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<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Summary method for class "saem.mmkin" — summary.saem.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="Summary method for class " saem.mmkin summary.saem.mmkin><meta property="og:description" content="Lists model equations, initial parameter values, optimised parameters
for fixed effects (population), random effects (deviations from the
population mean) and residual error model, as well as the resulting
endpoints such as formation fractions and DT50 values. Optionally
(default is FALSE), the data are listed in full."><!-- 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]>
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    <div class="page-header">
    <h1>Summary method for class "saem.mmkin"</h1>
    <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/summary.saem.mmkin.R" class="external-link"><code>R/summary.saem.mmkin.R</code></a></small>
    <div class="hidden name"><code>summary.saem.mmkin.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Lists model equations, initial parameter values, optimised parameters
for fixed effects (population), random effects (deviations from the
population mean) and residual error model, as well as the resulting
endpoints such as formation fractions and DT50 values. Optionally
(default is FALSE), the data are listed in full.</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for saem.mmkin</span></span>
<span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span></span>
<span>  <span class="va">object</span>,</span>
<span>  data <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span>  verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span>  covariates <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  covariate_quantile <span class="op">=</span> <span class="fl">0.5</span>,</span>
<span>  distimes <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span>  <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for summary.saem.mmkin</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="va">x</span><span class="op">$</span><span class="va">verbose</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
    </div>

    <div id="arguments">
    <h2>Arguments</h2>
    <dl><dt>object</dt>
<dd><p>an object of class <a href="saem.html">saem.mmkin</a></p></dd>


<dt>data</dt>
<dd><p>logical, indicating whether the full data should be included in
the summary.</p></dd>


<dt>verbose</dt>
<dd><p>Should the summary be verbose?</p></dd>


<dt>covariates</dt>
<dd><p>Numeric vector with covariate values for all variables in
any covariate models in the object. If given, it overrides 'covariate_quantile'.</p></dd>


<dt>covariate_quantile</dt>
<dd><p>This argument only has an effect if the fitted
object has covariate models. If so, the default is to show endpoints
for the median of the covariate values (50th percentile).</p></dd>


<dt>distimes</dt>
<dd><p>logical, indicating whether DT50 and DT90 values should be
included.</p></dd>


<dt>...</dt>
<dd><p>optional arguments passed to methods like <code>print</code>.</p></dd>


<dt>x</dt>
<dd><p>an object of class summary.saem.mmkin</p></dd>


<dt>digits</dt>
<dd><p>Number of digits to use for printing</p></dd>

</dl></div>
    <div id="value">
    <h2>Value</h2>
    

<p>The summary function returns a list based on the <a href="https://rdrr.io/pkg/saemix/man/SaemixObject-class.html" class="external-link">saemix::SaemixObject</a></p>


<p>obtained in the fit, with at least the following additional components</p>
<dl><dt>saemixversion, mkinversion, Rversion</dt>
<dd><p>The saemix, mkin and R versions used</p></dd>

<dt>date.fit, date.summary</dt>
<dd><p>The dates where the fit and the summary were
produced</p></dd>

<dt>diffs</dt>
<dd><p>The differential equations used in the degradation model</p></dd>

<dt>use_of_ff</dt>
<dd><p>Was maximum or minimum use made of formation fractions</p></dd>

<dt>data</dt>
<dd><p>The data</p></dd>

<dt>confint_trans</dt>
<dd><p>Transformed parameters as used in the optimisation, with confidence intervals</p></dd>

<dt>confint_back</dt>
<dd><p>Backtransformed parameters, with confidence intervals if available</p></dd>

<dt>confint_errmod</dt>
<dd><p>Error model parameters with confidence intervals</p></dd>

<dt>ff</dt>
<dd><p>The estimated formation fractions derived from the fitted
model.</p></dd>

<dt>distimes</dt>
<dd><p>The DT50 and DT90 values for each observed variable.</p></dd>

<dt>SFORB</dt>
<dd><p>If applicable, eigenvalues of SFORB components of the model.</p></dd>

