Update static docs

15 files changed, 655 insertions, 277 deletions

diff --git a/docs/404.html b/docs/404.html
index 750f0ae7..89c41d21 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -124,7 +124,7 @@ Content not found. Please use links in the navbar.
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.5.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 9a014b09..c3a39708 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -112,7 +112,7 @@
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.5.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer></div>
diff --git a/docs/authors.html b/docs/authors.html
index 9daad578..ab436c86 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -130,7 +130,7 @@ R package version 1.1.2, <a href="https://pkgdown.jrwb.de/mkin/">https://pkgdown
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.5.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer></div>
diff --git a/docs/index.html b/docs/index.html
index 6118572b..67e1702a 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -276,7 +276,7 @@
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.5.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer>
diff --git a/docs/news/index.html b/docs/news/index.html
index d5c30552..faaab288 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -83,12 +83,15 @@
 
     <div class="section level2">
 <h2 class="page-header" data-toc-text="1.1.2" id="mkin-112">mkin 1.1.2<a class="anchor" aria-label="anchor" href="#mkin-112"></a></h2>
-<ul><li><p>‘R/convergence.R’: New generic to show convergence information with a method for ‘mmin’ objects.</p></li>
-<li><p>‘R/illparms.R’: New generic to show ill-defined parameters with methods for ‘mkinfit’ and ‘mmkin’ objects.</p></li>
+<ul><li><p>‘R/mhmkin.R’: New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel.</p></li>
+<li><p>‘R/saem.R’: Implement and test saemix transformations for FOMC and HS. Also, error out if saemix transformations are requested but not supported.</p></li>
+<li><p>‘R/saem.R’: ‘logLik’ and ‘update’ methods for ‘saem.mmkin’ objects.</p></li>
+<li><p>‘R/convergence.R’: New generic to show convergence information with methods for ‘mmkin’ and ‘mhmkin’ objects.</p></li>
+<li><p>‘R/illparms.R’: New generic to show ill-defined parameters with methods for ‘mkinfit’, ‘mmkin’, ‘saem.mmkin’ and ‘mhmkin’ objects.</p></li>
 <li><p>‘R/summary.mmkin.R’: Summary method for mmkin objects.</p></li>
 </ul></div>
     <div class="section level2">
-<h2 class="page-header" data-toc-text="1.1.1" id="mkin-111">mkin 1.1.1<a class="anchor" aria-label="anchor" href="#mkin-111"></a></h2>
+<h2 class="page-header" data-toc-text="1.1.1" id="mkin-111-2022-07-12">mkin 1.1.1 (2022-07-12)<a class="anchor" aria-label="anchor" href="#mkin-111-2022-07-12"></a></h2>
 <ul><li><p>’R/{mkinmod,mkinpredict}.R: Store DLL information in mkinmod objects and use that information in mkinpredict to avoid a performance regression brought by a bugfix in R 4.2.x. Thanks to Tomas Kalibera for his analysis of the problem on the r-package-devel list and his suggestion on how to fix it.</p></li>
 <li><p>‘vignettes/FOCUS_L.rmd’: Remove an outdated note referring to a failure to calculate the covariance matrix for DFOP with the L2 dataset. Since 0.9.45.5 the covariance matrix is available</p></li>
 <li><p>‘vignettes/web_only/benchmarks.rmd’: Add the first benchmark data using my laptop system, therefore add the CPU when showing the benchmark results.</p></li>
@@ -600,7 +603,7 @@
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.5.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer></div>
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 9c5ace2f..b3090f05 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,5 +1,5 @@
 pandoc: 2.9.2.1
-pkgdown: 2.0.5
+pkgdown: 2.0.6
 pkgdown_sha: ~
 articles:
   FOCUS_D: FOCUS_D.html
@@ -11,7 +11,7 @@ articles:
   benchmarks: web_only/benchmarks.html
   compiled_models: web_only/compiled_models.html
   dimethenamid_2018: web_only/dimethenamid_2018.html
-last_built: 2022-07-22T09:39Z
+last_built: 2022-08-10T11:14Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png
index 17a35806..1ec32c4a 100644
--- a/docs/reference/Rplot001.png
+++ b/docs/reference/Rplot001.png
diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png
index f8bf10bb..1af5d4b4 100644
--- a/docs/reference/Rplot003.png
+++ b/docs/reference/Rplot003.png
diff --git a/docs/reference/illparms.html b/docs/reference/illparms.html
index 037d7a8c..cbdbfde2 100644
--- a/docs/reference/illparms.html
+++ b/docs/reference/illparms.html
@@ -1,5 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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>Method to get the names of ill-defined parameters — illparms • 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="Method to get the names of ill-defined parameters — illparms"><meta property="og:description" content="Method to get the names of ill-defined parameters"><!-- 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]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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>Method to get the names of ill-defined parameters — illparms • 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="Method to get the names of ill-defined parameters — illparms"><meta property="og:description" content="The method for generalised nonlinear regression fits as obtained
+with mkinfit and mmkin checks if the degradation parameters
+pass the Wald test (in degradation kinetics often simply called t-test) for
+significant difference from zero. For this test, the parameterisation
+without parameter transformations is used."><!-- 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">
@@ -83,7 +87,11 @@
     </div>
 
     <div class="ref-description">
-    <p>Method to get the names of ill-defined parameters</p>
+    <p>The method for generalised nonlinear regression fits as obtained
+with <a href="mkinfit.html">mkinfit</a> and <a href="mmkin.html">mmkin</a> checks if the degradation parameters
+pass the Wald test (in degradation kinetics often simply called t-test) for
+significant difference from zero. For this test, the parameterisation
+without parameter transformations is used.</p>
     </div>
 
     <div id="ref-usage">
@@ -96,6 +104,15 @@
 <span><span class="fu">illparms</span><span class="op">(</span><span class="va">object</span>, conf.level <span class="op">=</span> <span class="fl">0.95</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># S3 method for illparms.mmkin</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for saem.mmkin</span></span>
+<span><span class="fu">illparms</span><span class="op">(</span><span class="va">object</span>, conf.level <span class="op">=</span> <span class="fl">0.95</span>, random <span class="op">=</span> <span class="cn">TRUE</span>, errmod <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for mhmkin</span></span>
+<span><span class="fu">illparms</span><span class="op">(</span><span class="va">object</span>, conf.level <span class="op">=</span> <span class="fl">0.95</span>, random <span class="op">=</span> <span class="cn">TRUE</span>, errmod <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for illparms.mhmkin</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
@@ -116,14 +133,33 @@
 <dt>x</dt>
 <dd><p>The object to be printed</p></dd>
 
+
+<dt>random</dt>
+<dd><p>For hierarchical fits, should random effects be tested?</p></dd>
+
+
+<dt>errmod</dt>
+<dd><p>For hierarchical fits, should error model parameters be
+tested?</p></dd>
+
 </dl></div>
     <div id="value">
     <h2>Value</h2>
     
 
-<p>For <a href="mkinfit.html">mkinfit</a> objects, a character vector of parameter names
-For <a href="mmkin.html">mmkin</a> objects, an object of class 'illparms.mmkin' with a
-suitable printing method.</p>
+<p>For <a href="mkinfit.html">mkinfit</a> or <a href="saem.html">saem</a> objects, a character vector of parameter
+names. For <a href="mmkin.html">mmkin</a> or <a href="mhmkin.html">mhmkin</a> objects, a matrix like object of class
+'illparms.mmkin' or 'illparms.mhmkin'. The latter objects have a suitable
+printing method.</p>
+    </div>
+    <div id="details">
+    <h2>Details</h2>
+    <p>The method for hierarchical model fits, also known as nonlinear
+mixed-effects model fits as obtained with <a href="saem.html">saem</a> and <a href="mhmkin.html">mhmkin</a>
+checks if any of the confidence intervals for the random
+effects expressed as standard deviations include zero, and if
+the confidence intervals for the error model parameters include
+zero.</p>
     </div>
 
     <div id="ref-examples">
@@ -157,7 +193,7 @@ suitable printing method.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.5.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 482edf08..956648d2 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -98,9 +98,27 @@
