base/environment.html" class="external-link">globalenv</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"></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">m_nlme</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">value</span> <span class="op">~</span> <span class="fu">nlme_f</span><span class="op">(</span><span class="va">name</span>, <span class="va">time</span>, <span class="va">parent_0</span>, <span class="va">log_k_parent_sink</span><span class="op">)</span>,</span> +<span class="r-in"> data <span class="op">=</span> <span class="va">grouped_data</span>,</span> +<span class="r-in"> fixed <span class="op">=</span> <span class="va">parent_0</span> <span class="op">+</span> <span class="va">log_k_parent_sink</span> <span class="op">~</span> <span class="fl">1</span>,</span> +<span class="r-in"> 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">parent_0</span> <span class="op">+</span> <span class="va">log_k_parent_sink</span> <span class="op">~</span> <span class="fl">1</span><span class="op">)</span>,</span> +<span class="r-in"> start <span class="op">=</span> <span class="va">mean_dp</span><span class="op">)</span></span> +<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m_nlme</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> Nonlinear mixed-effects model fit by maximum likelihood</span> +<span class="r-out co"><span class="r-pr">#></span> Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink) </span> +<span class="r-out co"><span class="r-pr">#></span> Data: grouped_data </span> +<span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> +<span class="r-out co"><span class="r-pr">#></span> 300.6824 310.2426 -145.3412</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)</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 Residual</span> +<span class="r-out co"><span class="r-pr">#></span> StdDev: 1.697361 0.6801209 3.666073</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Fixed effects: parent_0 + log_k_parent_sink ~ 1 </span> +<span class="r-out co"><span class="r-pr">#></span> Value Std.Error DF t-value p-value</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 100.99378 1.3890416 46 72.70753 0</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink -3.07521 0.4018589 46 -7.65246 0</span> +<span class="r-out co"><span class="r-pr">#></span> Correlation: </span> +<span class="r-out co"><span class="r-pr">#></span> prnt_0</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink 0.027 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Standardized Within-Group Residuals:</span> +<span class="r-out co"><span class="r-pr">#></span> Min Q1 Med Q3 Max </span> +<span class="r-out co"><span class="r-pr">#></span> -1.9942823 -0.5622565 0.1791579 0.7165038 2.0704781 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Number of Observations: 50</span> +<span class="r-out co"><span class="r-pr">#></span> Number of Groups: 3 </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="fu"><a href="https://rdrr.io/pkg/nlme/man/augPred.html" class="external-link">augPred</a></span><span class="op">(</span><span class="va">m_nlme</span>, level <span class="op">=</span> <span class="fl">0</span><span class="op">:</span><span class="fl">1</span><span class="op">)</span>, layout <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-plt img"><img src="nlme-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span class="co"># augPred does not work on fits with more than one state</span></span> +<span class="r-in"><span class="co"># variable</span></span> +<span class="r-in"><span class="co">#</span></span> +<span class="r-in"><span class="co"># The procedure is greatly simplified by the nlme.mmkin function</span></span> +<span class="r-in"><span class="va">f_nlme</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> +<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</span><span class="op">)</span></span> +<span class="r-plt img"><img src="nlme-2.png" alt="" width="700" height="433"></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> |