Complete rebuild of static docs of dev version

author: Johannes Ranke <jranke@uni-bremen.de> 2020-11-30 16:05:10 +0100
committer: Johannes Ranke <jranke@uni-bremen.de> 2020-11-30 16:05:10 +0100
commit: 524a8bba89b95840b4e9215c403947a8bb76d7b2 (patch)
tree: f28717d46b0ac95bd56d4b84ee4fb770364b91ba
parent: 78884beed74c18c99521b9ceeaa643e13cf94c06 (diff)
120 files changed, 957 insertions, 2656 deletions
diff --git a/R/nlme.mmkin.R b/R/nlme.mmkin.R
index b434bbf4..0d6e6c37 100644
--- a/R/nlme.mmkin.R
+++ b/R/nlme.mmkin.R
@@ -29,8 +29,10 @@ get_deg_func <- function() {
 #' @param data Ignored, data are taken from the mmkin model
 #' @param fixed Ignored, all degradation parameters fitted in the
 #'   mmkin model are used as fixed parameters
-#' @param random If not specified, all fixed effects are complemented
-#'   with uncorrelated random effects
+#' @param random If not specified, correlated random effects are set up
+#'   for all optimised degradation model parameters using the log-Cholesky
+#'   parameterization [nlme::pdLogChol] that is also the default of
+#'   the generic [nlme] method.
 #' @param groups See the documentation of nlme
 #' @param start If not specified, mean values of the fitted degradation
 #'   parameters taken from the mmkin object are used
diff --git a/docs/dev/articles/FOCUS_D.html b/docs/dev/articles/FOCUS_D.html
index e526b3a7..dd86f677 100644
--- a/docs/dev/articles/FOCUS_D.html
+++ b/docs/dev/articles/FOCUS_D.html
@@ -102,7 +102,7 @@
       <h1 data-toc-skip>Example evaluation of FOCUS Example Dataset D</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2020-11-19</h4>
+            <h4 class="date">2020-11-30</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/FOCUS_D.rmd"><code>vignettes/FOCUS_D.rmd</code></a></small>
       <div class="hidden name"><code>FOCUS_D.rmd</code></div>
@@ -163,8 +163,8 @@
 <p>Next we specify the degradation model: The parent compound degrades with simple first-order kinetics (SFO) to one metabolite named m1, which also degrades with SFO kinetics.</p>
 <p>The call to mkinmod returns a degradation model. The differential equations represented in R code can be found in the character vector <code>$diffs</code> of the <code>mkinmod</code> object. If a C compiler (gcc) is installed and functional, the differential equation model will be compiled from auto-generated C code.</p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
-<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
+<code class="sourceCode R"><span class="va">SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
+<pre><code>## Temporary DLL for differentials generated and loaded</code></pre>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">SFO_SFO</span><span class="op">$</span><span class="va">diffs</span><span class="op">)</span></code></pre></div>
 <pre><code>##                                                    parent 
@@ -189,8 +189,8 @@
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.50.4 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Thu Nov 19 15:00:06 2020 
-## Date of summary: Thu Nov 19 15:00:06 2020 
+## Date of fit:     Mon Nov 30 16:01:50 2020 
+## Date of summary: Mon Nov 30 16:01:50 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -198,7 +198,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 401 model solutions performed in 0.188 s
+## Fitted using 401 model solutions performed in 0.161 s
 ## 
 ## Error model: Constant variance 
 ## 
diff --git a/docs/dev/articles/FOCUS_L.html b/docs/dev/articles/FOCUS_L.html
index 1fbe5c76..2695db5e 100644
--- a/docs/dev/articles/FOCUS_L.html
+++ b/docs/dev/articles/FOCUS_L.html
@@ -102,7 +102,7 @@
       <h1 data-toc-skip>Example evaluation of FOCUS Laboratory Data L1 to L3</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2020-11-19</h4>
+            <h4 class="date">2020-11-30</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/FOCUS_L.rmd"><code>vignettes/FOCUS_L.rmd</code></a></small>
       <div class="hidden name"><code>FOCUS_L.rmd</code></div>
@@ -130,15 +130,15 @@
 <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">m.L1.SFO</span><span class="op">)</span></code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.50.4 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Thu Nov 19 15:00:09 2020 
-## Date of summary: Thu Nov 19 15:00:09 2020 
+## Date of fit:     Mon Nov 30 16:01:52 2020 
+## Date of summary: Mon Nov 30 16:01:52 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.034 s
+## Fitted using 133 model solutions performed in 0.032 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -236,15 +236,15 @@
 ## doubtful</code></pre>
 <pre><code>## mkin version used for fitting:    0.9.50.4 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Thu Nov 19 15:00:09 2020 
-## Date of summary: Thu Nov 19 15:00:09 2020 
+## Date of fit:     Mon Nov 30 16:01:53 2020 
+## Date of summary: Mon Nov 30 16:01:53 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 380 model solutions performed in 0.085 s
+## Fitted using 380 model solutions performed in 0.087 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -348,15 +348,15 @@
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">m.L2.FOMC</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.50.4 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Thu Nov 19 15:00:10 2020 
-## Date of summary: Thu Nov 19 15:00:10 2020 
+## Date of fit:     Mon Nov 30 16:01:54 2020 
+## Date of summary: Mon Nov 30 16:01:54 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 239 model solutions performed in 0.051 s
+## Fitted using 239 model solutions performed in 0.05 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -429,8 +429,8 @@
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">m.L2.DFOP</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.50.4 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Thu Nov 19 15:00:10 2020 
-## Date of summary: Thu Nov 19 15:00:10 2020 
+## Date of fit:     Mon Nov 30 16:01:54 2020 
+## Date of summary: Mon Nov 30 16:01:54 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -439,7 +439,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 581 model solutions performed in 0.138 s
+## Fitted using 581 model solutions performed in 0.136 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -535,8 +535,8 @@
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">mm.L3</span><span class="op">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.50.4 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Thu Nov 19 15:00:11 2020 
-## Date of summary: Thu Nov 19 15:00:11 2020 
+## Date of fit:     Mon Nov 30 16:01:55 2020 
+## Date of summary: Mon Nov 30 16:01:55 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -545,7 +545,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 376 model solutions performed in 0.083 s
+## Fitted using 376 model solutions performed in 0.081 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -648,15 +648,15 @@
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"SFO"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.50.4 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Thu Nov 19 15:00:12 2020 
-## Date of summary: Thu Nov 19 15:00:12 2020 
+## Date of fit:     Mon Nov 30 16:01:55 2020 
+## Date of summary: Mon Nov 30 16:01:55 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 142 model solutions performed in 0.031 s
+## Fitted using 142 model solutions performed in 0.03 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -713,15 +713,15 @@
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.50.4 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Thu Nov 19 15:00:12 2020 
-## Date of summary: Thu Nov 19 15:00:12 2020 
+## Date of fit:     Mon Nov 30 16:01:55 2020 
+## Date of summary: Mon Nov 30 16:01:56 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 224 model solutions performed in 0.05 s
+## Fitted using 224 model solutions performed in 0.045 s
 ## 
 ## Error model: Constant variance 
 ## 
diff --git a/docs/dev/articles/mkin.html b/docs/dev/articles/mkin.html
index 75e53bbd..2de8b9f0 100644
--- a/docs/dev/articles/mkin.html
+++ b/docs/dev/articles/mkin.html
@@ -102,7 +102,7 @@
       <h1 data-toc-skip>Introduction to mkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2020-11-27</h4>
+            <h4 class="date">2020-11-30</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/mkin.rmd"><code>vignettes/mkin.rmd</code></a></small>
       <div class="hidden name"><code>mkin.rmd</code></div>
diff --git a/docs/dev/articles/twa.html b/docs/dev/articles/twa.html
index d778b773..42ed6fa5 100644
--- a/docs/dev/articles/twa.html
+++ b/docs/dev/articles/twa.html
@@ -102,7 +102,7 @@
       <h1 data-toc-skip>Calculation of time weighted average concentrations with mkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2020-11-19</h4>
+            <h4 class="date">2020-11-30</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/twa.rmd"><code>vignettes/twa.rmd</code></a></small>
       <div class="hidden name"><code>twa.rmd</code></div>
diff --git a/docs/dev/articles/web_only/FOCUS_Z.html b/docs/dev/articles/web_only/FOCUS_Z.html
index 4cfe6c31..15c41eb7 100644
--- a/docs/dev/articles/web_only/FOCUS_Z.html
+++ b/docs/dev/articles/web_only/FOCUS_Z.html
@@ -102,7 +102,7 @@
       <h1 data-toc-skip>Example evaluation of FOCUS dataset Z</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2020-11-19</h4>
+            <h4 class="date">2020-11-30</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/FOCUS_Z.rmd"><code>vignettes/web_only/FOCUS_Z.rmd</code></a></small>
       <div class="hidden name"><code>FOCUS_Z.rmd</code></div>
@@ -138,9 +138,9 @@
 <a href="#parent-and-one-metabolite" class="anchor"></a>Parent and one metabolite</h1>
 <p>The next step is to set up the models used for the kinetic analysis. As the simultaneous fit of parent and the first metabolite is usually straightforward, Step 1 (SFO for parent only) is skipped here. We start with the model 2a, with formation and decline of metabolite Z1 and the pathway from parent directly to sink included (default in mkin).</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">Z.2a</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span><span class="op">)</span>,
-                Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
-<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
+<code class="sourceCode R"><span class="va">Z.2a</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span><span class="op">)</span>,
+                Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
+<pre><code>## Temporary DLL for differentials generated and loaded</code></pre>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">m.Z.2a</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.2a</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
 <pre><code>## Warning in mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
@@ -159,10 +159,10 @@
 <p>As obvious from the parameter summary (the  component of the summary), the kinetic rate constant from parent compound Z to sink is very small and the t-test for this parameter suggests that it is not significantly different from zero. This suggests, in agreement with the analysis in the FOCUS kinetics report, to simplify the model by removing the pathway to sink.</p>
 <p>A similar result can be obtained when formation fractions are used in the model formulation:</p>
 <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">Z.2a.ff</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span><span class="op">)</span>,
-                   Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,
+<code class="sourceCode R"><span class="va">Z.2a.ff</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span><span class="op">)</span>,
+                   Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,
                    use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></code></pre></div>
-<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
+<pre><code>## Temporary DLL for differentials generated and loaded</code></pre>
 <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">m.Z.2a.ff</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.2a.ff</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
 <pre><code>## Warning in mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
@@ -182,9 +182,9 @@
 <p>A simplified model is obtained by removing the pathway to the sink. </p>
 <p>In the following, we use the parameterisation with formation fractions in order to be able to compare with the results in the FOCUS guidance, and as it makes it easier to use parameters obtained in a previous fit when adding a further metabolite.</p>
 <div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">Z.3</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-               Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></code></pre></div>
-<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
+<code class="sourceCode R"><span class="va">Z.3</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
+               Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></code></pre></div>