         <td><p>Fit one or more kinetic models with one or more state variables to one or
 more datasets</p></td>
       </tr><tr><td>
-          <p><code><a href="nafta.html">nafta()</a></code> <code><a href="nafta.html">print(<i>&lt;nafta&gt;</i>)</a></code> </p>
+          <p><code><a href="mhmkin.html">mhmkin()</a></code> <code><a href="mhmkin.html">`[`(<i>&lt;mhmkin&gt;</i>)</a></code> <code><a href="mhmkin.html">print(<i>&lt;mhmkin&gt;</i>)</a></code> </p>
         </td>
-        <td><p>Evaluate parent kinetics using the NAFTA guidance</p></td>
+        <td><p>Fit nonlinear mixed-effects models built from one or more kinetic
+degradation models and one or more error models</p></td>
+      </tr></tbody><tbody><tr><th colspan="2">
+          <h2 id="generics">Generics <a href="#generics" class="anchor" aria-hidden="true"></a></h2>
+          <p class="section-desc"></p><p>Generic functions introduced by the package</p>
+        </th>
+      </tr></tbody><tbody><tr><td>
+          <p><code><a href="convergence.html">convergence()</a></code> <code><a href="convergence.html">print(<i>&lt;convergence.mmkin&gt;</i>)</a></code> </p>
+        </td>
+        <td><p>Method to get convergence information</p></td>
+      </tr><tr><td>
+          <p><code><a href="illparms.html">illparms()</a></code> <code><a href="illparms.html">print(<i>&lt;illparms.mmkin&gt;</i>)</a></code> <code><a href="illparms.html">print(<i>&lt;illparms.mhmkin&gt;</i>)</a></code> </p>
+        </td>
+        <td><p>Method to get the names of ill-defined parameters</p></td>
+      </tr><tr><td>
+          <p><code><a href="endpoints.html">endpoints()</a></code> </p>
+        </td>
+        <td><p>Function to calculate endpoints for further use from kinetic models fitted
+with mkinfit</p></td>
       </tr></tbody><tbody><tr><th colspan="2">
           <h2 id="show-results">Show results <a href="#show-results" class="anchor" aria-hidden="true"></a></h2>
           <p class="section-desc"></p><p>Functions working with mkinfit objects</p>
@@ -138,11 +156,6 @@ more datasets</p></td>
         </td>
         <td><p>Calculate the minimum error to assume in order to pass the variance test</p></td>
       </tr><tr><td>
-          <p><code><a href="endpoints.html">endpoints()</a></code> </p>
-        </td>
-        <td><p>Function to calculate endpoints for further use from kinetic models fitted
-with mkinfit</p></td>
-      </tr><tr><td>
           <p><code><a href="aw.html">aw()</a></code> </p>
         </td>
         <td><p>Calculate Akaike weights for model averaging</p></td>
@@ -168,20 +181,12 @@ of an mmkin object</p></td>
         </td>
         <td><p>Calculate the AIC for a column of an mmkin object</p></td>
       </tr><tr><td>
-          <p><code><a href="convergence.html">convergence()</a></code> <code><a href="convergence.html">print(<i>&lt;convergence.mmkin&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>Method to get convergence information</p></td>
-      </tr><tr><td>
-          <p><code><a href="illparms.html">illparms()</a></code> <code><a href="illparms.html">print(<i>&lt;illparms.mmkin&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>Method to get the names of ill-defined parameters</p></td>
-      </tr><tr><td>
           <p><code><a href="summary.mmkin.html">summary(<i>&lt;mmkin&gt;</i>)</a></code> <code><a href="summary.mmkin.html">print(<i>&lt;summary.mmkin&gt;</i>)</a></code> </p>
         </td>
         <td><p>Summary method for class "mmkin"</p></td>
       </tr></tbody><tbody><tr><th colspan="2">
           <h2 id="mixed-models">Mixed models <a href="#mixed-models" class="anchor" aria-hidden="true"></a></h2>
-          <p class="section-desc"></p><p>Create and work with nonlinear mixed effects models</p>
+          <p class="section-desc"></p><p>Create and work with nonlinear hierarchical models</p>
         </th>
       </tr></tbody><tbody><tr><td>
           <p><code><a href="nlme.mmkin.html">nlme(<i>&lt;mmkin&gt;</i>)</a></code> <code><a href="nlme.mmkin.html">print(<i>&lt;nlme.mmkin&gt;</i>)</a></code> <code><a href="nlme.mmkin.html">update(<i>&lt;nlme.mmkin&gt;</i>)</a></code> </p>
@@ -192,6 +197,11 @@ of an mmkin object</p></td>
         </td>
         <td><p>Fit nonlinear mixed models with SAEM</p></td>
       </tr><tr><td>
+          <p><code><a href="mhmkin.html">mhmkin()</a></code> <code><a href="mhmkin.html">`[`(<i>&lt;mhmkin&gt;</i>)</a></code> <code><a href="mhmkin.html">print(<i>&lt;mhmkin&gt;</i>)</a></code> </p>
+        </td>
+        <td><p>Fit nonlinear mixed-effects models built from one or more kinetic
+degradation models and one or more error models</p></td>
+      </tr><tr><td>
           <p><code><a href="plot.mixed.mmkin.html">plot(<i>&lt;mixed.mmkin&gt;</i>)</a></code> </p>
         </td>
         <td><p>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</p></td>
@@ -216,7 +226,7 @@ of an mmkin object</p></td>
         </td>
         <td><p>Create a mixed effects model from an mmkin row object</p></td>
       </tr><tr><td>
-          <p><code><a href="reexports.html">reexports</a></code> </p>
+          <p><code><a href="reexports.html">reexports</a></code> <code><a href="reexports.html">intervals</a></code> <code><a href="reexports.html">lrtest</a></code> <code><a href="reexports.html">nlme</a></code> </p>
         </td>
         <td><p>Objects exported from other packages</p></td>
       </tr><tr><td>
@@ -441,7 +451,7 @@ kinetic models fitted with mkinfit</p></td>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.5.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/mhmkin.html b/docs/reference/mhmkin.html
new file mode 100644
index 00000000..25be0af6
--- /dev/null
+++ b/docs/reference/mhmkin.html
@@ -0,0 +1,213 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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>Fit nonlinear mixed-effects models built from one or more kinetic
+degradation models and one or more error models — mhmkin • 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="Fit nonlinear mixed-effects models built from one or more kinetic
+degradation models and one or more error models — mhmkin"><meta property="og:description" content="The name of the methods expresses that (multiple) hierarchichal
+(also known as multilevel) multicompartment kinetic models are
+fitted. Our kinetic models are nonlinear, so we can use various nonlinear
+mixed-effects model fitting functions."><!-- 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>
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+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
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+        <a class="navbar-link" href="../index.html">mkin</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span>
+      </span>
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+
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav"><li>
+  <a href="../reference/index.html">Functions and data</a>
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+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
+    Articles
+     
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+  </a>
+  <ul class="dropdown-menu" role="menu"><li>
+      <a href="../articles/mkin.html">Introduction to mkin</a>
+    </li>
+    <li>
+      <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+    </li>
+    <li>
+      <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+    </li>
+    <li>
+      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+    </li>
+  </ul></li>
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+  <a href="../news/index.html">News</a>
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+      </ul><ul class="nav navbar-nav navbar-right"><li>
+  <a href="https://github.com/jranke/mkin/" class="external-link">
+    <span class="fab fa-github fa-lg"></span>
+     
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+      </ul></div><!--/.nav-collapse -->
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+</div><!--/.navbar -->
+
+      
+
+      </header><div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Fit nonlinear mixed-effects models built from one or more kinetic
+degradation models and one or more error models</h1>
+    <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mhmkin.R" class="external-link"><code>R/mhmkin.R</code></a></small>
+    <div class="hidden name"><code>mhmkin.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>The name of the methods expresses that (<strong>m</strong>ultiple) <strong>h</strong>ierarchichal
+(also known as multilevel) <strong>m</strong>ulticompartment <strong>kin</strong>etic models are
+fitted. Our kinetic models are nonlinear, so we can use various nonlinear
+mixed-effects model fitting functions.</p>
+    </div>
+
+    <div id="ref-usage">
+    <div class="sourceCode"><pre><code>mhmkin(objects, backend = "saemix", algorithm = "saem", ...)