</dl><p>The print method is called for its side effect, i.e. printing the summary.</p>
    </div>
    <div id="author">
    <h2>Author</h2>
    <p>Johannes Ranke for the mkin specific parts
saemix authors for the parts inherited from saemix.</p>
    </div>

    <div id="ref-examples">
    <h2>Examples</h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Generate five datasets following DFOP-SFO kinetics</span></span></span>
<span class="r-in"><span><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>
<span class="r-in"><span><span class="va">dfop_sfo</span> <span class="op">&lt;-</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">"m1"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> m1 <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>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">1234</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">k1_in</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="fl">5</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.1</span><span class="op">)</span>, <span class="fl">0.3</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">k2_in</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="fl">5</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.02</span><span class="op">)</span>, <span class="fl">0.3</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">g_in</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">plogis</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">5</span>, <span class="fu"><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">qlogis</a></span><span class="op">(</span><span class="fl">0.5</span><span class="op">)</span>, <span class="fl">0.3</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">f_parent_to_m1_in</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">plogis</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">5</span>, <span class="fu"><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">qlogis</a></span><span class="op">(</span><span class="fl">0.3</span><span class="op">)</span>, <span class="fl">0.3</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">k_m1_in</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="fl">5</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.02</span><span class="op">)</span>, <span class="fl">0.3</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">pred_dfop_sfo</span> <span class="op">&lt;-</span> <span class="kw">function</span><span class="op">(</span><span class="va">k1</span>, <span class="va">k2</span>, <span class="va">g</span>, <span class="va">f_parent_to_m1</span>, <span class="va">k_m1</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span>  <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">dfop_sfo</span>,</span></span>
<span class="r-in"><span>    <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k1 <span class="op">=</span> <span class="va">k1</span>, k2 <span class="op">=</span> <span class="va">k2</span>, g <span class="op">=</span> <span class="va">g</span>, f_parent_to_m1 <span class="op">=</span> <span class="va">f_parent_to_m1</span>, k_m1 <span class="op">=</span> <span class="va">k_m1</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>    <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">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>    <span class="va">sampling_times</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">ds_mean_dfop_sfo</span> <span class="op">&lt;-</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="fl">1</span><span class="op">:</span><span class="fl">5</span>, <span class="kw">function</span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span>  <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">dfop_sfo</span>,</span></span>
<span class="r-in"><span>    <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k1 <span class="op">=</span> <span class="va">k1_in</span><span class="op">[</span><span class="va">i</span><span class="op">]</span>, k2 <span class="op">=</span> <span class="va">k2_in</span><span class="op">[</span><span class="va">i</span><span class="op">]</span>, g <span class="op">=</span> <span class="va">g_in</span><span class="op">[</span><span class="va">i</span><span class="op">]</span>,</span></span>
<span class="r-in"><span>      f_parent_to_m1 <span class="op">=</span> <span class="va">f_parent_to_m1_in</span><span class="op">[</span><span class="va">i</span><span class="op">]</span>, k_m1 <span class="op">=</span> <span class="va">k_m1_in</span><span class="op">[</span><span class="va">i</span><span class="op">]</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>    <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>    <span class="va">sampling_times</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">ds_mean_dfop_sfo</span><span class="op">)</span> <span class="op">&lt;-</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="st">"ds"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">5</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">ds_syn_dfop_sfo</span> <span class="op">&lt;-</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">ds_mean_dfop_sfo</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span>  <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">ds</span>,</span></span>
<span class="r-in"><span>    sdfunc <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="fl">1</span><span class="op">^</span><span class="fl">2</span> <span class="op">+</span> <span class="va">value</span><span class="op">^</span><span class="fl">2</span> <span class="op">*</span> <span class="fl">0.07</span><span class="op">^</span><span class="fl">2</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>    n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span></span></span>
<span class="r-in"><span><span class="op">}</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
<span class="r-in"><span><span class="co"># Evaluate using mmkin and saem</span></span></span>
<span class="r-in"><span><span class="va">f_mmkin_dfop_sfo</span> <span class="op">&lt;-</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="va">dfop_sfo</span><span class="op">)</span>, <span class="va">ds_syn_dfop_sfo</span>,</span></span>
