Update static docs

7 files changed, 482 insertions, 24 deletions

diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html
index 3980ea88..4f811b9f 100644
--- a/docs/dev/news/index.html
+++ b/docs/dev/news/index.html
@@ -146,6 +146,7 @@
 <a href="#mkin-0-9-50-4-unreleased" class="anchor"></a>mkin 0.9.50.4 (unreleased)<small> Unreleased </small>
 </h1>
 <ul>
+<li><p>‘saem’ generic function to fit saemix models, with a method ‘saem.mmkin’ and a corresponding ‘summary.saem.mmkin’</p></li>
 <li><p>‘transform_odeparms’, ‘backtransform_odeparms’: Use logit transformation for solitary fractions like the g parameter of the DFOP model, or formation fractions for a pathway to only one target variable</p></li>
 <li><p>‘update’ method for ‘mmkin’ objects</p></li>
 <li><p>‘plot’, ‘summary’ and ‘print’ methods for ‘nlme.mmkin’ objects</p></li>
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index aebac46b..120f4975 100644
--- a/docs/dev/pkgdown.yml
+++ b/docs/dev/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
   web_only/NAFTA_examples: NAFTA_examples.html
   web_only/benchmarks: benchmarks.html
   web_only/compiled_models: compiled_models.html
-last_built: 2020-11-07T12:14Z
+last_built: 2020-11-08T01:44Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/endpoints.html b/docs/dev/reference/endpoints.html
index 5a20a34c..db702c2e 100644
--- a/docs/dev/reference/endpoints.html
+++ b/docs/dev/reference/endpoints.html
@@ -165,8 +165,11 @@ advantage that the SFORB model can also be used for metabolites.</p>
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>fit</th>
-      <td><p>An object of class <code><a href='mkinfit.html'>mkinfit</a></code> or
-<code><a href='nlme.mmkin.html'>nlme.mmkin</a></code></p></td>
+      <td><p>An object of class <a href='mkinfit.html'>mkinfit</a>, <a href='nlme.mmkin.html'>nlme.mmkin</a> or
+<a href='saem.html'>saem.mmkin</a>. Or another object that has list components
+mkinmod containing an <a href='mkinmod.html'>mkinmod</a> degradation model, and two numeric vectors,
+bparms.optim and bparms.fixed, that contain parameter values
+for that model.</p></td>
     </tr>
     </table>
 
@@ -176,9 +179,14 @@ advantage that the SFORB model can also be used for metabolites.</p>
 and, if applicable, a vector of formation fractions named ff
 and, if the SFORB model was in use, a vector of eigenvalues
 of these SFORB models, equivalent to DFOP rate constants</p>
+    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+    <p>Additional DT50 values are calculated from the FOMC DT90 and k1 and k2 from
+HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models</p>
     <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
 
-    <p>The function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p>
+    <p>The function is used internally by <a href='summary.mkinfit.html'>summary.mkinfit</a>,
+<a href='summary.nlme.mmkin.html'>summary.nlme.mmkin</a> and <a href='summary.saem.mmkin.html'>summary.saem.mmkin</a>.</p>
     <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
 
     <p>Johannes Ranke</p>
diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html
index f1884d2b..825c4d27 100644
--- a/docs/dev/reference/index.html
+++ b/docs/dev/reference/index.html
@@ -343,6 +343,12 @@ of an mmkin object</p></td>
       </tr><tr>
         
         <td>
+          <p><code><a href="summary.saem.mmkin.html">summary(<i>&lt;saem.mmkin&gt;</i>)</a></code> <code><a href="summary.saem.mmkin.html">print(<i>&lt;summary.saem.mmkin&gt;</i>)</a></code> </p>
+        </td>
+        <td><p>Summary method for class "saem.mmkin"</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>Helper functions to create nlme models from mmkin row objects</p></td>
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html
index f883eb11..06fcfaa7 100644
--- a/docs/dev/reference/saem.html
+++ b/docs/dev/reference/saem.html
@@ -41,8 +41,8 @@
 
 <meta property="og:title" content="Fit nonlinear mixed models with SAEM — saem" />
 <meta property="og:description" content="This function uses saemix::saemix() as a backend for fitting nonlinear mixed
-effects models created from mmkin row objects using the stochastic approximation
-to the expectation maximisation algorithm (SAEM)." />
+effects models created from mmkin row objects using the Stochastic Approximation
+Expectation Maximisation algorithm (SAEM)." />
 
 
 <meta name="robots" content="noindex">
@@ -147,8 +147,8 @@ to the expectation maximisation algorithm (SAEM)." />
 
     <div class="ref-description">
     <p>This function uses <code><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix::saemix()</a></code> as a backend for fitting nonlinear mixed
-effects models created from <a href='mmkin.html'>mmkin</a> row objects using the stochastic approximation
-to the expectation maximisation algorithm (SAEM).</p>