+
+# S3 method for list
+mhmkin(
+  objects,
+  backend = "saemix",
+  ...,
+  cores = if (Sys.info()["sysname"] == "Windows") 1 else parallel::detectCores(),
+  cluster = NULL
+)
+
+# S3 method for mhmkin
+[(x, i, j, ..., drop = FALSE)
+
+# S3 method for mhmkin
+print(x, ...)</code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>objects</dt>
+<dd><p>A list of <a href="mmkin.html">mmkin</a> objects containing fits of the same
+degradation models to the same data, but using different error models.</p></dd>
+
+
+<dt>backend</dt>
+<dd><p>The backend to be used for fitting. Currently, only saemix is
+supported</p></dd>
+
+
+<dt>algorithm</dt>
+<dd><p>The algorithm to be used for fitting (currently not used)</p></dd>
+
+
+<dt>...</dt>
+<dd><p>Further arguments that will be passed to the nonlinear mixed-effects
+model fitting function.</p></dd>
+
+
+<dt>cores</dt>
+<dd><p>The number of cores to be used for multicore processing. This
+is only used when the <code>cluster</code> argument is <code>NULL</code>. On Windows
+machines, cores &gt; 1 is not supported, you need to use the <code>cluster</code>
+argument to use multiple logical processors. Per default, all cores detected
+by <code><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">parallel::detectCores()</a></code> are used, except on Windows where the default
+is 1.</p></dd>
+
+
+<dt>cluster</dt>
+<dd><p>A cluster as returned by makeCluster to be used for
+parallel execution.</p></dd>
+
+
+<dt>x</dt>
+<dd><p>An mhmkin object.</p></dd>
+
+
+<dt>i</dt>
+<dd><p>Row index selecting the fits for specific models</p></dd>
+
+
+<dt>j</dt>
+<dd><p>Column index selecting the fits to specific datasets</p></dd>
+
+
+<dt>drop</dt>
+<dd><p>If FALSE, the method always returns an mhmkin object, otherwise
+either a list of fit objects or a single fit object.</p></dd>
+
+</dl></div>
+    <div id="value">
+    <h2>Value</h2>
+    
+
+<p>A two-dimensional <a href="https://rdrr.io/r/base/array.html" class="external-link">array</a> of fit objects and/or try-errors that can
+be indexed using the degradation model names for the first index (row index)
+and the error model names for the second index (column index), with class
+attribute 'mhmkin'.</p>
+
+
+<p>An object of class <code>mhmkin</code>.</p>
+    </div>
+    <div id="see-also">
+    <h2>See also</h2>
+    <div class="dont-index"><p><code>[.mhmkin</code> for subsetting mhmkin objects</p></div>
+    </div>
+    <div id="author">
+    <h2>Author</h2>
+    <p>Johannes Ranke</p>
+    </div>
+
+  </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></p><p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+</div>
+
+      </footer></div>
+
+  
+
+
+  
+
+  </body></html>
+
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index e5bf1203..3b27ac7f 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -25,7 +25,7 @@ likelihood function."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span>
       </span>
     </div>
 
@@ -103,33 +103,33 @@ likelihood function.</p>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mkinfit</span><span class="op">(</span>
-  <span class="va">mkinmod</span>,
-  <span class="va">observed</span>,
-  parms.ini <span class="op">=</span> <span class="st">"auto"</span>,
-  state.ini <span class="op">=</span> <span class="st">"auto"</span>,
-  err.ini <span class="op">=</span> <span class="st">"auto"</span>,
-  fixed_parms <span class="op">=</span> <span class="cn">NULL</span>,
-  fixed_initials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">mkinmod</span><span class="op">$</span><span class="va">diffs</span><span class="op">)</span><span class="op">[</span><span class="op">-</span><span class="fl">1</span><span class="op">]</span>,
-  from_max_mean <span class="op">=</span> <span class="cn">FALSE</span>,
-  solution_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"auto"</span>, <span class="st">"analytical"</span>, <span class="st">"eigen"</span>, <span class="st">"deSolve"</span><span class="op">)</span>,
-  method.ode <span class="op">=</span> <span class="st">"lsoda"</span>,
-  use_compiled <span class="op">=</span> <span class="st">"auto"</span>,
-  control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>eval.max <span class="op">=</span> <span class="fl">300</span>, iter.max <span class="op">=</span> <span class="fl">200</span><span class="op">)</span>,
-  transform_rates <span class="op">=</span> <span class="cn">TRUE</span>,
-  transform_fractions <span class="op">=</span> <span class="cn">TRUE</span>,
-  quiet <span class="op">=</span> <span class="cn">FALSE</span>,
-  atol <span class="op">=</span> <span class="fl">1e-08</span>,
-  rtol <span class="op">=</span> <span class="fl">1e-10</span>,
-  error_model <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"const"</span>, <span class="st">"obs"</span>, <span class="st">"tc"</span><span class="op">)</span>,
-  error_model_algorithm <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"auto"</span>, <span class="st">"d_3"</span>, <span class="st">"direct"</span>, <span class="st">"twostep"</span>, <span class="st">"threestep"</span>,
-    <span class="st">"fourstep"</span>, <span class="st">"IRLS"</span>, <span class="st">"OLS"</span><span class="op">)</span>,
-  reweight.tol <span class="op">=</span> <span class="fl">1e-08</span>,
-  reweight.max.iter <span class="op">=</span> <span class="fl">10</span>,
-  trace_parms <span class="op">=</span> <span class="cn">FALSE</span>,
-  test_residuals <span class="op">=</span> <span class="cn">FALSE</span>,
-  <span class="va">...</span>
-<span class="op">)</span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinfit</span><span class="op">(</span></span>
+<span>  <span class="va">mkinmod</span>,</span>
+<span>  <span class="va">observed</span>,</span>
+<span>  parms.ini <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span>  state.ini <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span>  err.ini <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span>  fixed_parms <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  fixed_initials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">mkinmod</span><span class="op">$</span><span class="va">diffs</span><span class="op">)</span><span class="op">[</span><span class="op">-</span><span class="fl">1</span><span class="op">]</span>,</span>
+<span>  from_max_mean <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  solution_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"auto"</span>, <span class="st">"analytical"</span>, <span class="st">"eigen"</span>, <span class="st">"deSolve"</span><span class="op">)</span>,</span>
+<span>  method.ode <span class="op">=</span> <span class="st">"lsoda"</span>,</span>
+<span>  use_compiled <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span>  control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>eval.max <span class="op">=</span> <span class="fl">300</span>, iter.max <span class="op">=</span> <span class="fl">200</span><span class="op">)</span>,</span>
+<span>  transform_rates <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  transform_fractions <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  quiet <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  atol <span class="op">=</span> <span class="fl">1e-08</span>,</span>
+<span>  rtol <span class="op">=</span> <span class="fl">1e-10</span>,</span>
+<span>  error_model <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"const"</span>, <span class="st">"obs"</span>, <span class="st">"tc"</span><span class="op">)</span>,</span>
+<span>  error_model_algorithm <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"auto"</span>, <span class="st">"d_3"</span>, <span class="st">"direct"</span>, <span class="st">"twostep"</span>, <span class="st">"threestep"</span>, <span class="st">"fourstep"</span>,</span>
+<span>    <span class="st">"IRLS"</span>, <span class="st">"OLS"</span><span class="op">)</span>,</span>
+<span>  reweight.tol <span class="op">=</span> <span class="fl">1e-08</span>,</span>
+<span>  reweight.max.iter <span class="op">=</span> <span class="fl">10</span>,</span>
+<span>  trace_parms <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  test_residuals <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
@@ -140,6 +140,8 @@ model to be fitted to the data, or one of the shorthand names ("SFO",
 "FOMC", "DFOP", "HS", "SFORB", "IORE"). If a shorthand name is given, a
 parent only degradation model is generated for the variable with the
 highest value in <code>observed</code>.</p></dd>
+
+
 <dt>observed</dt>
 <dd><p>A dataframe with the observed data.  The first column called
 "name" must contain the name of the observed variable for each data point.