+<pre><code>## Temporary DLL for differentials generated and loaded</code></pre>
 <div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">m.Z.3</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.3</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
 <pre><code>## Warning in mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
@@ -206,10 +206,10 @@
 <a href="#metabolites-z2-and-z3" class="anchor"></a>Metabolites Z2 and Z3</h1>
 <p>As suggested in the FOCUS report, the pathway to sink was removed for metabolite Z1 as well in the next step. While this step appears questionable on the basis of the above results, it is followed here for the purpose of comparison. Also, in the FOCUS report, it is assumed that there is additional empirical evidence that Z1 quickly and exclusively hydrolyses to Z2.</p>
 <div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">Z.5</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-               Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-               Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></code></pre></div>
-<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
+<code class="sourceCode R"><span class="va">Z.5</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
+               Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
+               Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></code></pre></div>
+<pre><code>## Temporary DLL for differentials generated and loaded</code></pre>
 <div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">m.Z.5</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
 <pre><code>## Warning in mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
@@ -219,12 +219,12 @@
 <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png" width="700"></p>
 <p>Finally, metabolite Z3 is added to the model. We use the optimised differential equation parameter values from the previous fit in order to accelerate the optimization.</p>
 <div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">Z.FOCUS</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-                   Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-                   Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,
-                   Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,
+<code class="sourceCode R"><span class="va">Z.FOCUS</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
+                   Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
+                   Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,
+                   Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,
                    use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></code></pre></div>
-<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
+<pre><code>## Temporary DLL for differentials generated and loaded</code></pre>
 <div class="sourceCode" id="cb30"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">m.Z.FOCUS</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.FOCUS</span>, <span class="va">FOCUS_2006_Z_mkin</span>,
                      parms.ini <span class="op">=</span> <span class="va">m.Z.5</span><span class="op">$</span><span class="va">bparms.ode</span>,
@@ -266,11 +266,11 @@
 <p>As the FOCUS report states, there is a certain tailing of the time course of metabolite Z3. Also, the time course of the parent compound is not fitted very well using the SFO model, as residues at a certain low level remain.</p>
 <p>Therefore, an additional model is offered here, using the single first-order reversible binding (SFORB) model for metabolite Z3. As expected, the <span class="math inline">\(\chi^2\)</span> error level is lower for metabolite Z3 using this model and the graphical fit for Z3 is improved. However, the covariance matrix is not returned.</p>
 <div class="sourceCode" id="cb38"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">Z.mkin.1</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-                    Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-                    Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,
-                    Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
-<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
+<code class="sourceCode R"><span class="va">Z.mkin.1</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
+                    Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
+                    Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,
+                    Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
+<pre><code>## Temporary DLL for differentials generated and loaded</code></pre>
 <div class="sourceCode" id="cb40"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">m.Z.mkin.1</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.1</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
 <pre><code>## Warning in mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
@@ -283,10 +283,10 @@
 <pre><code>## NULL</code></pre>
 <p>Therefore, a further stepwise model building is performed starting from the stage of parent and two metabolites, starting from the assumption that the model fit for the parent compound can be improved by using the SFORB model.</p>
 <div class="sourceCode" id="cb45"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">Z.mkin.3</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-                    Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-                    Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
-<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
+<code class="sourceCode R"><span class="va">Z.mkin.3</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
+                    Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
+                    Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
+<pre><code>## Temporary DLL for differentials generated and loaded</code></pre>
 <div class="sourceCode" id="cb47"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">m.Z.mkin.3</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.3</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
 <pre><code>## Warning in mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
@@ -297,11 +297,11 @@
 <p>This results in a much better representation of the behaviour of the parent compound Z0.</p>
 <p>Finally, Z3 is added as well. These models appear overparameterised (no covariance matrix returned) if the sink for Z1 is left in the models.</p>
 <div class="sourceCode" id="cb50"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">Z.mkin.4</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-                    Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-                    Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,
-                    Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
-<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
+<code class="sourceCode R"><span class="va">Z.mkin.4</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
+                    Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
+                    Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,
+                    Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
+<pre><code>## Temporary DLL for differentials generated and loaded</code></pre>
 <div class="sourceCode" id="cb52"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">m.Z.mkin.4</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.4</span>, <span class="va">FOCUS_2006_Z_mkin</span>,
                       parms.ini <span class="op">=</span> <span class="va">m.Z.mkin.3</span><span class="op">$</span><span class="va">bparms.ode</span>,
@@ -313,11 +313,11 @@
 <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png" width="700"></p>
 <p>The error level of the fit, but especially of metabolite Z3, can be improved if the SFORB model is chosen for this metabolite, as this model is capable of representing the tailing of the metabolite decline phase.</p>
 <div class="sourceCode" id="cb55"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">Z.mkin.5</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-                    Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-                    Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,
-                    Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
-<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
+<code class="sourceCode R"><span class="va">Z.mkin.5</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
+                    Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
+                    Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,
+                    Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
+<pre><code>## Temporary DLL for differentials generated and loaded</code></pre>
 <div class="sourceCode" id="cb57"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">m.Z.mkin.5</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>,
                       parms.ini <span class="op">=</span> <span class="va">m.Z.mkin.4</span><span class="op">$</span><span class="va">bparms.ode</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">4</span><span class="op">]</span>,
diff --git a/docs/dev/articles/web_only/NAFTA_examples.html b/docs/dev/articles/web_only/NAFTA_examples.html
index c3192b37..fca15672 100644
--- a/docs/dev/articles/web_only/NAFTA_examples.html
+++ b/docs/dev/articles/web_only/NAFTA_examples.html
@@ -102,7 +102,7 @@
       <h1 data-toc-skip>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2020-11-19</h4>
+            <h4 class="date">2020-11-30</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/NAFTA_examples.rmd"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small>
       <div class="hidden name"><code>NAFTA_examples.rmd</code></div>
diff --git a/docs/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html
index ff70847e..8e157c0f 100644
--- a/docs/dev/articles/web_only/benchmarks.html
+++ b/docs/dev/articles/web_only/benchmarks.html
@@ -102,7 +102,7 @@
       <h1 data-toc-skip>Benchmark timings for mkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2020-11-19</h4>
+            <h4 class="date">2020-11-30</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/benchmarks.rmd"><code>vignettes/web_only/benchmarks.rmd</code></a></small>
       <div class="hidden name"><code>benchmarks.rmd</code></div>
@@ -127,14 +127,14 @@
 <p>One metabolite:</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>
-  parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,
-  m1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span>
+  parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,
+  m1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span>
 <span class="va">FOMC_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>
-  parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"m1"</span><span class="op">)</span>,
-  m1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span>
+  parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"m1"</span><span class="op">)</span>,
+  m1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span>
 <span class="va">DFOP_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>
-  parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"m1"</span><span class="op">)</span>,
-  m1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span>
+  parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"m1"</span><span class="op">)</span>,
+  m1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span>
 <span class="va">t3</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOMC_SFO</span>, <span class="va">DFOP_SFO</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="va">FOCUS_D</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span>
 <span class="va">t4</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOMC_SFO</span>, <span class="va">DFOP_SFO</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="va">FOCUS_D</span><span class="op">)</span>,
     error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></code></pre></div>
@@ -148,14 +148,14 @@
     error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></code></pre></div>
 <p>Two metabolites, synthetic data:</p>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">m_synth_SFO_lin</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M1"</span><span class="op">)</span>,
-                           M1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M2"</span><span class="op">)</span>,
-                           M2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,
+<code class="sourceCode R"><span class="va">m_synth_SFO_lin</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M1"</span><span class="op">)</span>,
+                           M1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M2"</span><span class="op">)</span>,
+                           M2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,
                            use_of_ff <span class="op">=</span> <span class="st">"max"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
 