+effects models created from <a href='mmkin.html'>mmkin</a> row objects using the Stochastic Approximation
+Expectation Maximisation algorithm (SAEM).</p>
     </div>
 
     <pre class="usage"><span class='fu'>saem</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>control</span>, <span class='va'>...</span><span class='op'>)</span>
@@ -205,7 +205,8 @@ by the saemix function?</p></td>
 
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>An <a href='https://rdrr.io/pkg/saemix/man/SaemixObject-class.html'>saemix::SaemixObject</a>.</p>
+    <p>An S3 object of class 'saem.mmkin', containing the fitted
+<a href='https://rdrr.io/pkg/saemix/man/SaemixObject-class.html'>saemix::SaemixObject</a> as a list component named 'so'.</p>
 <p>An <a href='https://rdrr.io/pkg/saemix/man/SaemixModel-class.html'>saemix::SaemixModel</a> object.</p>
 <p>An <a href='https://rdrr.io/pkg/saemix/man/SaemixData-class.html'>saemix::SaemixData</a> object.</p>
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
@@ -215,6 +216,9 @@ obtained by fitting the same model to a list of datasets using <a href='mkinfit.
 <p>Starting values for the fixed effects (population mean parameters, argument
 psi0 of <code><a href='https://rdrr.io/pkg/saemix/man/saemixModel.html'>saemix::saemixModel()</a></code> are the mean values of the parameters found
 using <a href='mmkin.html'>mmkin</a>.</p>
+    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+    <div class='dont-index'><p><a href='summary.saem.mmkin.html'>summary.saem.mmkin</a></p></div>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='co'># \dontrun{</span>
@@ -225,27 +229,27 @@ using <a href='mmkin.html'>mmkin</a>.</p>
   state.ini <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><span class='op'>)</span>, fixed_initials <span class='op'>=</span> <span class='st'>"parent"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 <span class='va'>f_saem_p0_fixed</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_p0_fixed</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Nov  7 13:14:50 2020"
+#&gt; [1] "Sun Nov  8 02:44:42 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Sat Nov  7 13:14:52 2020"</div><div class='input'>
+#&gt; [1] "Sun Nov  8 02:44:43 2020"</div><div class='input'>
 <span class='va'>f_mmkin_parent</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'>"FOMC"</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><span class='op'>)</span>
 <span class='va'>f_saem_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Nov  7 13:14:53 2020"
+#&gt; [1] "Sun Nov  8 02:44:45 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Sat Nov  7 13:14:55 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Sun Nov  8 02:44:46 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Nov  7 13:14:55 2020"
+#&gt; [1] "Sun Nov  8 02:44:47 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Sat Nov  7 13:14:57 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Sun Nov  8 02:44:49 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Nov  7 13:14:57 2020"
+#&gt; [1] "Sun Nov  8 02:44:49 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Sat Nov  7 13:15:00 2020"</div><div class='input'>
+#&gt; [1] "Sun Nov  8 02:44:52 2020"</div><div class='input'>
 <span class='co'># The returned saem.mmkin object contains an SaemixObject, we can use</span>
 <span class='co'># functions from saemix</span>
 <span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'>saemix</span><span class='op'>)</span>
@@ -258,10 +262,10 @@ using <a href='mmkin.html'>mmkin</a>.</p>
 <span class='va'>f_mmkin_parent_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_mmkin_parent</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
 <span class='va'>f_saem_fomc_tc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_tc</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Nov  7 13:15:02 2020"
+#&gt; [1] "Sun Nov  8 02:44:54 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Sat Nov  7 13:15:07 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</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='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
+#&gt; [1] "Sun Nov  8 02:44:59 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</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='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Likelihoods computed by importance sampling </div><div class='output co'>#&gt;        AIC      BIC
 #&gt; 1 467.7644 465.0305
 #&gt; 2 469.4862 466.3617</div><div class='input'>
@@ -271,20 +275,20 @@ using <a href='mmkin.html'>mmkin</a>.</p>
 <span class='co'># This takes about 4 minutes on my system</span>
 <span class='va'>f_saem</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Nov  7 13:15:08 2020"