<span class="r-in"><span>  quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, cores <span class="op">=</span> <span class="fl">5</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">f_saem_dfop_sfo</span> <span class="op">&lt;-</span> <span class="fu"><a href="saem.html">saem</a></span><span class="op">(</span><span class="va">f_mmkin_dfop_sfo</span><span class="op">)</span></span></span>
<span class="r-in"><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">f_saem_dfop_sfo</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Kinetic nonlinear mixed-effects model fit by SAEM</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Structural model:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>            time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>            * parent</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>            * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>            exp(-k2 * time))) * parent - k_m1 * m1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Data:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 171 observations of 2 variable(s) grouped in 5 datasets</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Likelihood computed by importance sampling</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>     AIC   BIC logLik</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   810.8 805.4 -391.4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted parameters:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>                      estimate     lower    upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0           100.966822  97.90584 104.0278</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_m1            -4.076164  -4.17485  -3.9775</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_qlogis     -0.940902  -1.35358  -0.5282</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_k1              -2.363988  -2.71690  -2.0111</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_k2              -4.060016  -4.21743  -3.9026</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> g_qlogis            -0.029999  -0.44766   0.3877</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> a.1                  0.876272   0.67308   1.0795</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> b.1                  0.079594   0.06399   0.0952</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SD.parent_0          0.076322 -76.47330  76.6259</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k_m1          0.005052  -1.09071   1.1008</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SD.f_parent_qlogis   0.446968   0.16577   0.7282</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k1            0.348786   0.09502   0.6025</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k2            0.147456   0.03111   0.2638</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SD.g_qlogis          0.348244   0.02794   0.6686</span>
<span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "sd(parent_0)" "sd(log_k_m1)"</span>
<span class="r-in"><span><span class="va">f_saem_dfop_sfo_2</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>,</span></span>
<span class="r-in"><span>  no_random_effect <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">"parent_0"</span>, <span class="st">"log_k_m1"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/intervals.html" class="external-link">intervals</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Approximate 95% confidence intervals</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  Fixed effects:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>                      lower         est.        upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0       98.04247057 101.09950884 104.15654711</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_m1            0.01528983   0.01687734   0.01862969</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_to_m1  0.20447650   0.27932896   0.36887691</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k1              0.06779844   0.09638524   0.13702550</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k2              0.01495629   0.01741775   0.02028431</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> g               0.37669311   0.48368409   0.59219202</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  Random effects:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>                          lower      est.     upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sd(f_parent_qlogis) 0.16515100 0.4448330 0.7245149</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sd(log_k1)          0.08982372 0.3447403 0.5996568</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sd(log_k2)          0.02806589 0.1419560 0.2558462</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sd(g_qlogis)        0.04908160 0.3801993 0.7113170</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>          lower       est.      upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> a.1 0.67539922 0.87630147 1.07720371</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> b.1 0.06401324 0.07920531 0.09439739</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> saemix version used for fitting:      3.2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting:  1.2.6 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:         4.3.1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Mon Oct 30 09:40:27 2023 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Mon Oct 30 09:40:27 2023 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>            time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>            * parent</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>            * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>            exp(-k2 * time))) * parent - k_m1 * m1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Data:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 171 observations of 2 variable(s) grouped in 5 datasets</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type analytical </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 19.763 