-<span class="va">m_synth_DFOP_par</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,
-                           M1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,
-                           M2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,
+<span class="va">m_synth_DFOP_par</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,
+                           M1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,
+                           M2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,
                            use_of_ff <span class="op">=</span> <span class="st">"max"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
 
 <span class="va">SFO_lin_a</span> <span class="op">&lt;-</span> <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>
@@ -232,8 +232,8 @@
 </tr>
 <tr class="even">
 <td align="left">0.9.50.4</td>
-<td align="right">1.702</td>
-<td align="right">3.717</td>
+<td align="right">1.786</td>
+<td align="right">3.729</td>
 </tr>
 </tbody>
 </table>
@@ -294,9 +294,9 @@
 </tr>
 <tr class="even">
 <td align="left">0.9.50.4</td>
-<td align="right">1.355</td>
-<td align="right">7.015</td>
-<td align="right">2.729</td>
+<td align="right">1.397</td>
+<td align="right">7.251</td>
+<td align="right">2.810</td>
 </tr>
 </tbody>
 </table>
@@ -381,12 +381,12 @@
 </tr>
 <tr class="even">
 <td align="left">0.9.50.4</td>
-<td align="right">0.759</td>
-<td align="right">1.245</td>
-<td align="right">1.436</td>
-<td align="right">3.687</td>
-<td align="right">1.886</td>
-<td align="right">3.028</td>
+<td align="right">0.783</td>
+<td align="right">1.282</td>
+<td align="right">1.486</td>
+<td align="right">3.815</td>
+<td align="right">1.958</td>
+<td align="right">3.105</td>
 </tr>
 </tbody>
 </table>
diff --git a/docs/dev/articles/web_only/compiled_models.html b/docs/dev/articles/web_only/compiled_models.html
index 3d1c7fcd..a444f4bc 100644
--- a/docs/dev/articles/web_only/compiled_models.html
+++ b/docs/dev/articles/web_only/compiled_models.html
@@ -102,7 +102,7 @@
       <h1 data-toc-skip>Performance benefit by using compiled model definitions in mkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2020-11-19</h4>
+            <h4 class="date">2020-11-30</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/compiled_models.rmd"><code>vignettes/web_only/compiled_models.rmd</code></a></small>
       <div class="hidden name"><code>compiled_models.rmd</code></div>
@@ -134,9 +134,9 @@
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="st"><a href="https://pkgdown.jrwb.de/mkin/">"mkin"</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
 <span class="va">SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>
-  parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,
-  m1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
-<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
+  parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,
+  m1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
+<pre><code>## Temporary DLL for differentials generated and loaded</code></pre>
 <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">FOCUS_D</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/subset.html">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></code></pre></div>
 <p>We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the benchmark package. In the output of below code, the warnings about zero being removed from the FOCUS D dataset are suppressed. Since mkin version 0.9.49.11, an analytical solution is also implemented, which is included in the tests below.</p>
@@ -160,10 +160,10 @@
   <span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="st">"R package rbenchmark is not available"</span><span class="op">)</span>
 <span class="op">}</span></code></pre></div>
 <pre><code>##                    test replications relative elapsed
-## 4            analytical            1    1.000   0.186
-## 3     deSolve, compiled            1    1.742   0.324
-## 2      Eigenvalue based            1    2.048   0.381
-## 1 deSolve, not compiled            1   42.532   7.911</code></pre>
+## 4            analytical            1    1.000   0.187
+## 3     deSolve, compiled            1    1.807   0.338
+## 2      Eigenvalue based            1    2.032   0.380
+## 1 deSolve, not compiled            1   43.048   8.050</code></pre>
 <p>We see that using the compiled model is by more than a factor of 10 faster than using deSolve without compiled code.</p>
 </div>
 <div id="model-without-analytical-solution" class="section level2">
@@ -173,8 +173,8 @@
 <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com">rbenchmark</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span>
   <span class="va">FOMC_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>
-    parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"m1"</span><span class="op">)</span>,
-    m1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span> <span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span>
+    parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"m1"</span><span class="op">)</span>,
+    m1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span> <span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span>
 
   <span class="va">b.2</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html">benchmark</a></span><span class="op">(</span>
     <span class="st">"deSolve, not compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">FOMC_SFO</span>, <span class="va">FOCUS_D</span>,
@@ -188,11 +188,11 @@
   <span class="va">factor_FOMC_SFO</span> <span class="op">&lt;-</span> <span class="cn">NA</span>
   <span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="st">"R package benchmark is not available"</span><span class="op">)</span>
 <span class="op">}</span></code></pre></div>
-<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
+<pre><code>## Temporary DLL for differentials generated and loaded</code></pre>
 <pre><code>##                    test replications relative elapsed
-## 2     deSolve, compiled            1    1.000   0.465
-## 1 deSolve, not compiled            1   30.852  14.346</code></pre>
-<p>Here we get a performance benefit of a factor of 31 using the version of the differential equation model compiled from C code!</p>
+## 2     deSolve, compiled            1    1.000   0.483
+## 1 deSolve, not compiled            1   29.969  14.475</code></pre>
+<p>Here we get a performance benefit of a factor of 30 using the version of the differential equation model compiled from C code!</p>
 <p>This vignette was built with mkin 0.9.50.4 on</p>
 <pre><code>## R version 4.0.3 (2020-10-10)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index f8ab4012..b3db5e23 100644
--- a/docs/dev/pkgdown.yml
+++ b/docs/dev/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
   web_only/NAFTA_examples: NAFTA_examples.html
   web_only/benchmarks: benchmarks.html
   web_only/compiled_models: compiled_models.html
-last_built: 2020-11-27T20:47Z
+last_built: 2020-11-30T14:47Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/CAKE_export.html b/docs/dev/reference/CAKE_export.html
index ce8a3444..d3f45bf0 100644
--- a/docs/dev/reference/CAKE_export.html
+++ b/docs/dev/reference/CAKE_export.html
@@ -73,7 +73,7 @@ specified as well." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -121,7 +121,7 @@ specified as well." />
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -140,7 +140,7 @@ specified as well." />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Export a list of datasets format to a CAKE study file</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/CAKE_export.R'><code>R/CAKE_export.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/CAKE_export.R'><code>R/CAKE_export.R</code></a></small>
     <div class="hidden name"><code>CAKE_export.Rd</code></div>
     </div>
 
@@ -149,21 +149,21 @@ specified as well." />
 specified as well.</p>
     </div>
 
-    <pre class="usage"><span class='fu'>CAKE_export</span>(
-  <span class='no'>ds</span>,
-  <span class='kw'>map</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='st'>"Parent"</span>),
-  <span class='kw'>links</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
-  <span class='kw'>filename</span> <span class='kw'>=</span> <span class='st'>"CAKE_export.csf"</span>,
-  <span class='kw'>path</span> <span class='kw'>=</span> <span class='st'>"."</span>,
-  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
-  <span class='kw'>study</span> <span class='kw'>=</span> <span class='st'>"Codlemone aerobic soil degradation"</span>,
-  <span class='kw'>description</span> <span class='kw'>=</span> <span class='st'>""</span>,
-  <span class='kw'>time_unit</span> <span class='kw'>=</span> <span class='st'>"days"</span>,
-  <span class='kw'>res_unit</span> <span class='kw'>=</span> <span class='st'>"% AR"</span>,
-  <span class='kw'>comment</span> <span class='kw'>=</span> <span class='st'>"Created using mkin::CAKE_export"</span>,
-  <span class='kw'>date</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span>(),
-  <span class='kw'>optimiser</span> <span class='kw'>=</span> <span class='st'>"IRLS"</span>
-)</pre>
+    <pre class="usage"><span class='fu'>CAKE_export</span><span class='op'>(</span>
+  <span class='va'>ds</span>,
+  map <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='st'>"Parent"</span><span class='op'>)</span>,
+  links <span class='op'>=</span> <span class='cn'>NA</span>,
+  filename <span class='op'>=</span> <span class='st'>"CAKE_export.csf"</span>,
+  path <span class='op'>=</span> <span class='st'>"."</span>,
+  overwrite <span class='op'>=</span> <span class='cn'>FALSE</span>,
+  study <span class='op'>=</span> <span class='st'>"Codlemone aerobic soil degradation"</span>,
+  description <span class='op'>=</span> <span class='st'>""</span>,
+  time_unit <span class='op'>=</span> <span class='st'>"days"</span>,
+  res_unit <span class='op'>=</span> <span class='st'>"% AR"</span>,
+  comment <span class='op'>=</span> <span class='st'>"Created using mkin::CAKE_export"</span>,
+  date <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span><span class='op'>(</span><span class='op'>)</span>,
+  optimiser <span class='op'>=</span> <span class='st'>"IRLS"</span>
+<span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -230,6 +230,9 @@ compatible with CAKE.</p></td>
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
     <p>The function is called for its side effect.</p>
+    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
+
+    <p>Johannes Ranke</p>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -246,7 +249,7 @@ compatible with CAKE.</p></td>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/D24_2014.html b/docs/dev/reference/D24_2014.html
index ba768186..e4a3216d 100644
--- a/docs/dev/reference/D24_2014.html
+++ b/docs/dev/reference/D24_2014.html
@@ -217,10 +217,10 @@ specific pieces of information in the comments.</p>
 #&gt; 10  114 18.0
 #&gt; 11  183 11.3
 #&gt; 12  273  9.9
-#&gt; 13  365  6.3</div><div class='input'><span class='va'>m_D24</span> <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>D24 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"DCP"</span><span class='op'>)</span>,
-  DCP <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"DCA"</span><span class='op'>)</span>,
-  DCA <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div></pre>
+#&gt; 13  365  6.3</div><div class='input'><span class='va'>m_D24</span> <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>D24 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"DCP"</span><span class='op'>)</span>,
+  DCP <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"DCA"</span><span class='op'>)</span>,
+  DCA <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>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">
diff --git a/docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html
index fcdfcf72..16d12378 100644
--- a/docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html
+++ b/docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html
@@ -76,7 +76,7 @@ in this fit." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -124,7 +124,7 @@ in this fit." />
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -155,12 +155,12 @@ the initial concentration of the parent compound was fixed to a value of 100
 in this fit.</p>
     </div>
 
-    <pre class="usage"><span class='no'>FOCUS_2006_DFOP_ref_A_to_B</span></pre>
+    <pre class="usage"><span class='va'>FOCUS_2006_DFOP_ref_A_to_B</span></pre>
 
 
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
-    <p>A data frame containing the following variables.</p><dl'>
+    <p>A data frame containing the following variables.</p><dl>
     <dt><code>package</code></dt><dd><p>a factor giving the name of the software package</p></dd>
     <dt><code>M0</code></dt><dd><p>The fitted initial concentration of the parent compound</p></dd>
     <dt><code>f</code></dt><dd><p>The fitted f parameter</p></dd>
@@ -181,7 +181,8 @@ in this fit.</p>
   <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>FOCUS_2006_DFOP_ref_A_to_B</span>)</div></pre>
+    <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_DFOP_ref_A_to_B</span><span class='op'>)</span>
+</div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">
@@ -197,7 +198,7 @@ in this fit.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html
index 666a1123..6b8a6119 100644
--- a/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html
+++ b/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html
@@ -76,7 +76,7 @@ in this fit." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -124,7 +124,7 @@ in this fit." />
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -155,12 +155,12 @@ the initial concentration of the parent compound was fixed to a value of 100
 in this fit.</p>
     </div>
 