@@ -150,6 +152,8 @@ order to avoid problems with fitting the two-component error model. This
 is not expected to be a problem, because in general, values of zero are
 not observed in degradation data, because there is a lower limit of
 detection.</p></dd>
+
+
 <dt>parms.ini</dt>
 <dd><p>A named vector of initial values for the parameters,
 including parameters to be optimised and potentially also fixed parameters
@@ -161,6 +165,8 @@ needs. You can use the parameter lists "bparms.ode" from a previously
 fitted model, which contains the differential equation parameters from
 this model.  This works nicely if the models are nested. An example is
 given below.</p></dd>
+
+
 <dt>state.ini</dt>
 <dd><p>A named vector of initial values for the state variables of
 the model. In case the observed variables are represented by more than one
@@ -170,26 +176,36 @@ is to set the initial value of the first model variable to the mean of the
 time zero values for the variable with the maximum observed value, and all
 others to 0.  If this variable has no time zero observations, its initial
 value is set to 100.</p></dd>
+
+
 <dt>err.ini</dt>
 <dd><p>A named vector of initial values for the error model
 parameters to be optimised.  If set to "auto", initial values are set to
 default values.  Otherwise, inital values for all error model parameters
 must be given.</p></dd>
+
+
 <dt>fixed_parms</dt>
 <dd><p>The names of parameters that should not be optimised but
 rather kept at the values specified in <code>parms.ini</code>. Alternatively,
 a named numeric vector of parameters to be fixed, regardless of the values
 in parms.ini.</p></dd>
+
+
 <dt>fixed_initials</dt>
 <dd><p>The names of model variables for which the initial
 state at time 0 should be excluded from the optimisation. Defaults to all
 state variables except for the first one.</p></dd>
+
+
 <dt>from_max_mean</dt>
 <dd><p>If this is set to TRUE, and the model has only one
 observed variable, then data before the time of the maximum observed value
 (after averaging for each sampling time) are discarded, and this time is
 subtracted from all remaining time values, so the time of the maximum
 observed mean value is the new time zero.</p></dd>
+
+
 <dt>solution_type</dt>
 <dd><p>If set to "eigen", the solution of the system of
 differential equations is based on the spectral decomposition of the
@@ -200,16 +216,24 @@ only implemented for relatively simple degradation models.  The default is
 "auto", which uses "analytical" if possible, otherwise "deSolve" if a
 compiler is present, and "eigen" if no compiler is present and the model
 can be expressed using eigenvalues and eigenvectors.</p></dd>
+
+
 <dt>method.ode</dt>
 <dd><p>The solution method passed via <code><a href="mkinpredict.html">mkinpredict()</a></code>
 to <code><a href="https://rdrr.io/pkg/deSolve/man/ode.html" class="external-link">deSolve::ode()</a></code> in case the solution type is "deSolve". The default
 "lsoda" is performant, but sometimes fails to converge.</p></dd>
+
+
 <dt>use_compiled</dt>
 <dd><p>If set to <code>FALSE</code>, no compiled version of the
 <a href="mkinmod.html">mkinmod</a> model is used in the calls to <code><a href="mkinpredict.html">mkinpredict()</a></code> even if a compiled
 version is present.</p></dd>
+
+
 <dt>control</dt>
 <dd><p>A list of control arguments passed to <code><a href="https://rdrr.io/r/stats/nlminb.html" class="external-link">stats::nlminb()</a></code>.</p></dd>
+
+
 <dt>transform_rates</dt>
 <dd><p>Boolean specifying if kinetic rate constants should
 be transformed in the model specification used in the fitting for better
@@ -218,6 +242,8 @@ TRUE, also alpha and beta parameters of the FOMC model are
 log-transformed, as well as k1 and k2 rate constants for the DFOP and HS
 models and the break point tb of the HS model.  If FALSE, zero is used as
 a lower bound for the rates in the optimisation.</p></dd>
+
+
 <dt>transform_fractions</dt>
 <dd><p>Boolean specifying if formation fractions
 should be transformed in the model specification used in the fitting for
@@ -225,16 +251,24 @@ better compliance with the assumption of normal distribution of the
 estimator. The default (TRUE) is to do transformations. If TRUE,
 the g parameter of the DFOP model is also transformed. Transformations
 are described in <a href="transform_odeparms.html">transform_odeparms</a>.</p></dd>
+
+
 <dt>quiet</dt>
 <dd><p>Suppress printing out the current value of the negative
 log-likelihood after each improvement?</p></dd>
+
+
 <dt>atol</dt>
 <dd><p>Absolute error tolerance, passed to <code><a href="https://rdrr.io/pkg/deSolve/man/ode.html" class="external-link">deSolve::ode()</a></code>. Default
 is 1e-8, which is lower than the default in the <code><a href="https://rdrr.io/pkg/deSolve/man/lsoda.html" class="external-link">deSolve::lsoda()</a></code>
 function which is used per default.</p></dd>
+
+
 <dt>rtol</dt>
 <dd><p>Absolute error tolerance, passed to <code><a href="https://rdrr.io/pkg/deSolve/man/ode.html" class="external-link">deSolve::ode()</a></code>. Default
 is 1e-10, much lower than in <code><a href="https://rdrr.io/pkg/deSolve/man/lsoda.html" class="external-link">deSolve::lsoda()</a></code>.</p></dd>
+
+
 <dt>error_model</dt>
 <dd><p>If the error model is "const", a constant standard
 deviation is assumed.</p>
@@ -246,6 +280,8 @@ used for setting up the likelihood function.  Note that this model
 deviates from the model by Rocke and Lorenzato, as their model implies
 that the errors follow a lognormal distribution for large values, not a
 normal distribution as assumed by this method.</p></dd>
+
+
 <dt>error_model_algorithm</dt>
 <dd><p>If "auto", the selected algorithm depends on
 the error model.  If the error model is "const", unweighted nonlinear
@@ -271,22 +307,35 @@ unweighted least squares, and then iterates optimization of the error
 model parameters and subsequent optimization of the degradation model
 using those error model parameters, until the error model parameters
 converge.</p></dd>
+
+
 <dt>reweight.tol</dt>
 <dd><p>Tolerance for the convergence criterion calculated from
 the error model parameters in IRLS fits.</p></dd>
+
+
 <dt>reweight.max.iter</dt>
 <dd><p>Maximum number of iterations in IRLS fits.</p></dd>
+
+
 <dt>trace_parms</dt>
 <dd><p>Should a trace of the parameter values be listed?</p></dd>
+
+
 <dt>test_residuals</dt>
 <dd><p>Should the residuals be tested for normal distribution?</p></dd>
+
+
 <dt>...</dt>
 <dd><p>Further arguments that will be passed on to
 <code><a href="https://rdrr.io/pkg/deSolve/man/ode.html" class="external-link">deSolve::ode()</a></code>.</p></dd>
+
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    <p>A list with "mkinfit" in the class attribute.</p>
+    
+
+<p>A list with "mkinfit" in the class attribute.</p>
     </div>
     <div id="details">
     <h2>Details</h2>
@@ -325,21 +374,21 @@ Degradation Data. <em>Environments</em> 6(12) 124
 
     <div id="ref-examples">
     <h2>Examples</h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span>
-<span class="r-in"><span class="co"># Use shorthand notation for parent only degradation</span></span>
-<span class="r-in"><span class="va">fit</span> <span class="op">&lt;-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for fitting:    1.1.0 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:       4.2.0 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Wed May 18 20:37:57 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Wed May 18 20:37:57 2022 </span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># Use shorthand notation for parent only degradation</span></span></span>
+<span class="r-in"><span><span class="va">fit</span> <span class="op">&lt;-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for fitting:    1.1.2 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:       4.2.1 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Wed Aug 10 13:14:25 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Wed Aug 10 13:14:25 2022 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type analytical </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted using 222 model solutions performed in 0.041 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted using 222 model solutions performed in 0.046 s</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Error model: Constant variance </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
@@ -374,10 +423,10 @@ Degradation Data. <em>Environments</em> 6(12) 124
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Parameter correlation:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>             parent_0  log_alpha   log_beta     sigma</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0   1.000e+00 -1.565e-01 -3.142e-01 4.770e-08</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> log_alpha -1.565e-01  1.000e+00  9.564e-01 9.974e-08</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> log_beta  -3.142e-01  9.564e-01  1.000e+00 8.468e-08</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> sigma      4.770e-08  9.974e-08  8.468e-08 1.000e+00</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0   1.000e+00 -1.565e-01 -3.142e-01 4.772e-08</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_alpha -1.565e-01  1.000e+00  9.564e-01 1.005e-07</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_beta  -3.142e-01  9.564e-01  1.000e+00 8.541e-08</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sigma      4.772e-08  1.005e-07  8.541e-08 1.000e+00</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Backtransformed parameters:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Confidence intervals for internally transformed parameters are asymmetric.</span>
@@ -409,24 +458,24 @@ Degradation Data. <em>Environments</em> 6(12) 124
 <span class="r-out co"><span class="r-pr">#&gt;</span>    63   parent      4.0     2.102   1.8977</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    91   parent      3.9     1.441   2.4590</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   119   parent      0.6     1.092  -0.4919</span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># One parent compound, one metabolite, both single first order.</span></span>
-<span class="r-in"><span class="co"># We remove zero values from FOCUS dataset D in order to avoid warnings</span></span>
-<span class="r-in"><span class="va">FOCUS_D</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span></span>
-<span class="r-in"><span class="co"># Use mkinsub for convenience in model formulation. Pathway to sink included per default.</span></span>
-<span class="r-in"><span class="va">SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span>
-<span class="r-in">  parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span>
-<span class="r-in">  m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># One parent compound, one metabolite, both single first order.</span></span></span>
+<span class="r-in"><span><span class="co"># We remove zero values from FOCUS dataset D in order to avoid warnings</span></span></span>
+<span class="r-in"><span><span class="va">FOCUS_D</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="co"># Use mkinsub for convenience in model formulation. Pathway to sink included per default.</span></span></span>
+<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span>
+<span class="r-in"><span>  parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># Fit the model quietly to the FOCUS example dataset D using defaults</span></span>
-<span class="r-in"><span class="va">fit</span> <span class="op">&lt;-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span class="r-in"><span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># Fit the model quietly to the FOCUS example dataset D using defaults</span></span></span>
+<span class="r-in"><span><span class="va">fit</span> <span class="op">&lt;-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="mkinfit-1.png" alt="" width="700" height="433"></span>
-<span class="r-in"><span class="co"># As lower parent values appear to have lower variance, we try an alternative error model</span></span>
-<span class="r-in"><span class="va">fit.tc</span> <span class="op">&lt;-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</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>
-<span class="r-in"><span class="co"># This avoids the warning, and the likelihood ratio test confirms it is preferable</span></span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">fit.tc</span>, <span class="va">fit</span><span class="op">)</span></span>
+<span class="r-in"><span><span class="co"># As lower parent values appear to have lower variance, we try an alternative error model</span></span></span>
+<span class="r-in"><span><span class="va">fit.tc</span> <span class="op">&lt;-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</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></span>
