A plot method for nlme.mmkin fits

7 files changed, 599 insertions, 16 deletions

diff --git a/docs/news/index.html b/docs/news/index.html
index c8d7ce3d..5fd97344 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -134,6 +134,7 @@
 <a href="#mkin-0-9-49-10-unreleased" class="anchor"></a>mkin 0.9.49.10 (unreleased)<small> Unreleased </small>
 </h1>
 <ul>
+<li><p>‘nlme.mmkin’: An nlme method for mmkin row objects and an associated class with plot method</p></li>
 <li><p>‘mean_degparms, nlme_data, nlme_function’: Three new functions to facilitate building nlme models from mmkin row objects</p></li>
 <li><p>‘endpoints’: Don’t return the SFORB list component if it’s empty. This reduces distraction and complies with the documentation</p></li>
 <li><p>Article in compiled models: Add some platform specific code and suppress warnings about zero values being removed from the FOCUS D dataset</p></li>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 31f7678c..3c5f1b38 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -270,12 +270,32 @@ of an mmkin object</p></td>
           <p><code><a href="AIC.mmkin.html">AIC(<i>&lt;mmkin&gt;</i>)</a></code> <code><a href="AIC.mmkin.html">BIC(<i>&lt;mmkin&gt;</i>)</a></code> </p>
         </td>
         <td><p>Calculate the AIC for a column of an mmkin object</p></td>
+      </tr>
+    </tbody><tbody>
+      <tr>
+        <th colspan="2">
+          <h2 id="section-mixed-models" class="hasAnchor"><a href="#section-mixed-models" class="anchor"></a>Mixed models</h2>
+          <p class="section-desc"><p>Create and work with nonlinear mixed models</p></p>
+        </th>
+      </tr>
+      <tr>
+        
+        <td>
+          <p><code><a href="nlme.mmkin.html">nlme(<i>&lt;mmkin&gt;</i>)</a></code> </p>
+        </td>
+        <td><p>Create an nlme model for an mmkin row object</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="plot.nlme.mmkin.html">plot(<i>&lt;nlme.mmkin&gt;</i>)</a></code> </p>
+        </td>
+        <td><p>Plot a fitted nonlinear mixed model obtained via an mmkin row object</p></td>
       </tr><tr>
         
         <td>
           <p><code><a href="nlme.html">nlme_function()</a></code> <code><a href="nlme.html">mean_degparms()</a></code> <code><a href="nlme.html">nlme_data()</a></code> </p>
         </td>
-        <td><p>Estimation of parameter distributions from mmkin row objects</p></td>
+        <td><p>Helper functions to create nlme models from mmkin row objects</p></td>
       </tr>
     </tbody><tbody>
       <tr>
@@ -576,6 +596,7 @@ kinetic models fitted with mkinfit</p></td>
       <li><a href="#section-main-functions">Main functions</a></li>
       <li><a href="#section-show-results">Show results</a></li>
       <li><a href="#section-work-with-mmkin-objects">Work with mmkin objects</a></li>
+      <li><a href="#section-mixed-models">Mixed models</a></li>
       <li><a href="#section-datasets-and-known-results">Datasets and known results</a></li>
       <li><a href="#section-nafta-guidance">NAFTA guidance</a></li>
       <li><a href="#section-helper-functions-mainly-used-internally">Helper functions mainly used internally</a></li>
diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html
index 1b05f882..981845fe 100644
--- a/docs/reference/nlme.html
+++ b/docs/reference/nlme.html
@@ -6,7 +6,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-<title>Estimation of parameter distributions from mmkin row objects — nlme_function • mkin</title>
+<title>Helper functions to create nlme models from mmkin row objects — nlme_function • mkin</title>
 
 
 <!-- jquery -->
@@ -35,7 +35,7 @@
 
 
 
-<meta property="og:title" content="Estimation of parameter distributions from mmkin row objects — nlme_function" />
+<meta property="og:title" content="Helper functions to create nlme models from mmkin row objects — nlme_function" />
 <meta property="og:description" content="These functions facilitate setting up a nonlinear mixed effects model for
 an mmkin row object. An mmkin row object is essentially a list of mkinfit
