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    <h1>Create an nlme model for an mmkin row object</h1>
    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/nlme.mmkin.R'><code>R/nlme.mmkin.R</code></a></small>
    <div class="hidden name"><code>nlme.mmkin.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>This functions sets up a nonlinear mixed effects model for an mmkin row
object. An mmkin row object is essentially a list of mkinfit objects that
have been obtained by fitting the same model to a list of datasets.</p>
    </div>

    <pre class="usage"><span class='co'># S3 method for mmkin</span>
<span class='fu'>nlme</span><span class='op'>(</span>
  <span class='va'>model</span>,
  data <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/sys.parent.html'>sys.frame</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/sys.parent.html'>sys.parent</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>,
  <span class='va'>fixed</span>,
  random <span class='op'>=</span> <span class='va'>fixed</span>,
  <span class='va'>groups</span>,
  <span class='va'>start</span>,
  correlation <span class='op'>=</span> <span class='cn'>NULL</span>,
  weights <span class='op'>=</span> <span class='cn'>NULL</span>,
  <span class='va'>subset</span>,
  method <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"ML"</span>, <span class='st'>"REML"</span><span class='op'>)</span>,
  na.action <span class='op'>=</span> <span class='va'>na.fail</span>,
  <span class='va'>naPattern</span>,
  control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='op'>)</span>,
  verbose <span class='op'>=</span> <span class='cn'>FALSE</span>
<span class='op'>)</span>

<span class='co'># S3 method for nlme.mmkin</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>

<span class='co'># S3 method for nlme.mmkin</span>
<span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre>

    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
    <table class="ref-arguments">
    <colgroup><col class="name" /><col class="desc" /></colgroup>
    <tr>
      <th>model</th>
      <td><p>An <code><a href='mmkin.html'>mmkin</a></code> row object.</p></td>
    </tr>
    <tr>
      <th>data</th>
      <td><p>Ignored, data are taken from the mmkin model</p></td>
    </tr>
    <tr>
      <th>fixed</th>
      <td><p>Ignored, all degradation parameters fitted in the
mmkin model are used as fixed parameters</p></td>
    </tr>
    <tr>
      <th>random</th>
      <td><p>If not specified, all fixed effects are complemented
with uncorrelated random effects</p></td>
    </tr>
    <tr>
      <th>groups</th>
      <td><p>See the documentation of nlme</p></td>
    </tr>
    <tr>
      <th>start</th>
      <td><p>If not specified, mean values of the fitted degradation
parameters taken from the mmkin object are used</p></td>
    </tr>
    <tr>
      <th>correlation</th>
      <td><p>See the documentation of nlme</p></td>
    </tr>
    <tr>
      <th>weights</th>
      <td><p>passed to nlme</p></td>
    </tr>
    <tr>
      <th>subset</th>
      <td><p>passed to nlme</p></td>
    </tr>
    <tr>
      <th>method</th>
      <td><p>passed to nlme</p></td>
    </tr>
    <tr>
      <th>na.action</th>
      <td><p>passed to nlme</p></td>
    </tr>
    <tr>
      <th>naPattern</th>
      <td><p>passed to nlme</p></td>
    </tr>
    <tr>
      <th>control</th>
      <td><p>passed to nlme</p></td>
    </tr>
    <tr>
      <th>verbose</th>
      <td><p>passed to nlme</p></td>
    </tr>
    <tr>
      <th>x</th>
      <td><p>An nlme.mmkin object to print</p></td>
    </tr>
    <tr>
      <th>...</th>
      <td><p>Update specifications passed to update.nlme</p></td>
    </tr>
    <tr>
      <th>object</th>
      <td><p>An nlme.mmkin object to update</p></td>
    </tr>
    </table>

    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>

    <p>Upon success, a fitted nlme.mmkin object, which is an nlme object
with additional elements</p>
    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>

    <div class='dont-index'><p><code><a href='nlme_function.html'>nlme_function</a></code></p></div>