+<span class="r-in"><span><span class="co"># This avoids the warning, and the likelihood ratio test confirms it is preferable</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">fit.tc</span>, <span class="va">fit</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Likelihood ratio test</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Model 1: SFO_SFO with error model tc and fixed parameter(s) m1_0</span>
@@ -436,10 +485,10 @@ Degradation Data. <em>Environments</em> 6(12) 124
 <span class="r-out co"><span class="r-pr">#&gt;</span> 2   5 -97.224 -1 64.483  9.737e-16 ***</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> ---</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span>
-<span class="r-in"><span class="co"># We can also allow for different variances of parent and metabolite as error model</span></span>
-<span class="r-in"><span class="va">fit.obs</span> <span class="op">&lt;-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</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>
-<span class="r-in"><span class="co"># The two-component error model has significantly higher likelihood</span></span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">fit.obs</span>, <span class="va">fit.tc</span><span class="op">)</span></span>
+<span class="r-in"><span><span class="co"># We can also allow for different variances of parent and metabolite as error model</span></span></span>
+<span class="r-in"><span><span class="va">fit.obs</span> <span class="op">&lt;-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</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></span>
+<span class="r-in"><span><span class="co"># The two-component error model has significantly higher likelihood</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">fit.obs</span>, <span class="va">fit.tc</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Likelihood ratio test</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Model 1: SFO_SFO with error model tc and fixed parameter(s) m1_0</span>
@@ -449,12 +498,12 @@ Degradation Data. <em>Environments</em> 6(12) 124
 <span class="r-out co"><span class="r-pr">#&gt;</span> 2   6 -96.936  0 63.907  &lt; 2.2e-16 ***</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> ---</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span>
-<span class="r-in"><span class="fu"><a href="parms.html">parms</a></span><span class="op">(</span><span class="va">fit.tc</span><span class="op">)</span></span>
+<span class="r-in"><span><span class="fu"><a href="parms.html">parms</a></span><span class="op">(</span><span class="va">fit.tc</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>       parent_0       k_parent           k_m1 f_parent_to_m1      sigma_low </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   1.007343e+02   1.005562e-01   5.166712e-03   5.083933e-01   3.049883e-03 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>       rsd_high </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   7.928118e-02 </span>
-<span class="r-in"><span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.tc</span><span class="op">)</span></span>
+<span class="r-in"><span><span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.tc</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $ff</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   parent_m1 parent_sink </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   0.5083933   0.4916067 </span>
@@ -462,38 +511,41 @@ Degradation Data. <em>Environments</em> 6(12) 124
 <span class="r-out co"><span class="r-pr">#&gt;</span> $distimes</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>             DT50      DT90</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> parent   6.89313  22.89848</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> m1     134.15634 445.65770</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># We can show a quick (only one replication) benchmark for this case, as we</span></span>
-<span class="r-in"><span class="co"># have several alternative solution methods for the model. We skip</span></span>
-<span class="r-in"><span class="co"># uncompiled deSolve, as it is so slow. More benchmarks are found in the</span></span>
-<span class="r-in"><span class="co"># benchmark vignette</span></span>
-<span class="r-in"><span class="co"># \dontrun{</span></span>
-<span class="r-in"><span class="kw">if</span><span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com" class="external-link">rbenchmark</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span>
-<span class="r-in">  <span class="fu">benchmark</span><span class="op">(</span>replications <span class="op">=</span> <span class="fl">1</span>, order <span class="op">=</span> <span class="st">"relative"</span>, columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"test"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span><span class="op">)</span>,</span>
-<span class="r-in">    deSolve_compiled <span class="op">=</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span>
-<span class="r-in">      solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, use_compiled <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span>
-<span class="r-in">    eigen <span class="op">=</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span>
-<span class="r-in">      solution_type <span class="op">=</span> <span class="st">"eigen"</span><span class="op">)</span>,</span>
-<span class="r-in">    analytical <span class="op">=</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span>
-<span class="r-in">      solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span><span class="op">)</span></span>
-<span class="r-in"><span class="op">}</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> m1     134.15634 445.65772</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># We can show a quick (only one replication) benchmark for this case, as we</span></span></span>
+<span class="r-in"><span><span class="co"># have several alternative solution methods for the model. We skip</span></span></span>
+<span class="r-in"><span><span class="co"># uncompiled deSolve, as it is so slow. More benchmarks are found in the</span></span></span>
+<span class="r-in"><span><span class="co"># benchmark vignette</span></span></span>
+<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span><span class="kw">if</span><span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com" class="external-link">rbenchmark</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
+<span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span>replications <span class="op">=</span> <span class="fl">1</span>, order <span class="op">=</span> <span class="st">"relative"</span>, columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"test"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>    deSolve_compiled <span class="op">=</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span></span>
+<span class="r-in"><span>      solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, use_compiled <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>    eigen <span class="op">=</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span></span>
+<span class="r-in"><span>      solution_type <span class="op">=</span> <span class="st">"eigen"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>    analytical <span class="op">=</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span></span>
+<span class="r-in"><span>      solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: rbenchmark</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>there is no package called ‘rbenchmark’</span>
-<span class="r-in"><span class="co"># }</span></span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span></span>
-<span class="r-in"><span class="co"># \dontrun{</span></span>
-<span class="r-in"><span class="va">FOMC_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span>
-<span class="r-in">  parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span>
-<span class="r-in">  m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>               test relative elapsed</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3       analytical    1.000   0.540</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 deSolve_compiled    1.537   0.830</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2            eigen    2.687   1.451</span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span></span></span>
+<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span><span class="va">FOMC_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span>
+<span class="r-in"><span>  parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
-<span class="r-in"><span class="va">fit.FOMC_SFO</span> <span class="op">&lt;-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">FOMC_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span class="r-in"><span class="co"># Again, we get a warning and try a more sophisticated error model</span></span>
-<span class="r-in"><span class="va">fit.FOMC_SFO.tc</span> <span class="op">&lt;-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">FOMC_SFO</span>, <span class="va">FOCUS_D</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>
-<span class="r-in"><span class="co"># This model has a higher likelihood, but not significantly so</span></span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">fit.tc</span>, <span class="va">fit.FOMC_SFO.tc</span><span class="op">)</span></span>
+<span class="r-in"><span><span class="va">fit.FOMC_SFO</span> <span class="op">&lt;-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">FOMC_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="co"># Again, we get a warning and try a more sophisticated error model</span></span></span>
+<span class="r-in"><span><span class="va">fit.FOMC_SFO.tc</span> <span class="op">&lt;-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">FOMC_SFO</span>, <span class="va">FOCUS_D</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></span>
+<span class="r-in"><span><span class="co"># This model has a higher likelihood, but not significantly so</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">fit.tc</span>, <span class="va">fit.FOMC_SFO.tc</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Likelihood ratio test</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Model 1: FOMC_SFO with error model tc and fixed parameter(s) m1_0</span>
@@ -501,16 +553,16 @@ Degradation Data. <em>Environments</em> 6(12) 124
 <span class="r-out co"><span class="r-pr">#&gt;</span>   #Df  LogLik Df  Chisq Pr(&gt;Chisq)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1   7 -64.829                     </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 2   6 -64.983 -1 0.3075     0.5792</span>
-<span class="r-in"><span class="co"># Also, the missing standard error for log_beta and the t-tests for alpha</span></span>
-<span class="r-in"><span class="co"># and beta indicate overparameterisation</span></span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.FOMC_SFO.tc</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
+<span class="r-in"><span><span class="co"># Also, the missing standard error for log_beta and the t-tests for alpha</span></span></span>
+<span class="r-in"><span><span class="co"># and beta indicate overparameterisation</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.FOMC_SFO.tc</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NaNs produced</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NaNs produced</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>diag(.) had 0 or NA entries; non-finite result is doubtful</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for fitting:    1.1.0 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:       4.2.0 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Wed May 18 20:38:07 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Wed May 18 20:38:07 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for fitting:    1.1.2 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:       4.2.1 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Wed Aug 10 13:14:36 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Wed Aug 10 13:14:36 2022 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span>
@@ -519,12 +571,12 @@ Degradation Data. <em>Environments</em> 6(12) 124
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type deSolve </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted using 3924 model solutions performed in 7.107 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted using 3729 model solutions performed in 2.488 s</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Error model: Two-component variance function </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Error model algorithm: d_3 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Three-step fitting yielded a higher likelihood than direct fitting </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Direct fitting and three-step fitting yield approximately the same likelihood </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Starting values for parameters to be optimised:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>                 value   type</span>