+#&gt; [1] "Sun Nov  8 02:45:00 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Sat Nov  7 13:19:07 2020"</div><div class='input'>
+#&gt; [1] "Sun Nov  8 02:49:01 2020"</div><div class='output co'>#&gt; <span class='error'>Error in exp(trans_k): non-numeric argument to mathematical function</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 317.7 169.9 258.9</span></div><div class='input'>
 <span class='va'>f_mmkin_des</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'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span><span class='op'>)</span>
 <span class='co'># Using a single core, the following takes about 6 minutes, using 10 cores</span>
 <span class='co'># it is slower instead of faster</span>
 <span class='va'>f_saem_des</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_des</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Nov  7 13:19:26 2020"
+#&gt; [1] "Sun Nov  8 02:49:20 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Sat Nov  7 13:27:33 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</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='va'>f_saemix</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saemix_des</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='error'>Error in compare.saemix(list(f_saemix$so, f_saemix_des$so)): object 'f_saemix' not found</span></div><div class='input'><span class='co'># }</span>
+#&gt; [1] "Sun Nov  8 02:57:30 2020"</div><div class='output co'>#&gt; <span class='error'>Error in exp(trans_k): non-numeric argument to mathematical function</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 591.7 205.6 521.4</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</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='va'>f_saem</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_des</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='error'>Error in compare.saemix(list(f_saem$so, f_saem_des$so)): object 'f_saem' not found</span></div><div class='input'><span class='co'># }</span>
 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html
new file mode 100644
index 00000000..01e8eb12
--- /dev/null
+++ b/docs/dev/reference/summary.saem.mmkin.html
@@ -0,0 +1,436 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+  <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Summary method for class "saem.mmkin" — summary.saem.mmkin • mkin</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+
+<meta property="og:title" content="Summary method for class "saem.mmkin" — summary.saem.mmkin" />
+<meta property="og:description" content="Lists model equations, initial parameter values, optimised parameters
+for fixed effects (population), random effects (deviations from the
+population mean) and residual error model, as well as the resulting
+endpoints such as formation fractions and DT50 values. Optionally
+(default is FALSE), the data are listed in full." />
+
+
+<meta name="robots" content="noindex">
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+
+  </head>
+
+  <body data-spy="scroll" data-target="#toc">
+    <div class="container template-reference-topic">
+      <header>
+      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+  <div class="container">
+    <div class="navbar-header">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
+        <span class="icon-bar"></span>
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+<div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Summary method for class "saem.mmkin"</h1>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/summary.saem.mmkin.R'><code>R/summary.saem.mmkin.R</code></a></small>
+    <div class="hidden name"><code>summary.saem.mmkin.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Lists model equations, initial parameter values, optimised parameters
+for fixed effects (population), random effects (deviations from the
+population mean) and residual error model, as well as the resulting
+endpoints such as formation fractions and DT50 values. Optionally
+(default is FALSE), the data are listed in full.</p>
+    </div>
+
+    <pre class="usage"><span class='co'># S3 method for saem.mmkin</span>
+<span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>object</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span>, verbose <span class='op'>=</span> <span class='cn'>FALSE</span>, distimes <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span>
+
+<span class='co'># S3 method for summary.saem.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>, verbose <span class='op'>=</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>verbose</span>, <span class='va'>...</span><span class='op'>)</span></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 object of class <a href='saem.html'>saem.mmkin</a></p></td>
+    </tr>
+    <tr>
+      <th>data</th>
+      <td><p>logical, indicating whether the full data should be included in