 objects that have been obtained by fitting the same model to a list of
@@ -130,7 +130,7 @@ datasets." />
 <div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
-    <h1>Estimation of parameter distributions from mmkin row objects</h1>
+    <h1>Helper functions to create nlme models from mmkin row objects</h1>
     
     <div class="hidden name"><code>nlme.Rd</code></div>
     </div>
@@ -255,37 +255,39 @@ datasets.</p>
   <span class='no'>nlme_f_sfo_sfo</span> <span class='kw'>&lt;-</span> <span class='fu'>nlme_function</span>(<span class='no'>f_2</span>[<span class='st'>"SFO-SFO"</span>, ])
   <span class='no'>nlme_f_sfo_sfo_ff</span> <span class='kw'>&lt;-</span> <span class='fu'>nlme_function</span>(<span class='no'>f_2</span>[<span class='st'>"SFO-SFO-ff"</span>, ])
   <span class='no'>nlme_f_fomc_sfo</span> <span class='kw'>&lt;-</span> <span class='fu'>nlme_function</span>(<span class='no'>f_2</span>[<span class='st'>"FOMC-SFO"</span>, ])
+  <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span>(<span class='st'>"nlme_f_sfo_sfo"</span>, <span class='no'>nlme_f_sfo_sfo</span>, <span class='fu'><a href='https://rdrr.io/r/base/environment.html'>globalenv</a></span>())
+  <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span>(<span class='st'>"nlme_f_sfo_sfo_ff"</span>, <span class='no'>nlme_f_sfo_sfo_ff</span>, <span class='fu'><a href='https://rdrr.io/r/base/environment.html'>globalenv</a></span>())
+  <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span>(<span class='st'>"nlme_f_fomc_sfo"</span>, <span class='no'>nlme_f_fomc_sfo</span>, <span class='fu'><a href='https://rdrr.io/r/base/environment.html'>globalenv</a></span>())
 
-  <span class='co'># Allowing for correlations between random effects leads to non-convergence</span>
+  <span class='co'># Allowing for correlations between random effects (not shown)</span>
+  <span class='co'># leads to non-convergence</span>
   <span class='no'>f_nlme_sfo_sfo</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>value</span> ~ <span class='fu'>nlme_f_sfo_sfo</span>(<span class='no'>name</span>, <span class='no'>time</span>,
        <span class='no'>parent_0</span>, <span class='no'>log_k_parent_sink</span>, <span class='no'>log_k_parent_A1</span>, <span class='no'>log_k_A1_sink</span>),
      <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>grouped_data_2</span>,
      <span class='kw'>fixed</span> <span class='kw'>=</span> <span class='no'>parent_0</span> + <span class='no'>log_k_parent_sink</span> + <span class='no'>log_k_parent_A1</span> + <span class='no'>log_k_A1_sink</span> ~ <span class='fl'>1</span>,
      <span class='kw'>random</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/pdDiag.html'>pdDiag</a></span>(<span class='no'>parent_0</span> + <span class='no'>log_k_parent_sink</span> + <span class='no'>log_k_parent_A1</span> + <span class='no'>log_k_A1_sink</span> ~ <span class='fl'>1</span>),
-     <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp_sfo_sfo</span>)</div><div class='output co'>#&gt; <span class='error'>Error in nlme_f_sfo_sfo(name, time, parent_0, log_k_parent_sink, log_k_parent_A1,     log_k_A1_sink): konnte Funktion "nlme_f_sfo_sfo" nicht finden</span></div><div class='input'>
+     <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp_sfo_sfo</span>)
+   <span class='co'># augPred does not see to work on this object, so no plot is shown</span>
+
   <span class='co'># The same model fitted with transformed formation fractions does not converge</span>
   <span class='no'>f_nlme_sfo_sfo_ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>value</span> ~ <span class='fu'>nlme_f_sfo_sfo_ff</span>(<span class='no'>name</span>, <span class='no'>time</span>,
        <span class='no'>parent_0</span>, <span class='no'>log_k_parent</span>, <span class='no'>log_k_A1</span>, <span class='no'>f_parent_ilr_1</span>),
      <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>grouped_data_2</span>,