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
    <pre class="examples"><div class='input'><span class='va'>ds</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>,
 <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span>, <span class='va'>name</span> <span class='op'>==</span> <span class='st'>"parent"</span><span class='op'>)</span><span class='op'>)</span>
<span class='va'>f</span> <span class='op'>&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/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p =  0.0195</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p =  0.00985</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p =  0.011</span></div><div class='input'><span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://svn.r-project.org/R-packages/trunk/nlme/'>nlme</a></span><span class='op'>)</span>
<span class='va'>f_nlme_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
<span class='va'>f_nlme_dfop</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo</span>, <span class='va'>f_nlme_dfop</span><span class='op'>)</span>
</div><div class='output co'>#&gt;             df      AIC
#&gt; f_nlme_sfo   5 625.0539
#&gt; f_nlme_dfop  9 495.1270</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by maximum likelihood
#&gt;   Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k1,      log_k2, g_ilr) 
#&gt;   Data: "Not shown" 
#&gt;   Log-likelihood: -238.5635
#&gt;   Fixed: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1) 
#&gt;    parent_0      log_k1      log_k2       g_ilr 
#&gt; 94.17015133 -1.80015306 -4.14738870  0.02290935 
#&gt; 
#&gt; Random effects:
#&gt;  Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1)
#&gt;  Level: ds
#&gt;  Structure: Diagonal
#&gt;         parent_0    log_k1  log_k2     g_ilr Residual
#&gt; StdDev: 2.488249 0.8447273 1.32965 0.3289311 2.321364
#&gt; 
#&gt; Number of Observations: 90
#&gt; Number of Groups: 5 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span>
</div><div class='output co'>#&gt; $distimes
#&gt;            DT50     DT90 DT50back  DT50_k1  DT50_k2
#&gt; parent 10.79857 100.7937 30.34193 4.193938 43.85443
#&gt; </div><div class='input'><span class='co'># \dontrun{</span>
  <span class='va'>f_nlme_2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span>, start <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent_0 <span class='op'>=</span> <span class='fl'>100</span>, log_k_parent <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span><span class='op'>)</span>
  <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_nlme_2</span>, random <span class='op'>=</span> <span class='va'>parent_0</span> <span class='op'>~</span> <span class='fl'>1</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by maximum likelihood
#&gt;   Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_parent) 
#&gt;   Data: "Not shown" 
#&gt;   Log-likelihood: -404.3729
#&gt;   Fixed: list(parent_0 ~ 1, log_k_parent ~ 1) 
#&gt;     parent_0 log_k_parent 
#&gt;    75.933480    -3.555983 
#&gt; 
#&gt; Random effects:
#&gt;  Formula: parent_0 ~ 1 | ds
#&gt;            parent_0 Residual
#&gt; StdDev: 0.002416792 21.63027
#&gt; 
#&gt; Number of Observations: 90
#&gt; Number of Groups: 5 </div><div class='input'>  <span class='va'>ds_2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>,
   <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span>
  <span class='va'>m_sfo_sfo</span> <span class='op'>&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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
    A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"min"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
  <span class='va'>m_sfo_sfo_ff</span> <span class='op'>&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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
    A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
  <span class='va'>m_fomc_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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
    A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
  <span class='va'>m_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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
    A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>