+the summary.</p></td>
+    </tr>
+    <tr>
+      <th>verbose</th>
+      <td><p>Should the summary be verbose?</p></td>
+    </tr>
+    <tr>
+      <th>distimes</th>
+      <td><p>logical, indicating whether DT50 and DT90 values should be
+included.</p></td>
+    </tr>
+    <tr>
+      <th>...</th>
+      <td><p>optional arguments passed to methods like <code>print</code>.</p></td>
+    </tr>
+    <tr>
+      <th>x</th>
+      <td><p>an object of class summary.saem.mmkin</p></td>
+    </tr>
+    <tr>
+      <th>digits</th>
+      <td><p>Number of digits to use for printing</p></td>
+    </tr>
+    </table>
+
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>The summary function returns a list based on the <a href='https://rdrr.io/pkg/saemix/man/SaemixObject-class.html'>saemix::SaemixObject</a>
+obtained in the fit, with at least the following additional components</p>
+<dt>saemixversion, mkinversion, Rversion</dt><dd><p>The saemix, mkin and R versions used</p></dd>
+<dt>date.fit, date.summary</dt><dd><p>The dates where the fit and the summary were
+produced</p></dd>
+<dt>diffs</dt><dd><p>The differential equations used in the degradation model</p></dd>
+<dt>use_of_ff</dt><dd><p>Was maximum or minimum use made of formation fractions</p></dd>
+<dt>data</dt><dd><p>The data</p></dd>
+<dt>confint_trans</dt><dd><p>Transformed parameters as used in the optimisation, with confidence intervals</p></dd>
+<dt>confint_back</dt><dd><p>Backtransformed parameters, with confidence intervals if available</p></dd>
+<dt>ff</dt><dd><p>The estimated formation fractions derived from the fitted
+model.</p></dd>
+<dt>distimes</dt><dd><p>The DT50 and DT90 values for each observed variable.</p></dd>
+<dt>SFORB</dt><dd><p>If applicable, eigenvalues of SFORB components of the model.</p></dd>
+The print method is called for its side effect, i.e. printing the summary.
+
+    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
+
+    <p>Johannes Ranke for the mkin specific parts
+saemix authors for the parts inherited from saemix.</p>
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'><span class='co'># Generate five datasets following SFO kinetics</span>
+<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'>dt50_sfo_in_pop</span> <span class='op'>&lt;-</span> <span class='fl'>50</span>
+<span class='va'>k_in_pop</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span> <span class='op'>/</span> <span class='va'>dt50_sfo_in_pop</span>
+<span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span><span class='op'>(</span><span class='fl'>1234</span><span class='op'>)</span>
+<span class='va'>k_in</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Lognormal.html'>rlnorm</a></span><span class='op'>(</span><span class='fl'>5</span>, <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='va'>k_in_pop</span><span class='op'>)</span>, <span class='fl'>0.5</span><span class='op'>)</span>
+<span class='va'>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='op'>)</span><span class='op'>)</span>
+
+<span class='va'>pred_sfo</span> <span class='op'>&lt;-</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>k</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'>SFO</span>,
+    <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='va'>k</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><span class='op'>)</span>,
+    <span class='va'>sampling_times</span><span class='op'>)</span>
+<span class='op'>}</span>
+
+<span class='va'>ds_sfo_mean</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'>k_in</span>, <span class='va'>pred_sfo</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>ds_sfo_mean</span><span class='op'>)</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"ds"</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>5</span><span class='op'>)</span>
+
+<span class='va'>ds_sfo_syn</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'>ds_sfo_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='fl'>1</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>+</span> <span class='va'>value</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>*</span> <span class='fl'>0.07</span><span class='op'>^</span><span class='fl'>2</span><span class='op'>)</span>,
+    n <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span>
+<span class='op'>}</span><span class='op'>)</span>
+
+<span class='co'># \dontrun{</span>
+<span class='co'># Evaluate using mmkin and saem</span>
+<span class='va'>f_mmkin</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>ds_sfo_syn</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>
+<span class='va'>f_saem</span> <span class='op'>&lt;-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Running main SAEM algorithm
+#&gt; [1] "Sun Nov  8 02:58:03 2020"
+#&gt; ....