      <span class='kw'>fixed</span> <span class='kw'>=</span> <span class='no'>parent_0</span> + <span class='no'>log_k_parent</span> + <span class='no'>log_k_A1</span> + <span class='no'>f_parent_ilr_1</span> ~ <span class='fl'>1</span>,
      <span class='kw'>random</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/pdDiag.html'>pdDiag</a></span>(<span class='no'>parent_0</span> + <span class='no'>log_k_parent</span> + <span class='no'>log_k_A1</span> + <span class='no'>f_parent_ilr_1</span> ~ <span class='fl'>1</span>),
-     <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp_sfo_sfo_ff</span>)</div><div class='output co'>#&gt; <span class='error'>Error in nlme_f_sfo_sfo_ff(name, time, parent_0, log_k_parent, log_k_A1,     f_parent_ilr_1): konnte Funktion "nlme_f_sfo_sfo_ff" nicht finden</span></div><div class='input'>
-  <span class='co'># It does converge with this version of reduced random effects</span>
-  <span class='no'>f_nlme_sfo_sfo_ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>value</span> ~ <span class='fu'>nlme_f_sfo_sfo_ff</span>(<span class='no'>name</span>, <span class='no'>time</span>,
-       <span class='no'>parent_0</span>, <span class='no'>log_k_parent</span>, <span class='no'>log_k_A1</span>, <span class='no'>f_parent_ilr_1</span>),
-     <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>grouped_data_2</span>,
-     <span class='kw'>fixed</span> <span class='kw'>=</span> <span class='no'>parent_0</span> + <span class='no'>log_k_parent</span> + <span class='no'>log_k_A1</span> + <span class='no'>f_parent_ilr_1</span> ~ <span class='fl'>1</span>,
-     <span class='kw'>random</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/pdDiag.html'>pdDiag</a></span>(<span class='no'>parent_0</span> + <span class='no'>log_k_parent</span> ~ <span class='fl'>1</span>),
-     <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp_sfo_sfo_ff</span>)</div><div class='output co'>#&gt; <span class='error'>Error in nlme_f_sfo_sfo_ff(name, time, parent_0, log_k_parent, log_k_A1,     f_parent_ilr_1): konnte Funktion "nlme_f_sfo_sfo_ff" nicht finden</span></div><div class='input'>
+     <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp_sfo_sfo_ff</span>)</div><div class='output co'>#&gt; <span class='error'>Error in nlme.formula(value ~ nlme_f_sfo_sfo_ff(name, time, parent_0,     log_k_parent, log_k_A1, f_parent_ilr_1), data = grouped_data_2,     fixed = parent_0 + log_k_parent + log_k_A1 + f_parent_ilr_1 ~         1, random = pdDiag(parent_0 + log_k_parent + log_k_A1 +         f_parent_ilr_1 ~ 1), start = mean_dp_sfo_sfo_ff): step halving factor reduced below minimum in PNLS step</span></div><div class='input'>
   <span class='no'>f_nlme_fomc_sfo</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>value</span> ~ <span class='fu'>nlme_f_fomc_sfo</span>(<span class='no'>name</span>, <span class='no'>time</span>,
        <span class='no'>parent_0</span>, <span class='no'>log_alpha</span>, <span class='no'>log_beta</span>, <span class='no'>log_k_A1</span>, <span class='no'>f_parent_ilr_1</span>),
      <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>grouped_data_2</span>,
      <span class='kw'>fixed</span> <span class='kw'>=</span> <span class='no'>parent_0</span> + <span class='no'>log_alpha</span> + <span class='no'>log_beta</span> + <span class='no'>log_k_A1</span> + <span class='no'>f_parent_ilr_1</span> ~ <span class='fl'>1</span>,
      <span class='kw'>random</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/pdDiag.html'>pdDiag</a></span>(<span class='no'>parent_0</span> + <span class='no'>log_alpha</span> + <span class='no'>log_beta</span> + <span class='no'>log_k_A1</span> + <span class='no'>f_parent_ilr_1</span> ~ <span class='fl'>1</span>),
-     <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp_fomc_sfo</span>)</div><div class='output co'>#&gt; <span class='error'>Error in nlme_f_fomc_sfo(name, time, parent_0, log_alpha, log_beta, log_k_A1,     f_parent_ilr_1): konnte Funktion "nlme_f_fomc_sfo" nicht finden</span></div><div class='input'>