-    <pre class="usage"><span class='no'>FOCUS_2006_FOMC_ref_A_to_F</span></pre>
+    <pre class="usage"><span class='va'>FOCUS_2006_FOMC_ref_A_to_F</span></pre>
 
 
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
-    <p>A data frame containing the following variables.</p><dl'>
+    <p>A data frame containing the following variables.</p><dl>
     <dt><code>package</code></dt><dd><p>a factor giving the name of the software package</p></dd>
     <dt><code>M0</code></dt><dd><p>The fitted initial concentration of the parent compound</p></dd>
     <dt><code>alpha</code></dt><dd><p>The fitted alpha parameter</p></dd>
@@ -180,7 +180,8 @@ in this fit.</p>
   <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>FOCUS_2006_FOMC_ref_A_to_F</span>)</div></pre>
+    <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_FOMC_ref_A_to_F</span><span class='op'>)</span>
+</div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">
@@ -196,7 +197,7 @@ in this fit.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html
index b07abb0d..076a66c6 100644
--- a/docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html
+++ b/docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html
@@ -76,7 +76,7 @@ in this fit." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -124,7 +124,7 @@ in this fit." />
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -155,12 +155,12 @@ the initial concentration of the parent compound was fixed to a value of 100
 in this fit.</p>
     </div>
 
-    <pre class="usage"><span class='no'>FOCUS_2006_HS_ref_A_to_F</span></pre>
+    <pre class="usage"><span class='va'>FOCUS_2006_HS_ref_A_to_F</span></pre>
 
 
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
-    <p>A data frame containing the following variables.</p><dl'>
+    <p>A data frame containing the following variables.</p><dl>
     <dt><code>package</code></dt><dd><p>a factor giving the name of the software package</p></dd>
     <dt><code>M0</code></dt><dd><p>The fitted initial concentration of the parent compound</p></dd>
     <dt><code>tb</code></dt><dd><p>The fitted tb parameter</p></dd>
@@ -181,7 +181,8 @@ in this fit.</p>
   <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>FOCUS_2006_HS_ref_A_to_F</span>)</div></pre>
+    <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_HS_ref_A_to_F</span><span class='op'>)</span>
+</div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">
@@ -197,7 +198,7 @@ in this fit.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html
index 1e3b91f6..08f1d416 100644
--- a/docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html
+++ b/docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html
@@ -76,7 +76,7 @@ in this fit." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -124,7 +124,7 @@ in this fit." />
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -155,12 +155,12 @@ the initial concentration of the parent compound was fixed to a value of 100
 in this fit.</p>
     </div>
 
-    <pre class="usage"><span class='no'>FOCUS_2006_SFO_ref_A_to_F</span></pre>
+    <pre class="usage"><span class='va'>FOCUS_2006_SFO_ref_A_to_F</span></pre>
 
 
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
-    <p>A data frame containing the following variables.</p><dl'>
+    <p>A data frame containing the following variables.</p><dl>
     <dt><code>package</code></dt><dd><p>a factor giving the name of the software package</p></dd>
     <dt><code>M0</code></dt><dd><p>The fitted initial concentration of the parent compound</p></dd>
     <dt><code>k</code></dt><dd><p>The fitted first-order degradation rate constant</p></dd>
@@ -179,7 +179,8 @@ in this fit.</p>
   <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>FOCUS_2006_SFO_ref_A_to_F</span>)</div></pre>
+    <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_SFO_ref_A_to_F</span><span class='op'>)</span>
+</div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">
@@ -195,7 +196,7 @@ in this fit.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/FOCUS_2006_datasets.html b/docs/dev/reference/FOCUS_2006_datasets.html
index 9836adac..df4651f8 100644
--- a/docs/dev/reference/FOCUS_2006_datasets.html
+++ b/docs/dev/reference/FOCUS_2006_datasets.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -120,7 +120,7 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -147,17 +147,17 @@
     <p>Data taken from FOCUS (2006), p. 258.</p>
     </div>
 
-    <pre class="usage"><span class='no'>FOCUS_2006_A</span>
-  <span class='no'>FOCUS_2006_B</span>
-  <span class='no'>FOCUS_2006_C</span>
-  <span class='no'>FOCUS_2006_D</span>
-  <span class='no'>FOCUS_2006_E</span>
-  <span class='no'>FOCUS_2006_F</span></pre>
+    <pre class="usage"><span class='va'>FOCUS_2006_A</span>
+  <span class='va'>FOCUS_2006_B</span>
+  <span class='va'>FOCUS_2006_C</span>
+  <span class='va'>FOCUS_2006_D</span>
+  <span class='va'>FOCUS_2006_E</span>
+  <span class='va'>FOCUS_2006_F</span></pre>
 
 
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
-    <p>6 datasets with observations on the following variables.</p><dl'>
+    <p>6 datasets with observations on the following variables.</p><dl>
     <dt><code>name</code></dt><dd><p>a factor containing the name of the observed variable</p></dd>
     <dt><code>time</code></dt><dd><p>a numeric vector containing time points</p></dd>
     <dt><code>value</code></dt><dd><p>a numeric vector containing concentrations in percent of applied radioactivity</p></dd>
@@ -173,7 +173,8 @@
   <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='no'>FOCUS_2006_C</span></div><div class='output co'>#&gt;     name time value
+    <pre class="examples"><div class='input'><span class='va'>FOCUS_2006_C</span>
+</div><div class='output co'>#&gt;     name time value
 #&gt; 1 parent    0  85.1
 #&gt; 2 parent    1  57.9
 #&gt; 3 parent    3  29.9
@@ -198,7 +199,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/NAFTA_SOP_2015-1.png b/docs/dev/reference/NAFTA_SOP_2015-1.png
index 9025f2bb..4d823d77 100644
--- a/docs/dev/reference/NAFTA_SOP_2015-1.png
+++ b/docs/dev/reference/NAFTA_SOP_2015-1.png
diff --git a/docs/dev/reference/NAFTA_SOP_2015.html b/docs/dev/reference/NAFTA_SOP_2015.html
index c7e20a45..4243faba 100644
--- a/docs/dev/reference/NAFTA_SOP_2015.html
+++ b/docs/dev/reference/NAFTA_SOP_2015.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -120,7 +120,7 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -147,13 +147,13 @@
     <p>Data taken from US EPA (2015), p. 19 and 23.</p>
     </div>
 
-    <pre class="usage"><span class='no'>NAFTA_SOP_Appendix_B</span>
-  <span class='no'>NAFTA_SOP_Appendix_D</span></pre>
+    <pre class="usage"><span class='va'>NAFTA_SOP_Appendix_B</span>
+  <span class='va'>NAFTA_SOP_Appendix_D</span></pre>
 
 
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
-    <p>2 datasets with observations on the following variables.</p><dl'>
+    <p>2 datasets with observations on the following variables.</p><dl>
     <dt><code>name</code></dt><dd><p>a factor containing the name of the observed variable</p></dd>
     <dt><code>time</code></dt><dd><p>a numeric vector containing time points</p></dd>
     <dt><code>value</code></dt><dd><p>a numeric vector containing concentrations</p></dd>
@@ -172,7 +172,9 @@
   <a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'>  <span class='no'>nafta_evaluation</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='nafta.html'>nafta</a></span>(<span class='no'>NAFTA_SOP_Appendix_D</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#&gt; <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#&gt; <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#&gt; <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#&gt; <span class='message'>The representative half-life obtained from the DFOP model may be used</span></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='output co'>#&gt; Sums of squares:
+    <pre class="examples"><div class='input'>  <span class='va'>nafta_evaluation</span> <span class='op'>&lt;-</span> <span class='fu'><a href='nafta.html'>nafta</a></span><span class='op'>(</span><span class='va'>NAFTA_SOP_Appendix_D</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#&gt; <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#&gt; <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#&gt; <span class='message'>The representative half-life obtained from the DFOP model may be used</span></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>nafta_evaluation</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Sums of squares:
 #&gt;       SFO      IORE      DFOP 
 #&gt; 1378.6832  615.7730  517.8836 
 #&gt; 
@@ -181,17 +183,17 @@
 #&gt; 
 #&gt; Parameters:
 #&gt; $SFO
-#&gt;               Estimate   Pr(&gt;t)    Lower   Upper
-#&gt; parent_0       83.7558 1.80e-14 77.18268 90.3288
-#&gt; k_parent_sink   0.0017 7.43e-05  0.00112  0.0026
-#&gt; sigma           8.7518 1.22e-05  5.64278 11.8608
+#&gt;          Estimate   Pr(&gt;t)    Lower   Upper
+#&gt; parent_0  83.7558 1.80e-14 77.18268 90.3288
+#&gt; k_parent   0.0017 7.43e-05  0.00112  0.0026
+#&gt; sigma      8.7518 1.22e-05  5.64278 11.8608
 #&gt; 
 #&gt; $IORE
-#&gt;                     Estimate Pr(&gt;t)    Lower    Upper
-#&gt; parent_0            9.69e+01     NA 8.88e+01 1.05e+02
-#&gt; k__iore_parent_sink 8.40e-14     NA 1.79e-18 3.94e-09
-#&gt; N_parent            6.68e+00     NA 4.19e+00 9.17e+00
-#&gt; sigma               5.85e+00     NA 3.76e+00 7.94e+00
+#&gt;                Estimate Pr(&gt;t)    Lower    Upper
+#&gt; parent_0       9.69e+01     NA 8.88e+01 1.05e+02
+#&gt; k__iore_parent 8.40e-14     NA 1.79e-18 3.94e-09
+#&gt; N_parent       6.68e+00     NA 4.19e+00 9.17e+00
+#&gt; sigma          5.85e+00     NA 3.76e+00 7.94e+00
 #&gt; 
 #&gt; $DFOP
 #&gt;          Estimate   Pr(&gt;t)    Lower    Upper
@@ -209,7 +211,8 @@
 #&gt; DFOP  429    2380      841
 #&gt; 
 #&gt; Representative half-life:
-#&gt; [1] 841.41</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='NAFTA_SOP_2015-1.png' alt='' width='700' height='433' /></div></pre>
+#&gt; [1] 841.41</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>nafta_evaluation</span><span class='op'>)</span>
+</div><div class='img'><img src='NAFTA_SOP_2015-1.png' alt='' width='700' height='433' /></div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">
@@ -225,7 +228,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/NAFTA_SOP_Attachment-1.png b/docs/dev/reference/NAFTA_SOP_Attachment-1.png
index 19da6da7..6eb10cde 100644
--- a/docs/dev/reference/NAFTA_SOP_Attachment-1.png
+++ b/docs/dev/reference/NAFTA_SOP_Attachment-1.png
diff --git a/docs/dev/reference/NAFTA_SOP_Attachment.html b/docs/dev/reference/NAFTA_SOP_Attachment.html
index 7bc7817e..de984984 100644
--- a/docs/dev/reference/NAFTA_SOP_Attachment.html
+++ b/docs/dev/reference/NAFTA_SOP_Attachment.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -120,7 +120,7 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -147,7 +147,7 @@
     <p>Data taken from from Attachment 1 of the SOP.</p>
     </div>
 