@@ -559,7 +611,7 @@ Degradation Data. <em>Environments</em> 6(12) 124
 <span class="r-out co"><span class="r-pr">#&gt;</span>                   Estimate Std. Error     Lower      Upper</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> parent_0        101.600000  2.6400000 96.240000 107.000000</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> log_k_m1         -5.284000  0.0929100 -5.474000  -5.095000</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_qlogis   0.001426  0.0766900 -0.155000   0.157800</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_qlogis   0.001426  0.0767000 -0.155000   0.157800</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> log_alpha         5.522000  0.0077320  5.506000   5.538000</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> log_beta          7.806000        NaN       NaN        NaN</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> sigma_low         0.002488  0.0002431  0.001992   0.002984</span>
@@ -567,31 +619,31 @@ Degradation Data. <em>Environments</em> 6(12) 124
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Parameter correlation:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>                  parent_0  log_k_m1 f_parent_qlogis log_alpha log_beta</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0         1.000000 -0.095145        -0.76674   0.70541      NaN</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_m1        -0.095145  1.000000         0.51428  -0.14381      NaN</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_qlogis -0.766743  0.514278         1.00000  -0.61392      NaN</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> log_alpha        0.705413 -0.143809        -0.61392   1.00000      NaN</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0         1.000000 -0.095226        -0.76678   0.70544      NaN</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_m1        -0.095226  1.000000         0.51432  -0.14387      NaN</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_qlogis -0.766780  0.514321         1.00000  -0.61396      NaN</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_alpha        0.705444 -0.143872        -0.61396   1.00000      NaN</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> log_beta              NaN       NaN             NaN       NaN        1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> sigma_low        0.016077  0.001586         0.01548   5.87034      NaN</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> rsd_high         0.006617 -0.011694        -0.05356   0.04848      NaN</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sigma_low        0.016073  0.001586         0.01548   5.87007      NaN</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> rsd_high         0.006626 -0.011700        -0.05357   0.04849      NaN</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>                 sigma_low  rsd_high</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0         0.016077  0.006617</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_m1         0.001586 -0.011694</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_qlogis  0.015476 -0.053560</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> log_alpha        5.870339  0.048481</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0         0.016073  0.006626</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_m1         0.001586 -0.011700</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_qlogis  0.015476 -0.053566</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_alpha        5.870075  0.048487</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> log_beta              NaN       NaN</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> sigma_low        1.000000 -0.652555</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> rsd_high        -0.652555  1.000000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sigma_low        1.000000 -0.652558</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> rsd_high        -0.652558  1.000000</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Backtransformed parameters:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Confidence intervals for internally transformed parameters are asymmetric.</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> t-test (unrealistically) based on the assumption of normal distribution</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> for estimators of untransformed parameters.</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>                 Estimate t value    Pr(&gt;t)     Lower     Upper</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0       1.016e+02 32.7800 6.312e-26 9.624e+01 1.070e+02</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0       1.016e+02 32.7800 6.311e-26 9.624e+01 1.070e+02</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> k_m1           5.072e-03 10.1200 1.216e-11 4.196e-03 6.130e-03</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_to_m1 5.004e-01 20.8300 4.318e-20 4.613e-01 5.394e-01</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> alpha          2.502e+02  0.5624 2.890e-01 2.463e+02 2.542e+02</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_to_m1 5.004e-01 20.8300 4.317e-20 4.613e-01 5.394e-01</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> alpha          2.502e+02  0.5624 2.889e-01 2.463e+02 2.542e+02</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> beta           2.455e+03  0.5549 2.915e-01        NA        NA</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> sigma_low      2.488e-03  0.4843 3.158e-01 1.992e-03 2.984e-03</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> rsd_high       7.921e-02  8.4300 8.001e-10 6.018e-02 9.823e-02</span>
@@ -611,12 +663,12 @@ Degradation Data. <em>Environments</em> 6(12) 124
 <span class="r-out co"><span class="r-pr">#&gt;</span>           DT50  DT90 DT50back</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> parent   6.812  22.7    6.834</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> m1     136.661 454.0       NA</span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># We can easily use starting parameters from the parent only fit (only for illustration)</span></span>
-<span class="r-in"><span class="va">fit.FOMC</span> <span class="op">=</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_D</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>
-<span class="r-in"><span class="va">fit.FOMC_SFO</span> <span class="op">&lt;-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">FOMC_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span class="r-in">  parms.ini <span class="op">=</span> <span class="va">fit.FOMC</span><span class="op">$</span><span class="va">bparms.ode</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span>
-<span class="r-in"><span class="co"># }</span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># We can easily use starting parameters from the parent only fit (only for illustration)</span></span></span>
+<span class="r-in"><span><span class="va">fit.FOMC</span> <span class="op">=</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_D</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></span>
+<span class="r-in"><span><span class="va">fit.FOMC_SFO</span> <span class="op">&lt;-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">FOMC_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span></span>
+<span class="r-in"><span>  parms.ini <span class="op">=</span> <span class="va">fit.FOMC</span><span class="op">$</span><span class="va">bparms.ode</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
   </div>
@@ -631,7 +683,7 @@ Degradation Data. <em>Environments</em> 6(12) 124
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/saem-3.png b/docs/reference/saem-3.png
index 99f2a2d6..08e0f544 100644
--- a/docs/reference/saem-3.png
+++ b/docs/reference/saem-3.png
diff --git a/docs/reference/saem.html b/docs/reference/saem.html
index e9898a73..1bc6308e 100644
--- a/docs/reference/saem.html
+++ b/docs/reference/saem.html
@@ -19,7 +19,7 @@ Expectation Maximisation algorithm (SAEM)."><!-- mathjax --><script src="https:/
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span>
       </span>
     </div>
 
@@ -91,40 +91,40 @@ Expectation Maximisation algorithm (SAEM).</p>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">saem</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="co"># S3 method for mmkin</span>
-<span class="fu">saem</span><span class="op">(</span>
-  <span class="va">object</span>,
-  transformations <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"mkin"</span>, <span class="st">"saemix"</span><span class="op">)</span>,
-  degparms_start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a></span><span class="op">(</span><span class="op">)</span>,
-  test_log_parms <span class="op">=</span> <span class="cn">TRUE</span>,
-  conf.level <span class="op">=</span> <span class="fl">0.6</span>,
-  solution_type <span class="op">=</span> <span class="st">"auto"</span>,
-  nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">300</span>, <span class="fl">100</span><span class="op">)</span>,
-  control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>displayProgress <span class="op">=</span> <span class="cn">FALSE</span>, print <span class="op">=</span> <span class="cn">FALSE</span>, nbiter.saemix <span class="op">=</span> <span class="va">nbiter.saemix</span>,
-    save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-  fail_with_errors <span class="op">=</span> <span class="cn">TRUE</span>,
-  verbose <span class="op">=</span> <span class="cn">FALSE</span>,
-  quiet <span class="op">=</span> <span class="cn">FALSE</span>,
-  <span class="va">...</span>
-<span class="op">)</span>
-
-<span class="co"># S3 method for saem.mmkin</span>
-<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">saemix_model</span><span class="op">(</span>
-  <span class="va">object</span>,
-  solution_type <span class="op">=</span> <span class="st">"auto"</span>,
-  transformations <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"mkin"</span>, <span class="st">"saemix"</span><span class="op">)</span>,
-  degparms_start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a></span><span class="op">(</span><span class="op">)</span>,
-  test_log_parms <span class="op">=</span> <span class="cn">FALSE</span>,
-  conf.level <span class="op">=</span> <span class="fl">0.6</span>,
-  verbose <span class="op">=</span> <span class="cn">FALSE</span>,
-  <span class="va">...</span>
-<span class="op">)</span>
-
-<span class="fu">saemix_data</span><span class="op">(</span><span class="va">object</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">saem</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for mmkin</span></span>
+<span><span class="fu">saem</span><span class="op">(</span></span>
+<span>  <span class="va">object</span>,</span>
+<span>  transformations <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"mkin"</span>, <span class="st">"saemix"</span><span class="op">)</span>,</span>
+<span>  degparms_start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  test_log_parms <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  conf.level <span class="op">=</span> <span class="fl">0.6</span>,</span>
+<span>  solution_type <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span>  nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">300</span>, <span class="fl">100</span><span class="op">)</span>,</span>
+<span>  control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>displayProgress <span class="op">=</span> <span class="cn">FALSE</span>, print <span class="op">=</span> <span class="cn">FALSE</span>, nbiter.saemix <span class="op">=</span> <span class="va">nbiter.saemix</span>,</span>
+<span>    save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>  fail_with_errors <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  quiet <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for saem.mmkin</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">saemix_model</span><span class="op">(</span></span>
+<span>  <span class="va">object</span>,</span>
+<span>  solution_type <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span>  transformations <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"mkin"</span>, <span class="st">"saemix"</span><span class="op">)</span>,</span>
+<span>  degparms_start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  test_log_parms <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  conf.level <span class="op">=</span> <span class="fl">0.6</span>,</span>
+<span>  verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">saemix_data</span><span class="op">(</span><span class="va">object</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
@@ -132,54 +132,87 @@ Expectation Maximisation algorithm (SAEM).</p>