s</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Using 300, 100 iterations and 10 chains</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Variance model: Two-component variance function </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Starting values for degradation parameters:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>        parent_0        log_k_m1 f_parent_qlogis          log_k1          log_k2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>       101.65645        -4.05368        -0.94311        -2.35943        -4.07006 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>        g_qlogis </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>        -0.01133 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Fixed degradation parameter values:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> None</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Starting values for random effects (square root of initial entries in omega):</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>                 parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 g_qlogis</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0           6.742   0.0000          0.0000 0.0000 0.0000    0.000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_m1           0.000   0.2236          0.0000 0.0000 0.0000    0.000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_qlogis    0.000   0.0000          0.5572 0.0000 0.0000    0.000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_k1             0.000   0.0000          0.0000 0.8031 0.0000    0.000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_k2             0.000   0.0000          0.0000 0.0000 0.2931    0.000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> g_qlogis           0.000   0.0000          0.0000 0.0000 0.0000    0.807</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Starting values for error model parameters:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> a.1 b.1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   1   1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Results:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Likelihood computed by importance sampling</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>     AIC   BIC logLik</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   806.9 802.2 -391.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Optimised parameters:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>                         est.    lower    upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0           101.09951 98.04247 104.1565</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_m1            -4.08178 -4.18057  -3.9830</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_qlogis     -0.94779 -1.35855  -0.5370</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_k1              -2.33940 -2.69122  -1.9876</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_k2              -4.05027 -4.20262  -3.8979</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> g_qlogis            -0.06529 -0.50361   0.3730</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> a.1                  0.87630  0.67540   1.0772</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> b.1                  0.07921  0.06401   0.0944</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SD.f_parent_qlogis   0.44483  0.16515   0.7245</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k1            0.34474  0.08982   0.5997</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k2            0.14196  0.02807   0.2558</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SD.g_qlogis          0.38020  0.04908   0.7113</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Correlation: </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>                 parnt_0 lg_k_m1 f_prnt_ log_k1  log_k2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_m1        -0.4716                                </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_qlogis -0.2394  0.2617                        </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_k1           0.1677 -0.1566 -0.0659                </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_k2           0.0165  0.0638  0.0045  0.2013        </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> g_qlogis         0.1118 -0.1118 -0.0340 -0.2324 -0.3419</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Random effects:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>                      est.   lower  upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SD.f_parent_qlogis 0.4448 0.16515 0.7245</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k1          0.3447 0.08982 0.5997</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k2          0.1420 0.02807 0.2558</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SD.g_qlogis        0.3802 0.04908 0.7113</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Variance model:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>        est.   lower  upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> a.1 0.87630 0.67540 1.0772</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> b.1 0.07921 0.06401 0.0944</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Backtransformed parameters:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>                     est.    lower     upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0       101.09951 98.04247 104.15655</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_m1             0.01688  0.01529   0.01863</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_to_m1   0.27933  0.20448   0.36888</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k1               0.09639  0.06780   0.13703</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k2               0.01742  0.01496   0.02028</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> g                0.48368  0.37669   0.59219</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Resulting formation fractions:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>                 ff</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_m1   