  <span class='va'>f_2</span> <span class='op'>&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'>list</a></span><span class='op'>(</span><span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>m_sfo_sfo</span>,
   <span class='st'>"SFO-SFO-ff"</span> <span class='op'>=</span> <span class='va'>m_sfo_sfo_ff</span>,
   <span class='st'>"FOMC-SFO"</span> <span class='op'>=</span> <span class='va'>m_fomc_sfo</span>,
   <span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>m_dfop_sfo</span><span class='op'>)</span>,
    <span class='va'>ds_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># Separate fits for datasets 3 and 4</span>
</div><div class='img'><img src='nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'>
  <span class='va'>f_nlme_sfo_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
  <span class='co'># plot(f_nlme_sfo_sfo) # not feasible with pkgdown figures</span>
  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>)</span> <span class='co'># Global mixed model: Fits for datasets 3 and 4</span>
</div><div class='img'><img src='nlme.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'>
  <span class='co'># With formation fractions</span>
  <span class='va'>f_nlme_sfo_sfo_ff</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"SFO-SFO-ff"</span>, <span class='op'>]</span><span class='op'>)</span>
  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo_ff</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>)</span> <span class='co'># chi2 different due to different df attribution</span>
</div><div class='img'><img src='nlme.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'>
  <span class='co'># For more parameters, we need to increase pnlsMaxIter and the tolerance</span>
  <span class='co'># to get convergence</span>
  <span class='va'>f_nlme_fomc_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"FOMC-SFO"</span>, <span class='op'>]</span>,
    control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>100</span>, tolerance <span class='op'>=</span> <span class='fl'>1e-4</span><span class='op'>)</span>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
</div><div class='output co'>#&gt; 
#&gt; **Iteration 1
#&gt; LME step: Loglik: -394.1603, nlminb iterations: 3
#&gt; reStruct  parameters:
#&gt;        ds1        ds2        ds3        ds4        ds5 
#&gt; -0.2079793  0.8563830  1.7454105  1.0917354  1.2756825 
#&gt;  Beginning PNLS step: ..  completed fit_nlme() step.
#&gt; PNLS step: RSS =  643.8803 
#&gt;  fixed effects: 94.17379  -5.473193  -0.6970236  -0.2025091  2.103883  
#&gt;  iterations: 100 
#&gt; Convergence crit. (must all become &lt;= tolerance = 0.0001):
#&gt;     fixed  reStruct 
#&gt; 0.7960134 0.1447728 
#&gt; 
#&gt; **Iteration 2
#&gt; LME step: Loglik: -396.3824, nlminb iterations: 7
#&gt; reStruct  parameters:
#&gt;           ds1           ds2           ds3           ds4           ds5 
#&gt; -1.712404e-01 -2.432655e-05  1.842120e+00  1.073975e+00  1.322925e+00 
#&gt;  Beginning PNLS step: ..  completed fit_nlme() step.
#&gt; PNLS step: RSS =  643.8035 
#&gt;  fixed effects: 94.17385  -5.473487  -0.6970404  -0.2025137  2.103871  
#&gt;  iterations: 100 
#&gt; Convergence crit. (must all become &lt;= tolerance = 0.0001):
#&gt;        fixed     reStruct 
#&gt; 5.382757e-05 1.236667e-03 
#&gt; 
#&gt; **Iteration 3
#&gt; LME step: Loglik: -396.3825, nlminb iterations: 7
#&gt; reStruct  parameters:
#&gt;           ds1           ds2           ds3           ds4           ds5 
#&gt; -0.1712499044 -0.0001499831  1.8420971364  1.0739799123  1.3229167796 
#&gt;  Beginning PNLS step: ..  completed fit_nlme() step.
#&gt; PNLS step: RSS =  643.7948 
#&gt;  fixed effects: 94.17386  -5.473521  -0.6970422  -0.2025144  2.10387  
#&gt;  iterations: 100 
#&gt; Convergence crit. (must all become &lt;= tolerance = 0.0001):
#&gt;        fixed     reStruct 
#&gt; 6.072817e-06 1.400857e-04 
#&gt; 
#&gt; **Iteration 4
#&gt; LME step: Loglik: -396.3825, nlminb iterations: 7
#&gt; reStruct  parameters:
#&gt;           ds1           ds2           ds3           ds4           ds5 
#&gt; -0.1712529502 -0.0001641277  1.8420957542  1.0739797181  1.3229173076 
#&gt;  Beginning PNLS step: ..  completed fit_nlme() step.
#&gt; PNLS step: RSS =  643.7936 
#&gt;  fixed effects: 94.17386  -5.473526  -0.6970426  -0.2025146  2.103869  
#&gt;  iterations: 100 
#&gt; Convergence crit. (must all become &lt;= tolerance = 0.0001):
#&gt;        fixed     reStruct 
#&gt; 1.027451e-06 2.275704e-05 </div><div class='input'>  <span class='va'>f_nlme_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>,
    control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>5e-4</span><span class='op'>)</span>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
</div><div class='output co'>#&gt; 
#&gt; **Iteration 1
#&gt; LME step: Loglik: -404.9582, nlminb iterations: 1
#&gt; reStruct  parameters:
#&gt;        ds1        ds2        ds3        ds4        ds5        ds6 
#&gt; -0.4114355  0.9798697  1.6990037  0.7293315  0.3354323  1.7113046 
#&gt;  Beginning PNLS step: ..  completed fit_nlme() step.
#&gt; PNLS step: RSS =  630.3644 
#&gt;  fixed effects: 93.82269  -5.455991  -0.6788957  -1.862196  -4.199671  0.05532828  
#&gt;  iterations: 120 
#&gt; Convergence crit. (must all become &lt;= tolerance = 0.0005):
#&gt;     fixed  reStruct 
#&gt; 0.7885368 0.5822683 
#&gt; 
#&gt; **Iteration 2
#&gt; LME step: Loglik: -407.7755, nlminb iterations: 11
#&gt; reStruct  parameters:
#&gt;          ds1          ds2          ds3          ds4          ds5          ds6 
#&gt; -0.371224133  0.003056179  1.789939402  0.724671158  0.301602977  1.754200729 
#&gt;  Beginning PNLS step: ..  completed fit_nlme() step.
#&gt; PNLS step: RSS =  630.3633 
#&gt;  fixed effects: 93.82269  -5.455992  -0.6788958  -1.862196  -4.199671  0.05532831  
#&gt;  iterations: 120 
#&gt; Convergence crit. (must all become &lt;= tolerance = 0.0005):
#&gt;        fixed     reStruct 
#&gt; 4.789774e-07 2.200661e-05 </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_2</span><span class='op'>[</span><span class='st'>"FOMC-SFO"</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>]</span><span class='op'>)</span>
</div><div class='img'><img src='nlme.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_fomc_sfo</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>)</span>
</div><div class='img'><img src='nlme.mmkin-5.png' alt='' width='700' height='433' /></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_2</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>]</span><span class='op'>)</span>
</div><div class='img'><img src='nlme.mmkin-6.png' alt='' width='700' height='433' /></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>)</span>
</div><div class='img'><img src='nlme.mmkin-7.png' alt='' width='700' height='433' /></div><div class='input'>
  <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='va'>f_nlme_fomc_sfo</span>, <span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span>
</div><div class='output co'>#&gt;                 Model df       AIC       BIC    logLik   Test   L.Ratio p-value
#&gt; f_nlme_dfop_sfo     1 13  843.8547  884.6201 -408.9273                         
#&gt; f_nlme_fomc_sfo     2 11  818.5149  853.0087 -398.2575 1 vs 2  21.33975  &lt;.0001
#&gt; f_nlme_sfo_sfo      3  9 1085.1821 1113.4043 -533.5910 2 vs 3 270.66716  &lt;.0001</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span> <span class='co'># if we ignore FOMC</span>
</div><div class='output co'>#&gt;                 Model df       AIC       BIC    logLik   Test  L.Ratio p-value
#&gt; f_nlme_dfop_sfo     1 13  843.8547  884.6201 -408.9273                        
#&gt; f_nlme_sfo_sfo      2  9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3274  &lt;.0001</div><div class='input'>
  <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span>
</div><div class='output co'>#&gt; $ff
#&gt; parent_sink   parent_A1     A1_sink 
#&gt;   0.5912432   0.4087568   1.0000000 
#&gt; 
#&gt; $distimes
#&gt;            DT50     DT90
#&gt; parent 19.13518  63.5657
#&gt; A1     66.02155 219.3189
#&gt; </div><div class='input'>  <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span><span class='op'>)</span>
</div><div class='output co'>#&gt; $ff
#&gt;   parent_A1 parent_sink 
#&gt;   0.2768574   0.7231426 
#&gt; 
#&gt; $distimes
#&gt;             DT50     DT90 DT50back  DT50_k1  DT50_k2
#&gt; parent  11.07091 104.6320 31.49738 4.462384 46.20825
#&gt; A1     162.30536 539.1667       NA       NA       NA
#&gt; </div><div class='input'>
  <span class='kw'>if</span> <span class='op'>(</span><span class='fu'>findFunction</span><span class='op'>(</span><span class='st'>"varConstProp"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span> <span class='co'># tc error model for nlme available</span>
    <span class='co'># Attempts to fit metabolite kinetics with the tc error model</span>
    <span class='co'>#f_2_tc &lt;- mmkin(list("SFO-SFO" = m_sfo_sfo,</span>
    <span class='co'>#  "SFO-SFO-ff" = m_sfo_sfo_ff,</span>
    <span class='co'>#  "FOMC-SFO" = m_fomc_sfo,</span>
    <span class='co'>#  "DFOP-SFO" = m_dfop_sfo),</span>
    <span class='co'>#   ds_2, quiet = TRUE,</span>
    <span class='co'>#   error_model = "tc")</span>
    <span class='co'>#f_nlme_sfo_sfo_tc &lt;- nlme(f_2_tc["SFO-SFO", ], control = list(maxIter = 100))</span>
    <span class='co'>#f_nlme_dfop_sfo_tc &lt;- nlme(f_2_tc["DFOP-SFO", ])</span>
    <span class='co'>#f_nlme_dfop_sfo_tc &lt;- update(f_nlme_dfop_sfo, weights = varConstProp(),</span>
    <span class='co'>#  control = list(sigma = 1, msMaxIter = 100, pnlsMaxIter = 15))</span>
    <span class='co'># Fitting metabolite kinetics with nlme.mmkin and the two-component</span>
    <span class='co'># error model currently does not work, at least not with these data.</span>