-    <pre class="usage"><span class='no'>NAFTA_SOP_Attachment</span></pre>
+    <pre class="usage"><span class='va'>NAFTA_SOP_Attachment</span></pre>
 
 
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -166,7 +166,9 @@
   <a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'>  <span class='no'>nafta_att_p5a</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='nafta.html'>nafta</a></span>(<span class='no'>NAFTA_SOP_Attachment</span><span class='kw'>[[</span><span class='st'>"p5a"</span>]], <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#&gt; <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#&gt; <span class='message'>The half-life obtained from the IORE model may be used</span></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>nafta_att_p5a</span>)</div><div class='output co'>#&gt; Sums of squares:
+    <pre class="examples"><div class='input'>  <span class='va'>nafta_att_p5a</span> <span class='op'>&lt;-</span> <span class='fu'><a href='nafta.html'>nafta</a></span><span class='op'>(</span><span class='va'>NAFTA_SOP_Attachment</span><span class='op'>[[</span><span class='st'>"p5a"</span><span class='op'>]</span><span class='op'>]</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#&gt; <span class='message'>The half-life obtained from the IORE model may be used</span></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>nafta_att_p5a</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Sums of squares:
 #&gt;       SFO      IORE      DFOP 
 #&gt; 465.21753  56.27506  32.06401 
 #&gt; 
@@ -175,23 +177,23 @@
 #&gt; 
 #&gt; Parameters:
 #&gt; $SFO
-#&gt;               Estimate   Pr(&gt;t)  Lower   Upper
-#&gt; parent_0       95.8401 4.67e-21 92.245 99.4357
-#&gt; k_parent_sink   0.0102 3.92e-12  0.009  0.0117
-#&gt; sigma           4.8230 3.81e-06  3.214  6.4318
+#&gt;          Estimate   Pr(&gt;t)  Lower   Upper
+#&gt; parent_0  95.8401 4.67e-21 92.245 99.4357
+#&gt; k_parent   0.0102 3.92e-12  0.009  0.0117
+#&gt; sigma      4.8230 3.81e-06  3.214  6.4318
 #&gt; 
 #&gt; $IORE
-#&gt;                     Estimate Pr(&gt;t)    Lower    Upper
-#&gt; parent_0            1.01e+02     NA 9.91e+01 1.02e+02
-#&gt; k__iore_parent_sink 1.54e-05     NA 4.08e-06 5.84e-05
-#&gt; N_parent            2.57e+00     NA 2.25e+00 2.89e+00
-#&gt; sigma               1.68e+00     NA 1.12e+00 2.24e+00
+#&gt;                Estimate Pr(&gt;t)    Lower    Upper
+#&gt; parent_0       1.01e+02     NA 9.91e+01 1.02e+02
+#&gt; k__iore_parent 1.54e-05     NA 4.08e-06 5.84e-05
+#&gt; N_parent       2.57e+00     NA 2.25e+00 2.89e+00
+#&gt; sigma          1.68e+00     NA 1.12e+00 2.24e+00
 #&gt; 
 #&gt; $DFOP
 #&gt;          Estimate   Pr(&gt;t)   Lower    Upper
 #&gt; parent_0 9.99e+01 1.41e-26 98.8116 101.0810
 #&gt; k1       2.67e-02 5.05e-06  0.0243   0.0295
-#&gt; k2       2.86e-12 5.00e-01  0.0000      Inf
+#&gt; k2       2.42e-12 5.00e-01  0.0000      Inf
 #&gt; g        6.47e-01 3.67e-06  0.6248   0.6677
 #&gt; sigma    1.27e+00 8.91e-06  0.8395   1.6929
 #&gt; 
@@ -200,10 +202,11 @@
 #&gt;      DT50     DT90 DT50_rep
 #&gt; SFO  67.7 2.25e+02 6.77e+01
 #&gt; IORE 58.2 1.07e+03 3.22e+02
-#&gt; DFOP 55.5 4.42e+11 2.42e+11
+#&gt; DFOP 55.5 5.22e+11 2.86e+11
 #&gt; 
 #&gt; Representative half-life:
-#&gt; [1] 321.51</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>nafta_att_p5a</span>)</div><div class='img'><img src='NAFTA_SOP_Attachment-1.png' alt='' width='700' height='433' /></div></pre>
+#&gt; [1] 321.51</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>nafta_att_p5a</span><span class='op'>)</span>
+</div><div class='img'><img src='NAFTA_SOP_Attachment-1.png' alt='' width='700' height='433' /></div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">
@@ -219,7 +222,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png
index f001da49..ae5db971 100644
--- a/docs/dev/reference/Rplot001.png
+++ b/docs/dev/reference/Rplot001.png
diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png
index c6c75f42..51e51cf4 100644
--- a/docs/dev/reference/Rplot002.png
+++ b/docs/dev/reference/Rplot002.png
diff --git a/docs/dev/reference/Rplot003.png b/docs/dev/reference/Rplot003.png
index 41711ba6..ff6bc722 100644
--- a/docs/dev/reference/Rplot003.png
+++ b/docs/dev/reference/Rplot003.png
diff --git a/docs/dev/reference/Rplot004.png b/docs/dev/reference/Rplot004.png
index 875d6daf..98dd019e 100644
--- a/docs/dev/reference/Rplot004.png
+++ b/docs/dev/reference/Rplot004.png
diff --git a/docs/dev/reference/Rplot008.png b/docs/dev/reference/Rplot008.png
deleted file mode 100644
index 5d1701b8..00000000
--- a/docs/dev/reference/Rplot008.png
+++ /dev/null
diff --git a/docs/dev/reference/Rplot009.png b/docs/dev/reference/Rplot009.png
deleted file mode 100644
index 7788b2d0..00000000
--- a/docs/dev/reference/Rplot009.png
+++ /dev/null
diff --git a/docs/dev/reference/Rplot010.png b/docs/dev/reference/Rplot010.png
deleted file mode 100644
index 86ddd790..00000000
--- a/docs/dev/reference/Rplot010.png
+++ /dev/null
diff --git a/docs/dev/reference/Rplot011.png b/docs/dev/reference/Rplot011.png
deleted file mode 100644
index 30861f3e..00000000
--- a/docs/dev/reference/Rplot011.png
+++ /dev/null
diff --git a/docs/dev/reference/Rplot012.png b/docs/dev/reference/Rplot012.png
deleted file mode 100644
index 4286bb2a..00000000
--- a/docs/dev/reference/Rplot012.png
+++ /dev/null
diff --git a/docs/dev/reference/Rplot013.png b/docs/dev/reference/Rplot013.png
deleted file mode 100644
index 65903441..00000000
--- a/docs/dev/reference/Rplot013.png
+++ /dev/null
diff --git a/docs/dev/reference/Rplot014.png b/docs/dev/reference/Rplot014.png
deleted file mode 100644
index fe2cf0d9..00000000
--- a/docs/dev/reference/Rplot014.png
+++ /dev/null
diff --git a/docs/dev/reference/Rplot015.png b/docs/dev/reference/Rplot015.png
deleted file mode 100644
index 65903441..00000000
--- a/docs/dev/reference/Rplot015.png
+++ /dev/null
diff --git a/docs/dev/reference/add_err.html b/docs/dev/reference/add_err.html
index ae10e863..6ea30515 100644
--- a/docs/dev/reference/add_err.html
+++ b/docs/dev/reference/add_err.html
@@ -224,7 +224,7 @@ https://jrwb.de/posters/piacenza_2015.pdf</p>
 <span class='co'># The kinetic model</span>
 <span class='va'>m_SFO_SFO</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"M1"</span><span class='op'>)</span>,
                      M1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
 <span class='co'># Generate a prediction for a specific set of parameters</span>
 <span class='va'>sampling_times</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span>
 
diff --git a/docs/dev/reference/aw.html b/docs/dev/reference/aw.html
index 267c3b0b..ef808dd8 100644
--- a/docs/dev/reference/aw.html
+++ b/docs/dev/reference/aw.html
@@ -74,7 +74,7 @@ by Burnham and Anderson (2004)." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -122,7 +122,7 @@ by Burnham and Anderson (2004)." />
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -141,7 +141,7 @@ by Burnham and Anderson (2004)." />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Calculate Akaike weights for model averaging</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/aw.R'><code>R/aw.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/aw.R'><code>R/aw.R</code></a></small>
     <div class="hidden name"><code>aw.Rd</code></div>
     </div>
 