0.2793</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_sink 0.7207</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Estimated disappearance times:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>         DT50   DT90 DT50back DT50_k1 DT50_k2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent 15.66  94.28    28.38   7.191    39.8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> m1     41.07 136.43       NA      NA      NA</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Data:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>    ds   name time observed  predicted  residual    std standardized</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1 parent    0     89.8  1.011e+02 -11.29951 8.0554    -1.402721</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1 parent    0    104.1  1.011e+02   3.00049 8.0554     0.372481</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1 parent    1     88.7  9.624e+01  -7.53600 7.6726    -0.982195</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1 parent    1     95.5  9.624e+01  -0.73600 7.6726    -0.095925</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1 parent    3     81.8  8.736e+01  -5.55672 6.9744    -0.796732</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1 parent    3     94.5  8.736e+01   7.14328 6.9744     1.024217</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1 parent    7     71.5  7.251e+01  -1.00511 5.8093    -0.173019</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1 parent    7     70.3  7.251e+01  -2.20511 5.8093    -0.379585</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1 parent   14     54.2  5.356e+01   0.63921 4.3319     0.147560</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1 parent   14     49.6  5.356e+01  -3.96079 4.3319    -0.914340</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1 parent   28     31.5  3.175e+01  -0.25429 2.6634    -0.095475</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1 parent   28     28.8  3.175e+01  -2.95429 2.6634    -1.109218</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1 parent   60     12.1  1.281e+01  -0.71388 1.3409    -0.532390</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1 parent   60     13.6  1.281e+01   0.78612 1.3409     0.586271</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1 parent   90      6.2  6.405e+00  -0.20462 1.0125    -0.202083</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1 parent   90      8.3  6.405e+00   1.89538 1.0125     1.871910</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1 parent  120      2.2  3.329e+00  -1.12941 0.9151    -1.234165</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1 parent  120      2.4  3.329e+00  -0.92941 0.9151    -1.015615</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1     m1    1      0.3  1.177e+00  -0.87699 0.8812    -0.995168</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1     m1    1      0.2  1.177e+00  -0.97699 0.8812    -1.108644</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1     m1    3      2.2  3.268e+00  -1.06821 0.9137    -1.169063</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1     m1    3      3.0  3.268e+00  -0.26821 0.9137    -0.293536</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1     m1    7      6.5  6.555e+00  -0.05539 1.0186    -0.054377</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1     m1    7      5.0  6.555e+00  -1.55539 1.0186    -1.527022</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1     m1   14     10.2  1.017e+01   0.03108 1.1902     0.026117</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1     m1   14      9.5  1.017e+01  -0.66892 1.1902    -0.562010</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1     m1   28     12.2  1.270e+01  -0.50262 1.3342    -0.376708</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1     m1   28     13.4  1.270e+01   0.69738 1.3342     0.522686</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1     m1   60     11.8  1.078e+01   1.01734 1.2236     0.831403</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1     m1   60     13.2  1.078e+01   2.41734 1.2236     1.975530</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1     m1   90      6.6  7.686e+00  -1.08586 1.0670    -1.017675</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1     m1   90      9.3  7.686e+00   1.61414 1.0670     1.512779</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1     m1  120      3.5  5.205e+00  -1.70467 0.9684    -1.760250</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 1     m1  120      5.4  5.205e+00   0.19533 0.9684     0.201701</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2 parent    0    118.0  1.011e+02  16.90049 8.0554     2.098026</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2 parent    0     99.8  1.011e+02  -1.29951 8.0554    -0.161321</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2 parent    1     90.2  9.574e+01  -5.53784 7.6334    -0.725473</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2 parent    1     94.6  9.574e+01  -1.13784 7.6334    -0.149060</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2 parent    3     96.1  8.638e+01   9.72233 6.8975     1.409551</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2 parent    3     78.4  8.638e+01  -7.97767 6.8975    -1.156610</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2 parent    7     77.9  7.194e+01   5.95854 5.7651     1.033547</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2 parent    7     77.7  7.194e+01   5.75854 5.7651     0.998856</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2 parent   14     56.0  5.558e+01   0.42141 4.4885     0.093888</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2 parent   14     54.7  5.558e+01  -0.87859 4.4885    -0.195742</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2 parent   28     36.6  3.852e+01  -1.92382 3.1746    -0.605999</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2 parent   28     36.8  3.852e+01  -1.72382 3.1746    -0.543000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2 parent   60     22.1  2.108e+01   1.02043 1.8856     0.541168</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2 