    <span class='va'>f_tc</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/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
    <span class='va'>f_nlme_sfo_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_tc</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
    <span class='va'>f_nlme_dfop_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_tc</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
    <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo</span>, <span class='va'>f_nlme_sfo_tc</span>, <span class='va'>f_nlme_dfop</span>, <span class='va'>f_nlme_dfop_tc</span><span class='op'>)</span>
    <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_tc</span><span class='op'>)</span>
  <span class='op'>}</span>
</div><div class='output co'>#&gt; <span class='error'>Error in if (findFunction("varConstProp")) {    f_tc &lt;- mmkin(c("SFO", "DFOP"), ds, quiet = TRUE, error_model = "tc")    f_nlme_sfo_tc &lt;- nlme(f_tc["SFO", ])    f_nlme_dfop_tc &lt;- nlme(f_tc["DFOP", ])    AIC(f_nlme_sfo, f_nlme_sfo_tc, f_nlme_dfop, f_nlme_dfop_tc)    print(f_nlme_dfop_tc)}: argument is not interpretable as logical</span></div><div class='input'>  <span class='va'>f_2_obs</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'>list</a></span><span class='op'>(</span><span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>m_sfo_sfo</span>,
   <span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>m_dfop_sfo</span><span class='op'>)</span>,
    <span class='va'>ds_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span><span class='op'>)</span>
  <span class='va'>f_nlme_sfo_sfo_obs</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2_obs</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
  <span class='co'># The same with DFOP-SFO does not converge, apparently the variances of</span>
  <span class='co'># parent and A1 are too similar in this case, so that the model is</span>
  <span class='co'># overparameterised</span>
  <span class='co'>#f_nlme_dfop_sfo_obs &lt;- nlme(f_2_obs["DFOP-SFO", ], control = list(maxIter = 100))</span>
<span class='co'># }</span>
</div></pre>
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