@@ -151,13 +151,13 @@ expected Kullback-Leibler information as specified
 by Burnham and Anderson (2004).</p>
     </div>
 
-    <pre class="usage"><span class='fu'>aw</span>(<span class='no'>object</span>, <span class='no'>...</span>)
+    <pre class="usage"><span class='fu'>aw</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span>
 
 <span class='co'># S3 method for mkinfit</span>
-<span class='fu'>aw</span>(<span class='no'>object</span>, <span class='no'>...</span>)
+<span class='fu'>aw</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'>aw</span>(<span class='no'>object</span>, <span class='no'>...</span>)</pre>
+<span class='fu'>aw</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -185,11 +185,16 @@ Inference: Understanding AIC and BIC in Model Selection.
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='co'># \dontrun{</span>
-<span class='no'>f_sfo</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFO"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='no'>f_dfop</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"DFOP"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='no'>aw_sfo_dfop</span> <span class='kw'>&lt;-</span> <span class='fu'>aw</span>(<span class='no'>f_sfo</span>, <span class='no'>f_dfop</span>)
-<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span>(<span class='no'>aw_sfo_dfop</span>)</div><div class='output co'>#&gt; [1] 1</div><div class='input'><span class='no'>aw_sfo_dfop</span> <span class='co'># SFO gets more weight as it has less parameters and a similar fit</span></div><div class='output co'>#&gt; [1] 0.5970258 0.4029742</div><div class='input'><span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span>), <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='st'>"FOCUS D"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_D</span>), <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>aw</span>(<span class='no'>f</span>)</div><div class='output co'>#&gt; [1] 0.4808722 0.1945539 0.3245740</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span>(<span class='fu'>aw</span>(<span class='no'>f</span>))</div><div class='output co'>#&gt; [1] 1</div><div class='input'><span class='fu'>aw</span>(<span class='no'>f</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"DFOP"</span>)])</div><div class='output co'>#&gt; [1] 0.5970258 0.4029742</div><div class='input'># }
+<span class='va'>f_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='va'>f_dfop</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='va'>aw_sfo_dfop</span> <span class='op'>&lt;-</span> <span class='fu'>aw</span><span class='op'>(</span><span class='va'>f_sfo</span>, <span class='va'>f_dfop</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='va'>aw_sfo_dfop</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; [1] 1</div><div class='input'><span class='va'>aw_sfo_dfop</span> <span class='co'># SFO gets more weight as it has less parameters and a similar fit</span>
+</div><div class='output co'>#&gt; [1] 0.5970258 0.4029742</div><div class='input'><span class='va'>f</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"FOCUS D"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_D</span><span class='op'>)</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='fu'>aw</span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; [1] 0.4808722 0.1945539 0.3245740</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='fu'>aw</span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; [1] 1</div><div class='input'><span class='fu'>aw</span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; [1] 0.5970258 0.4029742</div><div class='input'><span class='co'># }</span>
 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -206,7 +211,7 @@ Inference: Understanding AIC and BIC in Model Selection.
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/confint.mkinfit.html b/docs/dev/reference/confint.mkinfit.html
index 745f2dc4..515a7c9e 100644
--- a/docs/dev/reference/confint.mkinfit.html
+++ b/docs/dev/reference/confint.mkinfit.html
@@ -278,19 +278,19 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
 <span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.getenv.html'>Sys.getenv</a></span><span class='op'>(</span><span class='st'>"TRAVIS"</span><span class='op'>)</span> <span class='op'>!=</span> <span class='st'>""</span><span class='op'>)</span> <span class='va'>n_cores</span> <span class='op'>=</span> <span class='fl'>1</span>
 <span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.info.html'>Sys.info</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>[</span><span class='st'>"sysname"</span><span class='op'>]</span> <span class='op'>==</span> <span class='st'>"Windows"</span><span class='op'>)</span> <span class='va'>n_cores</span> <span class='op'>=</span> <span class='fl'>1</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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-<span class='va'>SFO_SFO.ff</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>,
+<span class='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'>"m1"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='va'>SFO_SFO.ff</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>,
   use_of_ff <span class='op'>=</span> <span class='st'>"max"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 <span class='va'>f_d_1</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>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>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>ci_profile</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"profile"</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span>
 </div><div class='output co'>#&gt;    user  system elapsed 
-#&gt;   3.829   1.000   3.519 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span>
+#&gt;   3.900   0.929   3.548 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span>
 <span class='co'># If we additionally exclude parent_0 (the confidence of which is often of</span>
 <span class='co'># minor interest), we get a nice performance improvement from about 50</span>
 <span class='co'># seconds to about 12 seconds if we use at least four cores</span>
 <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>ci_profile_no_parent_0</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"profile"</span>,
   <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"k_parent_sink"</span>, <span class='st'>"k_parent_m1"</span>, <span class='st'>"k_m1_sink"</span>, <span class='st'>"sigma"</span><span class='op'>)</span>, cores <span class='op'>=</span> <span class='va'>n_cores</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Profiling the likelihood</span></div><div class='output co'>#&gt; <span class='warning'>Warning: scheduled cores 2, 1, 3 encountered errors in user code, all values of the jobs will be affected</span></div><div class='output co'>#&gt; <span class='error'>Error in dimnames(x) &lt;- dn: length of 'dimnames' [2] not equal to array extent</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0.011 0.029 0.241</span></div><div class='input'><span class='va'>ci_profile</span>
+</div><div class='output co'>#&gt; <span class='message'>Profiling the likelihood</span></div><div class='output co'>#&gt; <span class='warning'>Warning: scheduled cores 3, 2, 1 encountered errors in user code, all values of the jobs will be affected</span></div><div class='output co'>#&gt; <span class='error'>Error in dimnames(x) &lt;- dn: length of 'dimnames' [2] not equal to array extent</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0.009 0.034 0.257</span></div><div class='input'><span class='va'>ci_profile</span>
 </div><div class='output co'>#&gt;                        2.5%        97.5%
 #&gt; parent_0       96.456003640 1.027703e+02
 #&gt; k_parent        0.090911032 1.071578e-01
@@ -386,9 +386,9 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
 #&gt; sigma          0.0550252516 0.0327066836</div><div class='input'>
 <span class='co'># The profiling for the following fit does not finish in a reasonable time,</span>
 <span class='co'># therefore we use the quadratic approximation</span>
-<span class='va'>m_synth_DFOP_par</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span><span class='op'>)</span>,
-  M1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>,
-  M2 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>,
+<span class='va'>m_synth_DFOP_par</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='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span><span class='op'>)</span>,
+  M1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>,
+  M2 <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>,
   use_of_ff <span class='op'>=</span> <span class='st'>"max"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 <span class='va'>DFOP_par_c</span> <span class='op'>&lt;-</span> <span class='va'>synthetic_data_for_UBA_2014</span><span class='op'>[[</span><span class='fl'>12</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span>
 <span class='va'>f_tc_2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_synth_DFOP_par</span>, <span class='va'>DFOP_par_c</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>,
diff --git a/docs/dev/reference/create_deg_func.html b/docs/dev/reference/create_deg_func.html
index 9f2e4deb..4945d157 100644
--- a/docs/dev/reference/create_deg_func.html
+++ b/docs/dev/reference/create_deg_func.html
@@ -169,9 +169,9 @@
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
 <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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>,
-  m1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='va'>FOCUS_D</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>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 class='co'># to avoid warnings</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>,
+  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>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>FOCUS_D</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>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 class='co'># to avoid warnings</span>
 <span class='va'>fit_1</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, solution_type <span class='op'>=</span> <span class='st'>"analytical"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 <span class='va'>fit_2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 <span class='co'># \dontrun{</span>
@@ -181,20 +181,20 @@
     deSolve <span class='op'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
     replications <span class='op'>=</span> <span class='fl'>2</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; <span class='message'>Loading required package: rbenchmark</span></div><div class='output co'>#&gt;         test replications elapsed relative user.self sys.self user.child
-#&gt; 1 analytical            2   0.397    1.000     0.397    0.001          0
-#&gt; 2    deSolve            2   0.684    1.723     0.683    0.000          0
+#&gt; 1 analytical            2   0.396    1.000     0.395        0          0
+#&gt; 2    deSolve            2   0.694    1.753     0.693        0          0
 #&gt;   sys.child
 #&gt; 1         0
 #&gt; 2         0</div><div class='input'>  <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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='st'>"m1"</span><span class='op'>)</span>,
-    m1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/pkg/rbenchmark/man/benchmark.html'>benchmark</a></span><span class='op'>(</span>
+    parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='st'>"m1"</span><span class='op'>)</span>,
+    m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/pkg/rbenchmark/man/benchmark.html'>benchmark</a></span><span class='op'>(</span>
     analytical <span class='op'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>DFOP_SFO</span>, <span class='va'>FOCUS_D</span>, solution_type <span class='op'>=</span> <span class='st'>"analytical"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
     deSolve <span class='op'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>DFOP_SFO</span>, <span class='va'>FOCUS_D</span>, solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
     replications <span class='op'>=</span> <span class='fl'>2</span><span class='op'>)</span>
 </div><div class='output co'>#&gt;         test replications elapsed relative user.self sys.self user.child
-#&gt; 1 analytical            2   0.834    1.000     0.833    0.001          0
-#&gt; 2    deSolve            2   1.545    1.853     1.541    0.001          0
+#&gt; 1 analytical            2   0.838    1.000     0.838    0.001          0
+#&gt; 2    deSolve            2   1.573    1.877     1.572    0.000          0
 #&gt;   sys.child
 #&gt; 1         0
 #&gt; 2         0</div><div class='input'><span class='co'># }</span>
diff --git a/docs/dev/reference/dot-plot_mixed.html b/docs/dev/reference/dot-plot_mixed.html
deleted file mode 100644
index e359c5ea..00000000
--- a/docs/dev/reference/dot-plot_mixed.html
+++ /dev/null
@@ -1,203 +0,0 @@
-<!-- Generated by pkgdown: do not edit by hand -->
-<!DOCTYPE html>
-<html lang="en">
-  <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Not intended to be called directly by the user — .plot_mixed • mkin</title>
-
-
-<!-- jquery -->
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-        <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
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-    <div class="page-header">
-    <h1>Not intended to be called directly by the user</h1>
-    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/plot_mixed.R'><code>R/plot_mixed.R</code></a></small>
-    <div class="hidden name"><code>dot-plot_mixed.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    <p>Not intended to be called directly by the user</p>
-    </div>
-
-    <pre class="usage"><span class='fu'>.plot_mixed</span><span class='op'>(</span>
-  <span class='va'>x</span>,
-  i <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin</span><span class='op'>)</span>,
-  <span class='va'>degparms_optim</span>,
-  <span class='va'>degparms_pop</span>,
-  <span class='va'>residuals</span>,
-  obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>,
-  standardized <span class='op'>=</span> <span class='cn'>TRUE</span>,
-  xlab <span class='op'>=</span> <span class='st'>"Time"</span>,
-  xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</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='va'>time</span><span class='op'>)</span>,
-  resplot <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"predicted"</span>, <span class='st'>"time"</span><span class='op'>)</span>,
-  ymax <span class='op'>=</span> <span class='st'>"auto"</span>,
-  maxabs <span class='op'>=</span> <span class='st'>"auto"</span>,
-  ncol.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>8</span>, <span class='fl'>3</span>, <span class='fl'>4</span><span class='op'>)</span><span class='op'>)</span>,
-  nrow.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>ceiling</a></span><span class='op'>(</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ncol.legend</span><span class='op'>)</span>,
-  rel.height.legend <span class='op'>=</span> <span class='fl'>0.03</span> <span class='op'>+</span> <span class='fl'>0.08</span> <span class='op'>*</span> <span class='va'>nrow.legend</span>,
-  rel.height.bottom <span class='op'>=</span> <span class='fl'>1.1</span>,
-  pch_ds <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span>,
-  col_ds <span class='op'>=</span> <span class='va'>pch_ds</span> <span class='op'>+</span> <span class='fl'>1</span>,
-  lty_ds <span class='op'>=</span> <span class='va'>col_ds</span>,
-  frame <span class='op'>=</span> <span class='cn'>TRUE</span>,
-  <span class='va'>...</span>
-<span class='op'>)</span></pre>
-
-
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-    <nav id="toc" data-toggle="toc" class="sticky-top">
-      <h2 data-toc-skip>Contents</h2>
-    </nav>
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-      <div class="copyright">
-  <p>Developed by Johannes Ranke.</p>
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diff --git a/docs/dev/reference/experimental_data_for_UBA.html b/docs/dev/reference/experimental_data_for_UBA.html
index cd098b7d..78e57fb0 100644
--- a/docs/dev/reference/experimental_data_for_UBA.html
+++ b/docs/dev/reference/experimental_data_for_UBA.html
@@ -242,31 +242,31 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
 
