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<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/master/R/mixed.mmkin.R'><code>R/mixed.mmkin.R</code></a></small>
<div class="hidden name"><code>mixed.Rd</code></div>
</div>
<div class="ref-description">
<p>Create a mixed effects model from an mmkin row object</p>
</div>
<pre class="usage"><span class='fu'>mixed</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='co'># S3 method for mmkin</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'>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 class='co'># S3 method for mixed.mmkin</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, digits <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"digits"</span><span class='op'>)</span> <span class='op'>-</span> <span class='fl'>3</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span></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 <a href='mmkin.html'>mmkin</a> row object</p></td>
</tr>
<tr>
<th>...</th>
<td><p>Currently not used</p></td>
</tr>
<tr>
<th>method</th>
<td><p>The method to be used</p></td>
</tr>
<tr>
<th>x</th>
<td><p>A mixed.mmkin object to print</p></td>
</tr>
<tr>
<th>digits</th>
<td><p>Number of digits to use for printing.</p></td>
</tr>
</table>
<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'>n_biphasic</span> <span class='op'><-</span> <span class='fl'>8</span>
<span class='va'>err_1</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>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 class='va'>DFOP_SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>
parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='st'>"m1"</span><span class='op'>)</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 class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span><span class='op'>(</span><span class='fl'>123456</span><span class='op'>)</span>
<span class='va'>log_sd</span> <span class='op'><-</span> <span class='fl'>0.3</span>
<span class='va'>syn_biphasic_parms</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>as.matrix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>
k1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/stats/Lognormal.html'>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'>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>,
k2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/stats/Lognormal.html'>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'>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>,
g <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/stats/Logistic.html'>plogis</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>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>,
f_parent_to_m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/stats/Logistic.html'>plogis</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>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>,
k_m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/stats/Lognormal.html'>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'>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 class='va'>ds_biphasic_mean</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='fl'>1</span><span class='op'>:</span><span class='va'>n_biphasic</span>,
<span class='kw'>function</span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>{</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 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'>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 class='op'>}</span>
<span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span><span class='op'>(</span><span class='fl'>123456L</span><span class='op'>)</span>
<span class='va'>ds_biphasic</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>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 class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>ds</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'>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>,
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 class='op'>}</span><span class='op'>)</span>
<span class='co'># \dontrun{</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'>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 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 class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_mixed</span><span class='op'>)</span>
</div><div class='output co'>#> Kinetic model fitted by nonlinear regression to each dataset
#> Structural model:
#> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
#> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))
#> * parent
#> d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)
#> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *
#> exp(-k2 * time))) * parent - k_m1 * m1
#>
#> Data:
#> 271 observations of 2 variable(s) grouped in 8 datasets
#>
#> <mmkin> object
#> Status of individual fits:
#>
#> dataset
#> model 1 2 3 4 5 6 7 8
#> DFOP-SFO OK OK OK OK OK C OK OK
#>
#> OK: No warnings
#> C: Optimisation did not converge:
#> iteration limit reached without convergence (10)
#>
#> Mean fitted parameters:
#> parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2
#> 100.606304 -8.759216 -0.002001 -3.350539 -3.989549
#> g_qlogis
#> -0.090353 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_mixed</span><span class='op'>)</span>
</div><div class='img'><img src='mixed-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
</div></pre>
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