+     <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp_fomc_sfo</span>)
+
   <span class='co'># DFOP-SFO and SFORB-SFO did not converge with full random effects</span>
 
-  <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span>(<span class='no'>f_nlme_fomc_sfo</span>, <span class='no'>f_nlme_sfo_sfo</span>)</div><div class='output co'>#&gt; <span class='error'>Error in anova(f_nlme_fomc_sfo, f_nlme_sfo_sfo): Objekt 'f_nlme_fomc_sfo' nicht gefunden</span></div><div class='input'># }
+  <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span>(<span class='no'>f_nlme_fomc_sfo</span>, <span class='no'>f_nlme_sfo_sfo</span>)</div><div class='output co'>#&gt;                 Model df       AIC       BIC    logLik   Test  L.Ratio p-value
+#&gt; f_nlme_fomc_sfo     1 11  932.5817  967.0755 -455.2909                        
+#&gt; f_nlme_sfo_sfo      2  9 1089.2492 1117.4714 -535.6246 1 vs 2 160.6675  &lt;.0001</div><div class='input'># }
 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html
new file mode 100644
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@@ -0,0 +1,301 @@
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+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." />
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+      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
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+      <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
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+      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
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+      <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
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+    <div class="page-header">
+    <h1>Create an nlme model for an mmkin row object</h1>
+    
+    <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='no'>model</span>,
+  <span class='kw'>data</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/sys.parent.html'>sys.frame</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/sys.parent.html'>sys.parent</a></span>()),
+  <span class='no'>fixed</span>,
+  <span class='kw'>random</span> <span class='kw'>=</span> <span class='no'>fixed</span>,
+  <span class='no'>groups</span>,
+  <span class='no'>start</span>,
+  <span class='kw'>correlation</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+  <span class='kw'>weights</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+  <span class='no'>subset</span>,
+  <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"ML"</span>, <span class='st'>"REML"</span>),
+  <span class='kw'>na.action</span> <span class='kw'>=</span> <span class='no'>na.fail</span>,
+  <span class='no'>naPattern</span>,
+  <span class='kw'>control</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(),
+  <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</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>
+    </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.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='no'>ds</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>6</span>:<span class='fl'>10</span>],
+ <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>x</span>$<span class='no'>data</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span>)], <span class='no'>name</span> <span class='kw'>==</span> <span class='st'>"parent"</span>))
+<span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='st'>"SFO"</span>, <span class='no'>ds</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)
+<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>nlme</span>)
+<span class='no'>f_nlme</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>)
+<span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>, <span class='kw'>random</span> <span class='kw'>=</span> <span class='no'>parent_0</span> ~ <span class='fl'>1</span>)</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by maximum likelihood