parent   60     24.7  2.108e+01   3.62043 1.8856     1.920034</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2 parent   90     12.4  1.250e+01  -0.09675 1.3220    -0.073184</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2 parent   90     10.8  1.250e+01  -1.69675 1.3220    -1.283492</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2 parent  120      6.8  7.426e+00  -0.62587 1.0554    -0.593027</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2 parent  120      7.9  7.426e+00   0.47413 1.0554     0.449242</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2     m1    1      1.3  1.417e+00  -0.11735 0.8835    -0.132825</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2     m1    3      3.7  3.823e+00  -0.12301 0.9271    -0.132673</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2     m1    3      4.7  3.823e+00   0.87699 0.9271     0.945909</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2     m1    7      8.1  7.288e+00   0.81180 1.0494     0.773619</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2     m1    7      7.9  7.288e+00   0.61180 1.0494     0.583025</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2     m1   14     10.1  1.057e+01  -0.46957 1.2119    -0.387459</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2     m1   14     10.3  1.057e+01  -0.26957 1.2119    -0.222432</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2     m1   28     10.7  1.234e+01  -1.63555 1.3124    -1.246185</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2     m1   28     12.2  1.234e+01  -0.13555 1.3124    -0.103281</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2     m1   60     10.7  1.065e+01   0.04641 1.2165     0.038151</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2     m1   60     12.5  1.065e+01   1.84641 1.2165     1.517773</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2     m1   90      9.1  8.177e+00   0.92337 1.0896     0.847403</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2     m1   90      7.4  8.177e+00  -0.77663 1.0896    -0.712734</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2     m1  120      6.1  5.966e+00   0.13404 0.9956     0.134631</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 2     m1  120      4.5  5.966e+00  -1.46596 0.9956    -1.472460</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3 parent    0    106.2  1.011e+02   5.10049 8.0554     0.633175</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3 parent    0    106.9  1.011e+02   5.80049 8.0554     0.720073</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3 parent    1    107.4  9.365e+01  13.74627 7.4695     1.840332</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3 parent    1     96.1  9.365e+01   2.44627 7.4695     0.327504</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3 parent    3     79.4  8.139e+01  -1.99118 6.5059    -0.306058</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3 parent    3     82.6  8.139e+01   1.20882 6.5059     0.185803</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3 parent    7     63.9  6.445e+01  -0.54666 5.1792    -0.105549</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3 parent    7     62.4  6.445e+01  -2.04666 5.1792    -0.395170</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3 parent   14     51.0  4.830e+01   2.69944 3.9247     0.687800</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3 parent   14     47.1  4.830e+01  -1.20056 3.9247    -0.305896</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3 parent   28     36.1  3.426e+01   1.83885 2.8516     0.644839</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3 parent   28     36.6  3.426e+01   2.33885 2.8516     0.820177</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3 parent   60     20.1  1.968e+01   0.42208 1.7881     0.236053</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3 parent   60     19.8  1.968e+01   0.12208 1.7881     0.068273</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3 parent   90     11.3  1.194e+01  -0.64013 1.2893    -0.496496</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3 parent   90     10.7  1.194e+01  -1.24013 1.2893    -0.961865</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3 parent  120      8.2  7.247e+00   0.95264 1.0476     0.909381</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3 parent  120      7.3  7.247e+00   0.05264 1.0476     0.050254</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3     m1    0      0.8 -2.956e-12   0.80000 0.8763     0.912928</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3     m1    1      1.8  1.757e+00   0.04318 0.8873     0.048666</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3     m1    1      2.3  1.757e+00   0.54318 0.8873     0.612186</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3     m1    3      4.2  4.566e+00  -0.36607 0.9480    -0.386149</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3     m1    3      4.1  4.566e+00  -0.46607 0.9480    -0.491634</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3     m1    7      6.8  8.157e+00  -1.35680 1.0887    -1.246241</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3     m1    7     10.1  8.157e+00   1.94320 1.0887     1.784855</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3     m1   14     11.4  1.085e+01   0.55367 1.2272     0.451182</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3     m1   14     12.8  1.085e+01   1.95367 1.2272     1.592023</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3     m1   28     11.5  1.149e+01   0.01098 1.2633     0.008689</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3     m1   28     10.6  1.149e+01  -0.88902 1.2633    -0.703717</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3     m1   60      7.5  9.295e+00  -1.79500 1.1445    -1.568351</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3     m1   60      8.6  9.295e+00  -0.69500 1.1445    -0.607245</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3     m1   90      7.3  7.017e+00   0.28305 1.0377     0.272775</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3     m1   90      8.1  7.017e+00   1.08305 1.0377     