 <span class='co'># Model definitions</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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"A1"</span><span class='op'>)</span>,
-  A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>,
+  parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"A1"</span><span class='op'>)</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>,
   use_of_ff <span class='op'>=</span> <span class='st'>"max"</span>
 <span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
 <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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, to <span class='op'>=</span> <span class='st'>"A1"</span><span class='op'>)</span>,
-  A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>,
+  parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, to <span class='op'>=</span> <span class='st'>"A1"</span><span class='op'>)</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>,
   use_of_ff <span class='op'>=</span> <span class='st'>"max"</span>
 <span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
 <span class='va'>sfo_sfo_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>
-  parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"A1"</span><span class='op'>)</span>,
-  A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"A2"</span><span class='op'>)</span>,
-  A2 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>,
+  parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"A1"</span><span class='op'>)</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>, to <span class='op'>=</span> <span class='st'>"A2"</span><span class='op'>)</span>,
+  A2 <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>,
   use_of_ff <span class='op'>=</span> <span class='st'>"max"</span>
 <span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
 <span class='va'>dfop_sfo_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>
-  parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, to <span class='op'>=</span> <span class='st'>"A1"</span><span class='op'>)</span>,
-  A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"A2"</span><span class='op'>)</span>,
-  A2 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>,
+  parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, to <span class='op'>=</span> <span class='st'>"A1"</span><span class='op'>)</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>, to <span class='op'>=</span> <span class='st'>"A2"</span><span class='op'>)</span>,
+  A2 <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>,
   use_of_ff <span class='op'>=</span> <span class='st'>"max"</span>
 <span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='va'>d_1_2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>2</span><span class='op'>]</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>d_1_2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>2</span><span class='op'>]</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>)</span>
 <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>d_1_2</span><span class='op'>)</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Soil"</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>2</span><span class='op'>)</span>
 
 
diff --git a/docs/dev/reference/loftest-1.png b/docs/dev/reference/loftest-1.png
index 3d20f41e..6b918fec 100644
--- a/docs/dev/reference/loftest-1.png
+++ b/docs/dev/reference/loftest-1.png
diff --git a/docs/dev/reference/loftest-2.png b/docs/dev/reference/loftest-2.png
index be8bf815..60874bd3 100644
--- a/docs/dev/reference/loftest-2.png
+++ b/docs/dev/reference/loftest-2.png
diff --git a/docs/dev/reference/loftest-3.png b/docs/dev/reference/loftest-3.png
index cb55838c..4837e7f2 100644
--- a/docs/dev/reference/loftest-3.png
+++ b/docs/dev/reference/loftest-3.png
diff --git a/docs/dev/reference/loftest-4.png b/docs/dev/reference/loftest-4.png
index e2b8ac5c..9c18ac30 100644
--- a/docs/dev/reference/loftest-4.png
+++ b/docs/dev/reference/loftest-4.png
diff --git a/docs/dev/reference/loftest-5.png b/docs/dev/reference/loftest-5.png
index a4d9fd48..11f2bda7 100644
--- a/docs/dev/reference/loftest-5.png
+++ b/docs/dev/reference/loftest-5.png
diff --git a/docs/dev/reference/loftest.html b/docs/dev/reference/loftest.html
index b93b3aa3..abbbd3b9 100644
--- a/docs/dev/reference/loftest.html
+++ b/docs/dev/reference/loftest.html
@@ -75,7 +75,7 @@ lrtest.default from the lmtest package." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -123,7 +123,7 @@ lrtest.default from the lmtest package." />
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -142,7 +142,7 @@ lrtest.default from the lmtest package." />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Lack-of-fit test for models fitted to data with replicates</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/loftest.R'><code>R/loftest.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/loftest.R'><code>R/loftest.R</code></a></small>
     <div class="hidden name"><code>loftest.Rd</code></div>
     </div>
 
@@ -153,10 +153,10 @@ compares the likelihoods using the likelihood ratio test
 <code><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest.default</a></code> from the lmtest package.</p>
     </div>
 
-    <pre class="usage"><span class='fu'>loftest</span>(<span class='no'>object</span>, <span class='no'>...</span>)
+    <pre class="usage"><span class='fu'>loftest</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span>
 