+#&gt;   Model: value ~ deg_func(name, time, parent_0, log_k_parent_sink) 
+#&gt;   Data: structure(list(ds = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,  1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L,  2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L,  3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L,  4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,  4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L,  5L, 5L), .Label = c("1", "2", "3", "4", "5"), class = c("ordered",  "factor")), name = c("parent", "parent", "parent", "parent",  "parent", "parent", "parent", "parent", "parent", "parent", "parent",  "parent", "parent", "parent", "parent", "parent", "parent", "parent",  "parent", "parent", "parent", "parent", "parent", "parent", "parent",  "parent", "parent", "parent", "parent", "parent", "parent", "parent",  "parent", "parent", "parent", "parent", "parent", "parent", "parent",  "parent", "parent", "parent", "parent", "parent", "parent", "parent",  "parent", "parent", "parent", "parent", "parent", "parent", "parent",  "parent", "parent", "parent", "parent", "parent", "parent", "parent",  "parent", "parent", "parent", "parent", "parent", "parent", "parent",  "parent", "parent", "parent", "parent", "parent", "parent", "parent",  "parent", "parent", "parent", "parent", "parent", "parent", "parent",  "parent", "parent", "parent", "parent", "parent", "parent", "parent",  "parent", "parent"), time = c(0, 0, 3, 3, 6, 6, 10, 10, 20, 20,  34, 34, 55, 55, 90, 90, 112, 112, 132, 132, 0, 0, 3, 3, 7, 7,  14, 14, 30, 30, 60, 60, 90, 90, 120, 120, 180, 180, 0, 0, 1,  1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 0, 0, 1, 1, 3,  3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 91, 91, 120, 120, 0,  0, 8, 8, 14, 14, 21, 21, 41, 41, 63, 63, 91, 91, 120, 120), value = c(97.2,  96.4, 71.1, 69.2, 58.1, 56.6, 44.4, 43.4, 33.3, 29.2, 17.6, 18,  10.5, 9.3, 4.5, 4.7, 3, 3.4, 2.3, 2.7, 93.6, 92.3, 87, 82.2,  74, 73.9, 64.2, 69.5, 54, 54.6, 41.1, 38.4, 32.5, 35.5, 28.1,  29, 26.5, 27.6, 91.9, 90.8, 64.9, 66.2, 43.5, 44.1, 18.3, 18.1,  10.2, 10.8, 4.9, 3.3, 1.6, 1.5, 1.1, 0.9, 99.8, 98.3, 77.1, 77.2,  59, 58.1, 27.4, 29.2, 19.1, 29.6, 10.1, 18.2, 4.5, 9.1, 2.3,  2.9, 2, 1.8, 2, 2.2, 96.1, 94.3, 73.9, 73.9, 69.4, 73.1, 65.6,  65.3, 55.9, 54.4, 47, 49.3, 44.7, 46.7, 42.1, 41.3)), row.names = c(NA,  -90L), class = c("nfnGroupedData", "nfGroupedData", "groupedData",  "data.frame"), formula = value ~ time | ds, FUN = function (x)  max(x, na.rm = TRUE), order.groups = FALSE) 
+#&gt;   Log-likelihood: -394.4901
+#&gt;   Fixed: list(parent_0 ~ 1, log_k_parent_sink ~ 1) 
+#&gt;          parent_0 log_k_parent_sink 
+#&gt;         73.985522         -3.869079 
+#&gt; 
+#&gt; Random effects:
+#&gt;  Formula: parent_0 ~ 1 | ds
+#&gt;         parent_0 Residual
+#&gt; StdDev:  18.6134 18.22029
+#&gt; 
+#&gt; Number of Observations: 90
+#&gt; Number of Groups: 5 </div><div class='input'><span class='no'>f_nlme</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>, <span class='kw'>start</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent_0</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>log_k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>))
+<span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>f_nlme</span>, <span class='kw'>random</span> <span class='kw'>=</span> <span class='no'>parent_0</span> ~ <span class='fl'>1</span>)</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by maximum likelihood
+#&gt;   Model: value ~ deg_func(name, time, parent_0, log_k_parent_sink) 