1.043720</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3     m1  120      5.3  5.087e+00   0.21272 0.9645     0.220547</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 3     m1  120      3.8  5.087e+00  -1.28728 0.9645    -1.334660</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent    0    104.7  1.011e+02   3.60049 8.0554     0.446965</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent    0     88.3  1.011e+02 -12.79951 8.0554    -1.588930</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent    1     94.2  9.755e+01  -3.35176 7.7762    -0.431030</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent    1     94.6  9.755e+01  -2.95176 7.7762    -0.379591</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent    3     78.1  9.095e+01 -12.85198 7.2570    -1.770981</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent    3     96.5  9.095e+01   5.54802 7.2570     0.764508</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent    7     76.2  7.949e+01  -3.29267 6.3569    -0.517966</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent    7     77.8  7.949e+01  -1.69267 6.3569    -0.266272</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent   14     70.8  6.384e+01   6.95621 5.1321     1.355423</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent   14     67.3  6.384e+01   3.45621 5.1321     0.673445</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent   28     43.1  4.345e+01  -0.35291 3.5515    -0.099370</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent   28     45.1  4.345e+01   1.64709 3.5515     0.463771</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent   60     21.3  2.137e+01  -0.07478 1.9063    -0.039229</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent   60     23.5  2.137e+01   2.12522 1.9063     1.114813</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent   90     11.8  1.205e+01  -0.24925 1.2957    -0.192375</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent   90     12.1  1.205e+01   0.05075 1.2957     0.039168</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent  120      7.0  6.967e+00   0.03315 1.0356     0.032013</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent  120      6.2  6.967e+00  -0.76685 1.0356    -0.740510</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4     m1    0      1.6  1.421e-13   1.60000 0.8763     1.825856</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4     m1    1      0.9  7.250e-01   0.17503 0.8782     0.199310</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4     m1    3      3.7  2.038e+00   1.66201 0.8910     1.865236</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4     m1    3      2.0  2.038e+00  -0.03799 0.8910    -0.042637</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4     m1    7      3.6  4.186e+00  -0.58623 0.9369    -0.625692</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4     m1    7      3.8  4.186e+00  -0.38623 0.9369    -0.412230</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4     m1   14      7.1  6.752e+00   0.34768 1.0266     0.338666</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4     m1   14      6.6  6.752e+00  -0.15232 1.0266    -0.148372</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4     m1   28      9.5  9.034e+00   0.46628 1.1313     0.412159</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4     m1   28      9.3  9.034e+00   0.26628 1.1313     0.235373</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4     m1   60      8.3  8.634e+00  -0.33359 1.1115    -0.300112</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4     m1   60      9.0  8.634e+00   0.36641 1.1115     0.329645</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4     m1   90      6.6  6.671e+00  -0.07091 1.0233    -0.069295</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4     m1   90      7.7  6.671e+00   1.02909 1.0233     1.005691</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4     m1  120      3.7  4.823e+00  -1.12301 0.9559    -1.174763</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4     m1  120      3.5  4.823e+00  -1.32301 0.9559    -1.383979</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent    0    110.4  1.011e+02   9.30049 8.0554     1.154563</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent    0    112.1  1.011e+02  11.00049 8.0554     1.365601</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent    1     93.5  9.440e+01  -0.90098 7.5282    -0.119681</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent    1     91.0  9.440e+01  -3.40098 7.5282    -0.451764</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent    3     71.0  8.287e+01 -11.86698 6.6217    -1.792122</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent    3     89.7  8.287e+01   6.83302 6.6217     1.031907</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent    7     60.4  6.562e+01  -5.22329 5.2711    -0.990936</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent    7     59.1  6.562e+01  -6.52329 5.2711    -1.237566</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent   14     56.5  4.739e+01   9.10588 3.8548     2.362225</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent   14     47.0  4.739e+01  -0.39412 3.8548    -0.102240</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent   28     30.2  3.118e+01  -0.98128 2.6206    -0.374451</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent   28     23.9  3.118e+01  -7.28128 2.6206    -2.778500</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent   60     17.0  1.804e+01  -1.03959 1.6761    -0.620224</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent   60     18.7  1.804e+01   0.66041 1.6761     0.394008</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent   90     11.3  1.165e+01  -0.35248 1.2727    -0.276958</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent   90     11.9  1.165e+01   0.24752 1.2727     0.194488</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent  120      9.0  7.556e+00   1.44368 1.0612     1.360449</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent  120      8.1  7.556e+00   0.54368 1.0612     0.512338</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5     