+#&gt;     Minimisation finished
+#&gt; [1] "Sun Nov  8 02:58:07 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; saemix version used for fitting:      3.1.9000 
+#&gt; mkin version used for pre-fitting:  0.9.50.4 
+#&gt; R version used for fitting:         4.0.3 
+#&gt; Date of fit:     Sun Nov  8 02:58:07 2020 
+#&gt; Date of summary: Sun Nov  8 02:58:07 2020 
+#&gt; 
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt; 
+#&gt; Data:
+#&gt; 90 observations of 1 variable(s) grouped in 5 datasets
+#&gt; 
+#&gt; Model predictions using solution type analytical 
+#&gt; 
+#&gt; Fitted in 4.175 s using 300, 100 iterations
+#&gt; 
+#&gt; Variance model: Two-component variance function 
+#&gt; 
+#&gt; Mean of starting values for individual parameters:
+#&gt;     parent_0 log_k_parent 
+#&gt;    97.849556    -4.455036 
+#&gt; 
+#&gt; Fixed degradation parameter values:
+#&gt; None
+#&gt; 
+#&gt; Results:
+#&gt; 
+#&gt; Likelihood computed by importance sampling
+#&gt;        AIC      BIC    logLik
+#&gt;   555.6718 553.3284 -271.8359
+#&gt; 
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt;                   est.     lower      upper
+#&gt; parent_0     97.840291 94.701895 100.978686
+#&gt; log_k_parent -4.464246 -5.001413  -3.927078
+#&gt; 
+#&gt; Correlation: 
+#&gt;              prnt_0
+#&gt; log_k_parent 0.022 
+#&gt; 
+#&gt; Random effects:
+#&gt;                      est.     lower     upper
+#&gt; SD.parent_0     3.0805465 0.4960170 5.6650760
+#&gt; SD.log_k_parent 0.6109508 0.2301398 0.9917617
+#&gt; 
+#&gt; Variance model:
+#&gt;           est.      lower      upper
+#&gt; a.1 1.06249961 0.23012265 1.89487657
+#&gt; b.1 0.04649661 0.03060849 0.06238473
+#&gt; 
+#&gt; Backtransformed parameters with asymmetric confidence intervals:
+#&gt;                 est.        lower        upper
+#&gt; parent_0 97.84029088 94.701895315 100.97868644
+#&gt; k_parent  0.01151338  0.006728434   0.01970115
+#&gt; 
+#&gt; Estimated disappearance times:
+#&gt;        DT50 DT90
+#&gt; parent 60.2  200
+#&gt; 
+#&gt; Data:
+#&gt;    ds   name time observed predicted   residual standardized
+#&gt;  ds 1 parent    0    103.6    97.303   6.297361     -1.12720
+#&gt;  ds 1 parent    0     95.9    97.303  -1.402639      0.25107
+#&gt;  ds 1 parent    1     95.4    96.599  -1.198705      0.21583
+#&gt;  ds 1 parent    1     95.3    96.599  -1.298705      0.23383
+#&gt;  ds 1 parent    3     91.6    95.206  -3.606076      0.65693
+#&gt;  ds 1 parent    3     94.5    95.206  -0.706076      0.12863
+#&gt;  ds 1 parent    7     88.1    92.481  -4.380761      0.81692
+#&gt;  ds 1 parent    7     89.6    92.481  -2.880761      0.53720
+#&gt;  ds 1 parent   14     90.3    87.898   2.402166     -0.46649
+#&gt;  ds 1 parent   14     96.0    87.898   8.102166     -1.57340
+#&gt;  ds 1 parent   28     80.2    79.402   0.797948     -0.16783
+#&gt;  ds 1 parent   28     77.9    79.402  -1.502052      0.31593
+#&gt;  ds 1 parent   60     59.3    62.940  -3.639829      0.91247