+#&gt;   Data: structure(list(ds = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,  1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L,  2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L,  3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L,  4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,  4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L,  5L, 5L), .Label = c("1", "2", "3", "4", "5"), class = c("ordered",  "factor")), name = c("parent", "parent", "parent", "parent",  "parent", "parent", "parent", "parent", "parent", "parent", "parent",  "parent", "parent", "parent", "parent", "parent", "parent", "parent",  "parent", "parent", "parent", "parent", "parent", "parent", "parent",  "parent", "parent", "parent", "parent", "parent", "parent", "parent",  "parent", "parent", "parent", "parent", "parent", "parent", "parent",  "parent", "parent", "parent", "parent", "parent", "parent", "parent",  "parent", "parent", "parent", "parent", "parent", "parent", "parent",  "parent", "parent", "parent", "parent", "parent", "parent", "parent",  "parent", "parent", "parent", "parent", "parent", "parent", "parent",  "parent", "parent", "parent", "parent", "parent", "parent", "parent",  "parent", "parent", "parent", "parent", "parent", "parent", "parent",  "parent", "parent", "parent", "parent", "parent", "parent", "parent",  "parent", "parent"), time = c(0, 0, 3, 3, 6, 6, 10, 10, 20, 20,  34, 34, 55, 55, 90, 90, 112, 112, 132, 132, 0, 0, 3, 3, 7, 7,  14, 14, 30, 30, 60, 60, 90, 90, 120, 120, 180, 180, 0, 0, 1,  1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 0, 0, 1, 1, 3,  3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 91, 91, 120, 120, 0,  0, 8, 8, 14, 14, 21, 21, 41, 41, 63, 63, 91, 91, 120, 120), value = c(97.2,  96.4, 71.1, 69.2, 58.1, 56.6, 44.4, 43.4, 33.3, 29.2, 17.6, 18,  10.5, 9.3, 4.5, 4.7, 3, 3.4, 2.3, 2.7, 93.6, 92.3, 87, 82.2,  74, 73.9, 64.2, 69.5, 54, 54.6, 41.1, 38.4, 32.5, 35.5, 28.1,  29, 26.5, 27.6, 91.9, 90.8, 64.9, 66.2, 43.5, 44.1, 18.3, 18.1,  10.2, 10.8, 4.9, 3.3, 1.6, 1.5, 1.1, 0.9, 99.8, 98.3, 77.1, 77.2,  59, 58.1, 27.4, 29.2, 19.1, 29.6, 10.1, 18.2, 4.5, 9.1, 2.3,  2.9, 2, 1.8, 2, 2.2, 96.1, 94.3, 73.9, 73.9, 69.4, 73.1, 65.6,  65.3, 55.9, 54.4, 47, 49.3, 44.7, 46.7, 42.1, 41.3)), row.names = c(NA,  -90L), class = c("nfnGroupedData", "nfGroupedData", "groupedData",  "data.frame"), formula = value ~ time | ds, FUN = function (x)  max(x, na.rm = TRUE), order.groups = FALSE) 
+#&gt;   Log-likelihood: -404.3729
+#&gt;   Fixed: list(parent_0 ~ 1, log_k_parent_sink ~ 1) 
+#&gt;          parent_0 log_k_parent_sink 
+#&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></pre>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+    <h2>Contents</h2>
+    <ul class="nav nav-pills nav-stacked">
+      <li><a href="#arguments">Arguments</a></li>
+      <li><a href="#value">Value</a></li>
+      <li><a href="#see-also">See also</a></li>
+      <li><a href="#examples">Examples</a></li>
+    </ul>
+
+  </div>
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diff --git a/docs/reference/plot.nlme.mmkin-1.png b/docs/reference/plot.nlme.mmkin-1.png
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+    <h1>Plot a fitted nonlinear mixed model obtained via an mmkin row object</h1>
+    
+    <div class="hidden name"><code>plot.nlme.mmkin.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Plot a fitted nonlinear mixed model obtained via an mmkin row object</p>
+    </div>
+
+    <pre class="usage"><span class='co'># S3 method for nlme.mmkin</span>
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(
+  <span class='no'>x</span>,
+  <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span>(<span class='no'>x</span>$<span class='no'>mmkin_orig</span>),
+  <span class='kw'>main</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+  <span class='kw'>legends</span> <span class='kw'>=</span> <span class='fl'>1</span>,
+  <span class='kw'>resplot</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"time"</span>, <span class='st'>"errmod"</span>),
+  <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+  <span class='kw'>cex</span> <span class='kw'>=</span> <span class='fl'>0.7</span>,
+  <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>,
+  <span class='kw'>ymax</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+  <span class='no'>...</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>x</th>
+      <td><p>An object of class <code><a href='nlme.mmkin.html'>nlme.mmkin</a></code></p></td>