     <dl><dt>object</dt>
 <dd><p>An <a href="mmkin.html">mmkin</a> row object containing several fits of the same
 <a href="mkinmod.html">mkinmod</a> model to different datasets</p></dd>
+
+
 <dt>...</dt>
 <dd><p>Further parameters passed to <a href="https://rdrr.io/pkg/saemix/man/saemixModel.html" class="external-link">saemix::saemixModel</a>.</p></dd>
+
+
 <dt>transformations</dt>
 <dd><p>Per default, all parameter transformations are done
 in mkin. If this argument is set to 'saemix', parameter transformations
-are done in 'saemix' for the supported cases. Currently this is only
-supported in cases where the initial concentration of the parent is not fixed,
-SFO or DFOP is used for the parent and there is either no metabolite or one.</p></dd>
+are done in 'saemix' for the supported cases, i.e. (as of version 1.1.2)
+SFO, FOMC, DFOP and HS without fixing <code>parent_0</code>, and SFO or DFOP with
+one SFO metabolite.</p></dd>
+
+
 <dt>degparms_start</dt>
 <dd><p>Parameter values given as a named numeric vector will
 be used to override the starting values obtained from the 'mmkin' object.</p></dd>
+
+
 <dt>test_log_parms</dt>
 <dd><p>If TRUE, an attempt is made to use more robust starting
 values for population parameters fitted as log parameters in mkin (like
 rate constants) by only considering rate constants that pass the t-test
 when calculating mean degradation parameters using <a href="mean_degparms.html">mean_degparms</a>.</p></dd>
+
+
 <dt>conf.level</dt>
 <dd><p>Possibility to adjust the required confidence level
 for parameter that are tested if requested by 'test_log_parms'.</p></dd>
+
+
 <dt>solution_type</dt>
 <dd><p>Possibility to specify the solution type in case the
 automatic choice is not desired</p></dd>
+
+
 <dt>nbiter.saemix</dt>
 <dd><p>Convenience option to increase the number of
 iterations</p></dd>
+
+
 <dt>control</dt>
 <dd><p>Passed to <a href="https://rdrr.io/pkg/saemix/man/saemix.html" class="external-link">saemix::saemix</a>.</p></dd>
+
+
 <dt>fail_with_errors</dt>
 <dd><p>Should a failure to compute standard errors
 from the inverse of the Fisher Information Matrix be a failure?</p></dd>
+
+
 <dt>verbose</dt>
 <dd><p>Should we print information about created objects of
 type <a href="https://rdrr.io/pkg/saemix/man/SaemixModel-class.html" class="external-link">saemix::SaemixModel</a> and <a href="https://rdrr.io/pkg/saemix/man/SaemixData-class.html" class="external-link">saemix::SaemixData</a>?</p></dd>
+
+
 <dt>quiet</dt>
 <dd><p>Should we suppress the messages saemix prints at the beginning
 and the end of the optimisation process?</p></dd>
+
+
 <dt>x</dt>
 <dd><p>An saem.mmkin object to print</p></dd>
+
+
 <dt>digits</dt>
 <dd><p>Number of digits to use for printing</p></dd>
+
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    <p>An S3 object of class 'saem.mmkin', containing the fitted
+    
+
+<p>An S3 object of class 'saem.mmkin', containing the fitted
 <a href="https://rdrr.io/pkg/saemix/man/SaemixObject-class.html" class="external-link">saemix::SaemixObject</a> as a list component named 'so'. The
-object also inherits from 'mixed.mmkin'.
-An <a href="https://rdrr.io/pkg/saemix/man/SaemixModel-class.html" class="external-link">saemix::SaemixModel</a> object.
-An <a href="https://rdrr.io/pkg/saemix/man/SaemixData-class.html" class="external-link">saemix::SaemixData</a> object.</p>
+object also inherits from 'mixed.mmkin'.</p>
+
+
+<p>An <a href="https://rdrr.io/pkg/saemix/man/SaemixModel-class.html" class="external-link">saemix::SaemixModel</a> object.</p>
+
+
+<p>An <a href="https://rdrr.io/pkg/saemix/man/SaemixData-class.html" class="external-link">saemix::SaemixData</a> object.</p>
     </div>
     <div id="details">
     <h2>Details</h2>
@@ -196,77 +229,105 @@ using <a href="mmkin.html">mmkin</a>.</p>
 
     <div id="ref-examples">
     <h2>Examples</h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="co"># \dontrun{</span></span>
-<span class="r-in"><span class="va">ds</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">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>
-<span class="r-in"> <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" class="external-link">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" class="external-link">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="op">)</span></span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">)</span></span>
-<span class="r-in"><span class="va">f_mmkin_parent_p0_fixed</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">ds</span>,</span>
-<span class="r-in">  state.ini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>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>
-<span class="r-in"><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></span>
-<span class="r-in"></span>
-<span class="r-in"><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" class="external-link">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>
-<span class="r-in"><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></span>
-<span class="r-in"><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></span>
-<span class="r-in"><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></span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span></span>
-<span class="r-in"><span class="co"># functions from saemix</span></span>
-<span class="r-in"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">saemix</span><span class="op">)</span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span><span class="va">ds</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">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></span>
+<span class="r-in"><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" class="external-link">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" class="external-link">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="op">)</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">f_mmkin_parent_p0_fixed</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">ds</span>,</span></span>
+<span class="r-in"><span>  state.ini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>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></span>
+<span class="r-in"><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></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><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" class="external-link">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></span>
+<span class="r-in"><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></span></span>
+<span class="r-in"><span><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></span></span>
+<span class="r-in"><span><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></span></span>
+<span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_dfop</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "sd(g_qlogis)"</span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_dfop</span>, covariance.model <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/diag.html" class="external-link">diag</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">1</span>, <span class="fl">1</span>, <span class="fl">0</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Kinetic nonlinear mixed-effects model fit by SAEM</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Structural model:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>            time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>            * parent</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Data:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 90 observations of 1 variable(s) grouped in 5 datasets</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Likelihood computed by importance sampling</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>     AIC   BIC logLik</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   490.6 487.5 -237.3</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted parameters:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>             estimate   lower   upper</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0      93.902 91.3695 96.4339</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k1        -2.936 -3.9950 -1.8762</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k2        -3.091 -4.9290 -1.2523</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> g_qlogis      -0.366 -0.6484 -0.0836</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> a.1            2.385  2.0033  2.7664</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SD.parent_0    2.476  0.3890  4.5623</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k1      1.195  0.4381  1.9517</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k2      2.092  0.7906  3.3932</span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_saem_dfop</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 493.9811</span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span></span></span>
+<span class="r-in"><span><span class="co"># functions from saemix</span></span></span>
+<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">saemix</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: npde</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Package saemix, version 3.0</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Package saemix, version 3.1</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Attaching package: ‘saemix’</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> The following objects are masked from ‘package:npde’:</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>     kurtosis, skewness</span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/compare.saemix.html" class="external-link">compare.saemix</a></span><span class="op">(</span><span class="va">f_saem_sfo</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_saem_dfop</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/compare.saemix.html" class="external-link">compare.saemix</a></span><span class="op">(</span><span class="va">f_saem_sfo</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_saem_dfop</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Likelihoods calculated by importance sampling</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>        AIC      BIC</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1 624.2598 622.3070</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 2 467.8664 465.1324</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 3 493.9811 490.4660</span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="saem-1.png" alt="" width="700" height="433"></span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"individual.fit"</span><span class="op">)</span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"individual.fit"</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="saem-2.png" alt="" width="700" height="433"></span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"npde"</span><span class="op">)</span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"npde"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Simulating data using nsim = 1000 simulated datasets</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Computing WRES and npde .</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Please use npdeSaemix to obtain VPC and npde</span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"vpc"</span><span class="op">)</span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"vpc"</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="saem-3.png" alt="" width="700" height="433"></span>
-<span class="r-in"></span>
-<span class="r-in"><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" class="external-link">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>
-<span class="r-in"><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></span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/compare.saemix.html" class="external-link">compare.saemix</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>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><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" class="external-link">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></span>
+<span class="r-in"><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></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/compare.saemix.html" class="external-link">compare.saemix</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></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Likelihoods calculated by importance sampling</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>        AIC      BIC</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1 467.8664 465.1324</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 2 469.9096 466.7851</span>
-<span class="r-in"></span>
-<span class="r-in"><span class="va">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="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span>
