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<h6 class="dropdown-header" data-toc-skip>Example evaluations with hierarchical models (nonlinear mixed-effects models)</h6>
<a class="dropdown-item" href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a>
<a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a>
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<main id="main" class="col-md-9"><div class="page-header">
<img src="" class="logo" alt=""><h1>Create a mixed effects model from an mmkin row object</h1>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mixed.mmkin.R" class="external-link"><code>R/mixed.mmkin.R</code></a></small>
<div class="d-none name"><code>mixed.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>Create a mixed effects model from an mmkin row object</p>
</div>
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mixed</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for mmkin</span></span>
<span><span class="fu">mixed</span><span class="op">(</span><span class="va">object</span>, method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"none"</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for mixed.mmkin</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>object</dt>
<dd><p>An <a href="mmkin.html">mmkin</a> row object</p></dd>
<dt>...</dt>
<dd><p>Currently not used</p></dd>
<dt>method</dt>
<dd><p>The method to be used</p></dd>
<dt>x</dt>
<dd><p>A mixed.mmkin object to print</p></dd>
<dt>digits</dt>
<dd><p>Number of digits to use for printing.</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>An object of class 'mixed.mmkin' which has the observed data in a
single dataframe which is convenient for plotting</p>
</div>
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><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">n_biphasic</span> <span class="op"><-</span> <span class="fl">8</span></span></span>
<span class="r-in"><span><span class="va">err_1</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>const <span class="op">=</span> <span class="fl">1</span>, prop <span class="op">=</span> <span class="fl">0.07</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">DFOP_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span>
<span class="r-in"><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>,</span></span>
<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><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">123456</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">log_sd</span> <span class="op"><-</span> <span class="fl">0.3</span></span></span>
<span class="r-in"><span><span class="va">syn_biphasic_parms</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">as.matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> k1 <span class="op">=</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="va">n_biphasic</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">0.05</span><span class="op">)</span>, <span class="va">log_sd</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> k2 <span class="op">=</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="va">n_biphasic</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">0.01</span><span class="op">)</span>, <span class="va">log_sd</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> g <span class="op">=</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="va">n_biphasic</span>, <span class="fl">0</span>, <span class="va">log_sd</span><span class="op">)</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> f_parent_to_m1 <span class="op">=</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="va">n_biphasic</span>, <span class="fl">0</span>, <span class="va">log_sd</span><span class="op">)</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> k_m1 <span class="op">=</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="va">n_biphasic</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">0.002</span><span class="op">)</span>, <span class="va">log_sd</span><span class="op">)</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="va">ds_biphasic_mean</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="va">n_biphasic</span>,</span></span>
<span class="r-in"><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 class="va">syn_biphasic_parms</span><span class="op">[</span><span class="va">i</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 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 class="op">)</span></span></span>
<span class="r-in"><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">123456L</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">ds_biphasic</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">ds_biphasic_mean</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="va">err_1</span><span class="op">$</span><span class="va">const</span><span class="op">^</span><span class="fl">2</span> <span class="op">+</span> <span class="va">value</span><span class="op">^</span><span class="fl">2</span> <span class="op">*</span> <span class="va">err_1</span><span class="op">$</span><span class="va">prop</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>, secondary <span class="op">=</span> <span class="st">"m1"</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="va">f_mmkin</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"DFOP-SFO"</span> <span class="op">=</span> <span class="va">DFOP_SFO</span><span class="op">)</span>, <span class="va">ds_biphasic</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">f_mixed</span> <span class="op"><-</span> <span class="fu">mixed</span><span class="op">(</span><span class="va">f_mmkin</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_mixed</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> Kinetic model fitted by nonlinear regression to each dataset</span>
<span class="r-out co"><span class="r-pr">#></span> Structural model:</span>
<span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span>
<span class="r-out co"><span class="r-pr">#></span> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))</span>
<span class="r-out co"><span class="r-pr">#></span> * parent</span>
<span class="r-out co"><span class="r-pr">#></span> 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">#></span> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *</span>
<span class="r-out co"><span class="r-pr">#></span> exp(-k2 * time))) * parent - k_m1 * m1</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> Data:</span>
<span class="r-out co"><span class="r-pr">#></span> 271 observations of 2 variable(s) grouped in 8 datasets</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> <mmkin> object</span>
<span class="r-out co"><span class="r-pr">#></span> Status of individual fits:</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> dataset</span>
<span class="r-out co"><span class="r-pr">#></span> model 1 2 3 4 5 6 7 8 </span>
<span class="r-out co"><span class="r-pr">#></span> DFOP-SFO OK OK OK OK OK C OK OK</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> C: Optimisation did not converge:</span>
<span class="r-out co"><span class="r-pr">#></span> iteration limit reached without convergence (10)</span>
<span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> Mean fitted parameters:</span>
<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 </span>
<span class="r-out co"><span class="r-pr">#></span> 100.605312 -8.758664 -0.001917 -3.350887 -3.990017 </span>
<span class="r-out co"><span class="r-pr">#></span> g_qlogis </span>
<span class="r-out co"><span class="r-pr">#></span> -0.091167 </span>
<span class="r-in"><span><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_mixed</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="mixed-1.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
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