+    </tr>
+    <tr>
+      <th>i</th>
+      <td><p>A numeric index to select datasets for which to plot the nlme fit,
+in case plots get too large</p></td>
+    </tr>
+    <tr>
+      <th>main</th>
+      <td><p>The main title placed on the outer margin of the plot.</p></td>
+    </tr>
+    <tr>
+      <th>legends</th>
+      <td><p>An index for the fits for which legends should be shown.</p></td>
+    </tr>
+    <tr>
+      <th>resplot</th>
+      <td><p>Should the residuals plotted against time, using
+<code><a href='mkinresplot.html'>mkinresplot</a></code>, or as squared residuals against predicted
+values, with the error model, using <code><a href='mkinerrplot.html'>mkinerrplot</a></code>.</p></td>
+    </tr>
+    <tr>
+      <th>standardized</th>
+      <td><p>Should the residuals be standardized? This option
+is passed to <code><a href='mkinresplot.html'>mkinresplot</a></code>, it only takes effect if
+`resplot = "time"`.</p></td>
+    </tr>
+    <tr>
+      <th>cex</th>
+      <td><p>Passed to the plot functions and <code><a href='https://rdrr.io/r/graphics/mtext.html'>mtext</a></code>.</p></td>
+    </tr>
+    <tr>
+      <th>rel.height.middle</th>
+      <td><p>The relative height of the middle plot, if more
+than two rows of plots are shown.</p></td>
+    </tr>
+    <tr>
+      <th>ymax</th>
+      <td><p>Maximum y axis value for <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p></td>
+    </tr>
+    <tr>
+      <th>...</th>
+      <td><p>Further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and
+<code><a href='mkinresplot.html'>mkinresplot</a></code>.</p></td>
+    </tr>
+    </table>
+
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>The function is called for its side effect.</p>
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'><span class='no'>ds</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>6</span>:<span class='fl'>10</span>],
+ <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>x</span>$<span class='no'>data</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span>)], <span class='no'>name</span> <span class='kw'>==</span> <span class='st'>"parent"</span>))
+<span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='st'>"SFO"</span>, <span class='no'>ds</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)
+<span class='co'>#plot(f) # too many panels for pkgdown</span>
+<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>nlme</span>)
+<span class='no'>f_nlme</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>)
+
+<span class='co'>#plot(f_nlme) # too many panels for pkgdown</span>
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>f_nlme</span>, <span class='fl'>1</span>:<span class='fl'>2</span>)</div><div class='img'><img src='plot.nlme.mmkin-1.png' alt='' width='700' height='433' /></div></pre>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+    <h2>Contents</h2>
+    <ul class="nav nav-pills nav-stacked">
+      <li><a href="#arguments">Arguments</a></li>
+      <li><a href="#value">Value</a></li>
+      <li><a href="#examples">Examples</a></li>
+    </ul>
+
+    <h2>Author</h2>
+    <p>Johannes Ranke</p>
+  </div>
+</div>
+
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+      </footer>
+   </div>
+
+  
+
+
+  </body>
+</html>
+
+
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index 8ba032de..d1c86707 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -133,6 +133,9 @@
     <loc>https://pkgdown.jrwb.de/mkin/reference/nlme.html</loc>
   </url>
   <url>
+    <loc>https://pkgdown.jrwb.de/mkin/reference/nlme.mmkin.html</loc>
+  </url>
+  <url>
     <loc>https://pkgdown.jrwb.de/mkin/reference/nobs.mkinfit.html</loc>
   </url>
   <url>
@@ -148,6 +151,9 @@
     <loc>https://pkgdown.jrwb.de/mkin/reference/plot.nafta.html</loc>
   </url>
   <url>
+    <loc>https://pkgdown.jrwb.de/mkin/reference/plot.nlme.mmkin.html</loc>
+  </url>
+  <url>
     <loc>https://pkgdown.jrwb.de/mkin/reference/print.mkinds.html</loc>
   </url>
   <url>