-<span class="r-in">  A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="va">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="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
-<span class="r-in"><span class="va">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="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span>
-<span class="r-in">  A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span>
+<span class="r-in"><span><span class="va">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="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
-<span class="r-in"><span class="va">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="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span>
-<span class="r-in">  A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span>
+<span class="r-in"><span><span class="va">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="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
-<span class="r-in"><span class="co"># The following fit uses analytical solutions for SFO-SFO and DFOP-SFO,</span></span>
-<span class="r-in"><span class="co"># and compiled ODEs for FOMC that are much slower</span></span>
-<span class="r-in"><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="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span>
-<span class="r-in">    <span class="st">"SFO-SFO"</span> <span class="op">=</span> <span class="va">sfo_sfo</span>, <span class="st">"FOMC-SFO"</span> <span class="op">=</span> <span class="va">fomc_sfo</span>, <span class="st">"DFOP-SFO"</span> <span class="op">=</span> <span class="va">dfop_sfo</span><span class="op">)</span>,</span>
-<span class="r-in">  <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span class="r-in"><span class="co"># saem fits of SFO-SFO and DFOP-SFO to these data take about five seconds</span></span>
-<span class="r-in"><span class="co"># each on this system, as we use analytical solutions written for saemix.</span></span>
-<span class="r-in"><span class="co"># When using the analytical solutions written for mkin this took around</span></span>
-<span class="r-in"><span class="co"># four minutes</span></span>
-<span class="r-in"><span class="va">f_saem_sfo_sfo</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><span class="st">"SFO-SFO"</span>, <span class="op">]</span><span class="op">)</span></span>
-<span class="r-in"><span class="va">f_saem_dfop_sfo</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><span class="st">"DFOP-SFO"</span>, <span class="op">]</span><span class="op">)</span></span>
-<span class="r-in"><span class="co"># We can use print, plot and summary methods to check the results</span></span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span><span class="op">)</span></span>
+<span class="r-in"><span><span class="co"># The following fit uses analytical solutions for SFO-SFO and DFOP-SFO,</span></span></span>
+<span class="r-in"><span><span class="co"># and compiled ODEs for FOMC that are much slower</span></span></span>
+<span class="r-in"><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="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span></span>
+<span class="r-in"><span>    <span class="st">"SFO-SFO"</span> <span class="op">=</span> <span class="va">sfo_sfo</span>, <span class="st">"FOMC-SFO"</span> <span class="op">=</span> <span class="va">fomc_sfo</span>, <span class="st">"DFOP-SFO"</span> <span class="op">=</span> <span class="va">dfop_sfo</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="co"># saem fits of SFO-SFO and DFOP-SFO to these data take about five seconds</span></span></span>
+<span class="r-in"><span><span class="co"># each on this system, as we use analytical solutions written for saemix.</span></span></span>
+<span class="r-in"><span><span class="co"># When using the analytical solutions written for mkin this took around</span></span></span>
+<span class="r-in"><span><span class="co"># four minutes</span></span></span>
+<span class="r-in"><span><span class="va">f_saem_sfo_sfo</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><span class="st">"SFO-SFO"</span>, <span class="op">]</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">f_saem_dfop_sfo</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><span class="st">"DFOP-SFO"</span>, <span class="op">]</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="co"># We can use print, plot and summary methods to check the results</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Kinetic nonlinear mixed-effects model fit by SAEM</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Structural model:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span>
@@ -291,21 +352,21 @@ using <a href="mmkin.html">mmkin</a>.</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span> log_k1              -2.5841 -3.6876 -1.4805</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> log_k2              -3.5228 -5.3254 -1.7203</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> g_qlogis            -0.1027 -0.8719  0.6665</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> a.1                  1.8856  1.6770  2.0943</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> SD.parent_0          2.7682  0.7669  4.7695</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> a.1                  1.8856  1.6676  2.1037</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SD.parent_0          2.7682  0.7668  4.7695</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k_A1          1.7447  0.4047  3.0848</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> SD.f_parent_qlogis   0.4525  0.1620  0.7431</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k1            1.2423  0.4560  2.0285</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k2            2.0390  0.7601  3.3180</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> SD.g_qlogis          0.4439 -0.3068  1.1946</span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span><span class="op">)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SD.g_qlogis          0.4439 -0.3069  1.1947</span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="saem-4.png" alt="" width="700" height="433"></span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> saemix version used for fitting:      3.0 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting:  1.1.0 </span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> saemix version used for fitting:      3.1 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting:  1.1.2 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:         4.2.1 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Thu Jun 30 10:23:53 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Thu Jun 30 10:23:53 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Wed Aug 10 13:15:20 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Wed Aug 10 13:15:20 2022 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span>
@@ -320,7 +381,7 @@ using <a href="mmkin.html">mmkin</a>.</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type analytical </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 8.85 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 9.258 s</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Using 300, 100 iterations and 10 chains</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Variance model: Constant variance </span>
@@ -359,16 +420,16 @@ using <a href="mmkin.html">mmkin</a>.</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Random effects:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>                      est.   lower  upper</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> SD.parent_0        2.7682  0.7669 4.7695</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SD.parent_0        2.7682  0.7668 4.7695</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k_A1        1.7447  0.4047 3.0848</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> SD.f_parent_qlogis 0.4525  0.1620 0.7431</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k1          1.2423  0.4560 2.0285</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k2          2.0390  0.7601 3.3180</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> SD.g_qlogis        0.4439 -0.3068 1.1946</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SD.g_qlogis        0.4439 -0.3069 1.1947</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Variance model:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>      est. lower upper</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> a.1 1.886 1.677 2.094</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> a.1 1.886 1.668 2.104</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Backtransformed parameters:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>                     est.     lower    upper</span>
@@ -554,27 +615,27 @@ using <a href="mmkin.html">mmkin</a>.</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Dataset 10     A1   21      6.4   7.59693 -1.19693 1.886    -0.634761</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Dataset 10     A1   21      7.2   7.59693 -0.39693 1.886    -0.210502</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Dataset 10     A1   41      9.1   9.86436 -0.76436 1.886    -0.405361</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  Dataset 10     A1   41      8.5   9.86436 -1.36436 1.886    -0.723556</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  Dataset 10     A1   41      8.5   9.86436 -1.36436 1.886    -0.723555</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Dataset 10     A1   63     11.7  10.99397  0.70603 1.886     0.374425</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Dataset 10     A1   63     12.0  10.99397  1.00603 1.886     0.533522</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Dataset 10     A1   91     13.3  11.91274  1.38726 1.886     0.735696</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Dataset 10     A1   91     13.2  11.91274  1.28726 1.886     0.682663</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Dataset 10     A1  120     14.3  12.66519  1.63481 1.886     0.866981</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Dataset 10     A1  120     12.1  12.66519 -0.56519 1.886    -0.299733</span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># The following takes about 6 minutes</span></span>
-<span class="r-in"><span class="co">#f_saem_dfop_sfo_deSolve &lt;- saem(f_mmkin["DFOP-SFO", ], solution_type = "deSolve",</span></span>
-<span class="r-in"><span class="co">#  control = list(nbiter.saemix = c(200, 80), nbdisplay = 10))</span></span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co">#saemix::compare.saemix(list(</span></span>
-<span class="r-in"><span class="co">#  f_saem_dfop_sfo$so,</span></span>
-<span class="r-in"><span class="co">#  f_saem_dfop_sfo_deSolve$so))</span></span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># If the model supports it, we can also use eigenvalue based solutions, which</span></span>
-<span class="r-in"><span class="co"># take a similar amount of time</span></span>
-<span class="r-in"><span class="co">#f_saem_sfo_sfo_eigen &lt;- saem(f_mmkin["SFO-SFO", ], solution_type = "eigen",</span></span>
-<span class="r-in"><span class="co">#  control = list(nbiter.saemix = c(200, 80), nbdisplay = 10))</span></span>
-<span class="r-in"><span class="co"># }</span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># The following takes about 6 minutes</span></span></span>
+<span class="r-in"><span><span class="co">#f_saem_dfop_sfo_deSolve &lt;- saem(f_mmkin["DFOP-SFO", ], solution_type = "deSolve",</span></span></span>
+<span class="r-in"><span><span class="co">#  control = list(nbiter.saemix = c(200, 80), nbdisplay = 10))</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co">#saemix::compare.saemix(list(</span></span></span>
+<span class="r-in"><span><span class="co">#  f_saem_dfop_sfo$so,</span></span></span>
+<span class="r-in"><span><span class="co">#  f_saem_dfop_sfo_deSolve$so))</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># If the model supports it, we can also use eigenvalue based solutions, which</span></span></span>
+<span class="r-in"><span><span class="co"># take a similar amount of time</span></span></span>
+<span class="r-in"><span><span class="co">#f_saem_sfo_sfo_eigen &lt;- saem(f_mmkin["SFO-SFO", ], solution_type = "eigen",</span></span></span>
+<span class="r-in"><span><span class="co">#  control = list(nbiter.saemix = c(200, 80), nbdisplay = 10))</span></span></span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
   </div>
@@ -589,7 +650,7 @@ using <a href="mmkin.html">mmkin</a>.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer></div>
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index ba8f37e6..b30d21a1 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -163,6 +163,9 @@
     <loc>https://pkgdown.jrwb.de/mkin/reference/mean_degparms.html</loc>
   </url>
   <url>
+    <loc>https://pkgdown.jrwb.de/mkin/reference/mhmkin.html</loc>
+  </url>
+  <url>
     <loc>https://pkgdown.jrwb.de/mkin/reference/mixed.html</loc>
   </url>
   <url>