+#&gt;  ds 1 parent   60     59.6    62.940  -3.339829      0.83726
+#&gt;  ds 1 parent   90     59.4    50.620   8.779547     -2.56999
+#&gt;  ds 1 parent   90     51.0    50.620   0.379547     -0.11110
+#&gt;  ds 1 parent  120     38.8    40.712  -1.912380      0.64706
+#&gt;  ds 1 parent  120     38.9    40.712  -1.812380      0.61323
+#&gt;  ds 2 parent    0    103.2    97.185   6.015158     -1.07774
+#&gt;  ds 2 parent    0     95.1    97.185  -2.084842      0.37354
+#&gt;  ds 2 parent    1     88.3    95.609  -7.309466      1.32706
+#&gt;  ds 2 parent    1    102.4    95.609   6.790534     -1.23285
+#&gt;  ds 2 parent    3     88.4    92.535  -4.134911      0.77071
+#&gt;  ds 2 parent    3     95.2    92.535   2.665089     -0.49675
+#&gt;  ds 2 parent    7     83.5    86.679  -3.179231      0.62426
+#&gt;  ds 2 parent    7     96.4    86.679   9.720769     -1.90873
+#&gt;  ds 2 parent   14     77.3    77.309  -0.009268      0.00199
+#&gt;  ds 2 parent   14     76.0    77.309  -1.309268      0.28113
+#&gt;  ds 2 parent   28     61.7    61.499   0.201491     -0.05137
+#&gt;  ds 2 parent   28     56.5    61.499  -4.998509      1.27449
+#&gt;  ds 2 parent   60     35.1    36.454  -1.353571      0.49087
+#&gt;  ds 2 parent   60     32.2    36.454  -4.253571      1.54256
+#&gt;  ds 2 parent   90     21.2    22.326  -1.125996      0.53604
+#&gt;  ds 2 parent   90     23.3    22.326   0.974004     -0.46368
+#&gt;  ds 2 parent  120     14.1    13.674   0.426440     -0.25110
+#&gt;  ds 2 parent  120     16.9    13.674   3.226440     -1.89983
+#&gt;  ds 3 parent    0     92.4    93.838  -1.437848      0.26501
+#&gt;  ds 3 parent    0     94.0    93.838   0.162152     -0.02989
+#&gt;  ds 3 parent    1     95.7    91.709   3.991384     -0.74932
+#&gt;  ds 3 parent    1     90.8    91.709  -0.908616      0.17058
+#&gt;  ds 3 parent    3     86.7    87.594  -0.893997      0.17409
+#&gt;  ds 3 parent    3     85.8    87.594  -1.793997      0.34934
+#&gt;  ds 3 parent    7     77.1    79.910  -2.810299      0.58817
+#&gt;  ds 3 parent    7     81.5    79.910   1.589701     -0.33271
+#&gt;  ds 3 parent   14     69.1    68.050   1.050102     -0.24845
+#&gt;  ds 3 parent   14     62.4    68.050  -5.649898      1.33675
+#&gt;  ds 3 parent   28     49.1    49.349  -0.248837      0.07412
+#&gt;  ds 3 parent   28     47.2    49.349  -2.148837      0.64010
+#&gt;  ds 3 parent   60     21.9    23.676  -1.775776      0.82085
+#&gt;  ds 3 parent   60     23.6    23.676  -0.075776      0.03503
+#&gt;  ds 3 parent   90     12.4    11.892   0.507660     -0.31425
+#&gt;  ds 3 parent   90     13.8    11.892   1.907660     -1.18088
+#&gt;  ds 3 parent  120      4.9     5.974  -1.073521      0.80099
+#&gt;  ds 3 parent  120      7.5     5.974   1.526479     -1.13895
+#&gt;  ds 4 parent    0     91.8   102.087 -10.287197      1.77084
+#&gt;  ds 4 parent    0    104.6   102.087   2.512803     -0.43256
+#&gt;  ds 4 parent    1    117.5   101.632  15.867689     -2.74145