m1    0      0.7 -1.421e-14   0.70000 0.8763     0.798812</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5     m1    1      3.0  3.160e+00  -0.15979 0.9113    -0.175340</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5     m1    1      2.6  3.160e+00  -0.55979 0.9113    -0.614254</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5     m1    3      5.1  8.448e+00  -3.34789 1.1026    -3.036487</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5     m1    3      7.5  8.448e+00  -0.94789 1.1026    -0.859720</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5     m1    7     16.5  1.581e+01   0.68760 1.5286     0.449839</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5     m1    7     19.0  1.581e+01   3.18760 1.5286     2.085373</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5     m1   14     22.9  2.218e+01   0.71983 1.9632     0.366658</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5     m1   14     23.2  2.218e+01   1.01983 1.9632     0.519469</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5     m1   28     22.2  2.425e+01  -2.05105 2.1113    -0.971479</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5     m1   28     24.4  2.425e+01   0.14895 2.1113     0.070552</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5     m1   60     15.5  1.876e+01  -3.25968 1.7250    -1.889646</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5     m1   60     19.8  1.876e+01   1.04032 1.7250     0.603074</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5     m1   90     14.9  1.365e+01   1.25477 1.3914     0.901806</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5     m1   90     14.2  1.365e+01   0.55477 1.3914     0.398714</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5     m1  120     10.9  9.726e+00   1.17443 1.1667     1.006587</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5     m1  120     10.4  9.726e+00   0.67443 1.1667     0.578044</span>
<span class="r-in"><span><span class="co"># Add a correlation between random effects of g and k2</span></span></span>
<span class="r-in"><span><span class="va">cov_model_3</span> <span class="op">&lt;-</span> <span class="va">f_saem_dfop_sfo_2</span><span class="op">$</span><span class="va">so</span><span class="op">@</span><span class="va">model</span><span class="op">@</span><span class="va">covariance.model</span></span></span>
<span class="r-in"><span><span class="va">cov_model_3</span><span class="op">[</span><span class="st">"log_k2"</span>, <span class="st">"g_qlogis"</span><span class="op">]</span> <span class="op">&lt;-</span> <span class="fl">1</span></span></span>
<span class="r-in"><span><span class="va">cov_model_3</span><span class="op">[</span><span class="st">"g_qlogis"</span>, <span class="st">"log_k2"</span><span class="op">]</span> <span class="op">&lt;-</span> <span class="fl">1</span></span></span>
<span class="r-in"><span><span class="va">f_saem_dfop_sfo_3</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>,</span></span>
<span class="r-in"><span>  covariance.model <span class="op">=</span> <span class="va">cov_model_3</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/intervals.html" class="external-link">intervals</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_3</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Approximate 95% confidence intervals</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  Fixed effects:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>                      lower         est.        upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0       98.42519529 101.51623115 104.60726702</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_m1            0.01505059   0.01662123   0.01835577</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_to_m1  0.20100222   0.27477835   0.36332008</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k1              0.07347479   0.10139028   0.13991179</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k2              0.01469861   0.01771120   0.02134125</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> g               0.35506898   0.46263682   0.57379888</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  Random effects:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>                            lower       est.      upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sd(f_parent_qlogis)    0.3827416  0.4435866  0.5044315</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sd(log_k1)             0.1226277  0.2981783  0.4737289</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sd(log_k2)            -0.5457764  0.1912531  0.9282825</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sd(g_qlogis)           0.1483976  0.3997298  0.6510619</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> corr(log_k2,g_qlogis) -0.8537145 -0.5845703 -0.3154261</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>         lower       est.     upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> a.1 0.6732869 0.87421677 1.0751467</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> b.1 0.0640392 0.07925135 0.0944635</span>
<span class="r-in"><span><span class="co"># The correlation does not improve the fit judged by AIC and BIC, although</span></span></span>
<span class="r-in"><span><span class="co"># the likelihood is higher with the additional parameter</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, <span class="va">f_saem_dfop_sfo_2</span>, <span class="va">f_saem_dfop_sfo_3</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Data: 171 observations of 2 variable(s) grouped in 5 datasets</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>                   npar    AIC    BIC     Lik</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_saem_dfop_sfo_2   12 806.91 802.23 -391.46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_saem_dfop_sfo_3   13 807.96 802.88 -390.98</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_saem_dfop_sfo     14 810.83 805.36 -391.41</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
<span class="r-in"><span></span></span>
</code></pre></div>
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