+#&gt;  ds 4 parent    1     99.3   101.632  -2.332311      0.40295
+#&gt;  ds 4 parent    3     94.0   100.729  -6.728610      1.17100
+#&gt;  ds 4 parent    3     98.7   100.729  -2.028610      0.35304
+#&gt;  ds 4 parent    7    109.2    98.945  10.254756     -1.81080
+#&gt;  ds 4 parent    7     89.2    98.945  -9.745244      1.72083
+#&gt;  ds 4 parent   14    103.3    95.900   7.400009     -1.34021
+#&gt;  ds 4 parent   14    103.0    95.900   7.100009     -1.28588
+#&gt;  ds 4 parent   28     90.8    90.088   0.712227     -0.13563
+#&gt;  ds 4 parent   28     88.7    90.088  -1.387773      0.26427
+#&gt;  ds 4 parent   60     74.8    78.091  -3.291273      0.70124
+#&gt;  ds 4 parent   60     75.3    78.091  -2.791273      0.59471
+#&gt;  ds 4 parent   90     71.1    68.300   2.800407     -0.66075
+#&gt;  ds 4 parent   90     78.0    68.300   9.700407     -2.28880
+#&gt;  ds 4 parent  120     59.1    59.736  -0.635668      0.16554
+#&gt;  ds 4 parent  120     53.8    59.736  -5.935668      1.54574
+#&gt;  ds 5 parent    0     94.9    98.353  -3.452694      0.61266
+#&gt;  ds 5 parent    0    101.8    98.353   3.447306     -0.61171
+#&gt;  ds 5 parent    1     96.1    96.722  -0.621996      0.11187
+#&gt;  ds 5 parent    1     97.1    96.722   0.378004     -0.06799
+#&gt;  ds 5 parent    3     93.8    93.541   0.258738     -0.04781
+#&gt;  ds 5 parent    3     85.8    93.541  -7.741262      1.43043
+#&gt;  ds 5 parent    7     87.6    87.490   0.109848     -0.02141
+#&gt;  ds 5 parent    7     94.0    87.490   6.509848     -1.26885
+#&gt;  ds 5 parent   14     82.5    77.827   4.672679     -0.99818
+#&gt;  ds 5 parent   14     81.7    77.827   3.872679     -0.82728
+#&gt;  ds 5 parent   28     60.0    61.585  -1.585419      0.40382
+#&gt;  ds 5 parent   28     61.0    61.585  -0.585419      0.14911
+#&gt;  ds 5 parent   60     32.5    36.068  -3.568284      1.30251
+#&gt;  ds 5 parent   60     35.5    36.068  -0.568284      0.20744
+#&gt;  ds 5 parent   90     21.8    21.842  -0.042136      0.02028
+#&gt;  ds 5 parent   90     24.4    21.842   2.557864     -1.23088
+#&gt;  ds 5 parent  120     14.1    13.227   0.872898     -0.52035
+#&gt;  ds 5 parent  120     12.1    13.227  -1.127102      0.67189</div><div class='input'><span class='co'># }</span>
+
+</div></pre>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
+  </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> 1.6.1.</p>
+</div>
+
+      </footer>
+   </div>
+
+  
+
+
+  </body>
+</html>
+
+
diff --git a/docs/dev/sitemap.xml b/docs/dev/sitemap.xml
index c5f285f1..d9ef2228 100644
--- a/docs/dev/sitemap.xml
+++ b/docs/dev/sitemap.xml
@@ -190,6 +190,9 @@
     <loc>https://pkgdown.jrwb.de/mkin/reference/summary.nlme.mmkin.html</loc>
   </url>
   <url>
+    <loc>https://pkgdown.jrwb.de/mkin/reference/summary.saem.mmkin.html</loc>
+  </url>
+  <url>
     <loc>https://pkgdown.jrwb.de/mkin/reference/synthetic_data_for_UBA_2014.html</loc>
   </url>
   <url>