 <span class='co'># S3 method for mkinfit</span>
-<span class='fu'>loftest</span>(<span class='no'>object</span>, <span class='no'>...</span>)</pre>
+<span class='fu'>loftest</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -183,9 +183,11 @@ of replicate samples.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='co'># \dontrun{</span>
-<span class='no'>test_data</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>12</span>]]$<span class='no'>data</span>, <span class='no'>name</span> <span class='kw'>==</span> <span class='st'>"parent"</span>)
-<span class='no'>sfo_fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFO"</span>, <span class='no'>test_data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span>(<span class='no'>sfo_fit</span>) <span class='co'># We see a clear pattern in the residuals</span></div><div class='img'><img src='loftest-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>loftest</span>(<span class='no'>sfo_fit</span>)  <span class='co'># We have a clear lack of fit</span></div><div class='output co'>#&gt; Likelihood ratio test
+<span class='va'>test_data</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>synthetic_data_for_UBA_2014</span><span class='op'>[[</span><span class='fl'>12</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span>, <span class='va'>name</span> <span class='op'>==</span> <span class='st'>"parent"</span><span class='op'>)</span>
+<span class='va'>sfo_fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>test_data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span><span class='op'>(</span><span class='va'>sfo_fit</span><span class='op'>)</span> <span class='co'># We see a clear pattern in the residuals</span>
+</div><div class='img'><img src='loftest-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>loftest</span><span class='op'>(</span><span class='va'>sfo_fit</span><span class='op'>)</span>  <span class='co'># We have a clear lack of fit</span>
+</div><div class='output co'>#&gt; Likelihood ratio test
 #&gt; 
 #&gt; Model 1: ANOVA with error model const
 #&gt; Model 2: SFO with error model const
@@ -195,9 +197,11 @@ of replicate samples.</p>
 #&gt; ---
 #&gt; Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='co'>#</span>
 <span class='co'># We try a different model (the one that was used to generate the data)</span>
-<span class='no'>dfop_fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"DFOP"</span>, <span class='no'>test_data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span>(<span class='no'>dfop_fit</span>) <span class='co'># We don't see systematic deviations, but heteroscedastic residuals</span></div><div class='img'><img src='loftest-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># therefore we should consider adapting the error model, although we have</span>
-<span class='fu'>loftest</span>(<span class='no'>dfop_fit</span>) <span class='co'># no lack of fit</span></div><div class='output co'>#&gt; Likelihood ratio test
+<span class='va'>dfop_fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='va'>test_data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span><span class='op'>(</span><span class='va'>dfop_fit</span><span class='op'>)</span> <span class='co'># We don't see systematic deviations, but heteroscedastic residuals</span>
+</div><div class='img'><img src='loftest-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># therefore we should consider adapting the error model, although we have</span>
+<span class='fu'>loftest</span><span class='op'>(</span><span class='va'>dfop_fit</span><span class='op'>)</span> <span class='co'># no lack of fit</span>
+</div><div class='output co'>#&gt; Likelihood ratio test
 #&gt; 
 #&gt; Model 1: ANOVA with error model const
 #&gt; Model 2: DFOP with error model const
@@ -205,10 +209,11 @@ of replicate samples.</p>
 #&gt; 1  10 -40.710                    
 #&gt; 2   5 -42.453 -5 3.485     0.6257</div><div class='input'><span class='co'>#</span>
 <span class='co'># This is the anova model used internally for the comparison</span>
-<span class='no'>test_data_anova</span> <span class='kw'>&lt;-</span> <span class='no'>test_data</span>
-<span class='no'>test_data_anova</span>$<span class='no'>time</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/factor.html'>as.factor</a></span>(<span class='no'>test_data_anova</span>$<span class='no'>time</span>)
-<span class='no'>anova_fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/lm.html'>lm</a></span>(<span class='no'>value</span> ~ <span class='no'>time</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>test_data_anova</span>)
-<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>anova_fit</span>)</div><div class='output co'>#&gt; 
+<span class='va'>test_data_anova</span> <span class='op'>&lt;-</span> <span class='va'>test_data</span>
+<span class='va'>test_data_anova</span><span class='op'>$</span><span class='va'>time</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/factor.html'>as.factor</a></span><span class='op'>(</span><span class='va'>test_data_anova</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span>
+<span class='va'>anova_fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/lm.html'>lm</a></span><span class='op'>(</span><span class='va'>value</span> <span class='op'>~</span> <span class='va'>time</span>, data <span class='op'>=</span> <span class='va'>test_data_anova</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>anova_fit</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; 
 #&gt; Call:
 #&gt; lm(formula = value ~ time, data = test_data_anova)
 #&gt; 
@@ -233,12 +238,16 @@ of replicate samples.</p>
 #&gt; Residual standard error: 3.285 on 9 degrees of freedom
 #&gt; Multiple R-squared:  0.9953,	Adjusted R-squared:  0.9912 
 #&gt; F-statistic: 240.5 on 8 and 9 DF,  p-value: 1.417e-09
-#&gt; </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/logLik.html'>logLik</a></span>(<span class='no'>anova_fit</span>) <span class='co'># We get the same likelihood and degrees of freedom</span></div><div class='output co'>#&gt; 'log Lik.' -40.71015 (df=10)</div><div class='input'><span class='co'>#</span>
-<span class='no'>test_data_2</span> <span class='kw'>&lt;-</span> <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>12</span>]]$<span class='no'>data</span>
-<span class='no'>m_synth_SFO_lin</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M1"</span>),
-  <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M2"</span>),
-  <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>sfo_lin_fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_SFO_lin</span>, <span class='no'>test_data_2</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span>(<span class='no'>sfo_lin_fit</span>) <span class='co'># not a good model, we try parallel formation</span></div><div class='img'><img src='loftest-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>loftest</span>(<span class='no'>sfo_lin_fit</span>)</div><div class='output co'>#&gt; Likelihood ratio test
+#&gt; </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/logLik.html'>logLik</a></span><span class='op'>(</span><span class='va'>anova_fit</span><span class='op'>)</span> <span class='co'># We get the same likelihood and degrees of freedom</span>
+</div><div class='output co'>#&gt; 'log Lik.' -40.71015 (df=10)</div><div class='input'><span class='co'>#</span>
+<span class='va'>test_data_2</span> <span class='op'>&lt;-</span> <span class='va'>synthetic_data_for_UBA_2014</span><span class='op'>[[</span><span class='fl'>12</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span>
+<span class='va'>m_synth_SFO_lin</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='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"M1"</span><span class='op'>)</span>,
+  M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"M2"</span><span class='op'>)</span>,
+  M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>sfo_lin_fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_synth_SFO_lin</span>, <span class='va'>test_data_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span><span class='op'>(</span><span class='va'>sfo_lin_fit</span><span class='op'>)</span> <span class='co'># not a good model, we try parallel formation</span>
+</div><div class='img'><img src='loftest-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>loftest</span><span class='op'>(</span><span class='va'>sfo_lin_fit</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Likelihood ratio test
 #&gt; 
 #&gt; Model 1: ANOVA with error model const
 #&gt; Model 2: m_synth_SFO_lin with error model const and fixed parameter(s) M1_0, M2_0
@@ -247,10 +256,13 @@ of replicate samples.</p>
 #&gt; 2   7 -171.927 -21 156.64  &lt; 2.2e-16 ***
 #&gt; ---
 #&gt; Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='co'>#</span>
-<span class='no'>m_synth_SFO_par</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)),
-  <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
-  <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>sfo_par_fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_SFO_par</span>, <span class='no'>test_data_2</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span>(<span class='no'>sfo_par_fit</span>) <span class='co'># much better for metabolites</span></div><div class='img'><img src='loftest-4.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>loftest</span>(<span class='no'>sfo_par_fit</span>)</div><div class='output co'>#&gt; Likelihood ratio test
+<span class='va'>m_synth_SFO_par</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='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span><span class='op'>)</span>,
+  M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>,
+  M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>sfo_par_fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_synth_SFO_par</span>, <span class='va'>test_data_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span><span class='op'>(</span><span class='va'>sfo_par_fit</span><span class='op'>)</span> <span class='co'># much better for metabolites</span>
+</div><div class='img'><img src='loftest-4.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>loftest</span><span class='op'>(</span><span class='va'>sfo_par_fit</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Likelihood ratio test
 #&gt; 
 #&gt; Model 1: ANOVA with error model const
 #&gt; Model 2: m_synth_SFO_par with error model const and fixed parameter(s) M1_0, M2_0
@@ -259,10 +271,13 @@ of replicate samples.</p>
 #&gt; 2   7 -156.331 -21 125.45  &lt; 2.2e-16 ***
 #&gt; ---
 #&gt; Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='co'>#</span>
-<span class='no'>m_synth_DFOP_par</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"DFOP"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)),
-  <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
-  <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>dfop_par_fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_DFOP_par</span>, <span class='no'>test_data_2</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span>(<span class='no'>dfop_par_fit</span>) <span class='co'># No visual lack of fit</span></div><div class='img'><img src='loftest-5.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>loftest</span>(<span class='no'>dfop_par_fit</span>)  <span class='co'># no lack of fit found by the test</span></div><div class='output co'>#&gt; Likelihood ratio test
+<span class='va'>m_synth_DFOP_par</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='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"DFOP"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span><span class='op'>)</span>,
+  M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>,
+  M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>dfop_par_fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_synth_DFOP_par</span>, <span class='va'>test_data_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span><span class='op'>(</span><span class='va'>dfop_par_fit</span><span class='op'>)</span> <span class='co'># No visual lack of fit</span>
+</div><div class='img'><img src='loftest-5.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>loftest</span><span class='op'>(</span><span class='va'>dfop_par_fit</span><span class='op'>)</span>  <span class='co'># no lack of fit found by the test</span>
+</div><div class='output co'>#&gt; Likelihood ratio test
 #&gt; 
 #&gt; Model 1: ANOVA with error model const
 #&gt; Model 2: m_synth_DFOP_par with error model const and fixed parameter(s) M1_0, M2_0
@@ -270,11 +285,12 @@ of replicate samples.</p>
 #&gt; 1  28  -93.606                      
 #&gt; 2   9 -102.763 -19 18.313     0.5016</div><div class='input'><span class='co'>#</span>
 <span class='co'># The anova model used for comparison in the case of transformation products</span>
-<span class='no'>test_data_anova_2</span> <span class='kw'>&lt;-</span> <span class='no'>dfop_par_fit</span>$<span class='no'>data</span>
-<span class='no'>test_data_anova_2</span>$<span class='no'>variable</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/factor.html'>as.factor</a></span>(<span class='no'>test_data_anova_2</span>$<span class='no'>variable</span>)
-<span class='no'>test_data_anova_2</span>$<span class='no'>time</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/factor.html'>as.factor</a></span>(<span class='no'>test_data_anova_2</span>$<span class='no'>time</span>)
-<span class='no'>anova_fit_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/lm.html'>lm</a></span>(<span class='no'>observed</span> ~ <span class='no'>time</span>:<span class='no'>variable</span> - <span class='fl'>1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>test_data_anova_2</span>)
-<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>anova_fit_2</span>)</div><div class='output co'>#&gt; 
+<span class='va'>test_data_anova_2</span> <span class='op'>&lt;-</span> <span class='va'>dfop_par_fit</span><span class='op'>$</span><span class='va'>data</span>
+<span class='va'>test_data_anova_2</span><span class='op'>$</span><span class='va'>variable</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/factor.html'>as.factor</a></span><span class='op'>(</span><span class='va'>test_data_anova_2</span><span class='op'>$</span><span class='va'>variable</span><span class='op'>)</span>
+<span class='va'>test_data_anova_2</span><span class='op'>$</span><span class='va'>time</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/factor.html'>as.factor</a></span><span class='op'>(</span><span class='va'>test_data_anova_2</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span>
+<span class='va'>anova_fit_2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/lm.html'>lm</a></span><span class='op'>(</span><span class='va'>observed</span> <span class='op'>~</span> <span class='va'>time</span><span class='op'>:</span><span class='va'>variable</span> <span class='op'>-</span> <span class='fl'>1</span>, data <span class='op'>=</span> <span class='va'>test_data_anova_2</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>anova_fit_2</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; 
 #&gt; Call:
 #&gt; lm(formula = observed ~ time:variable - 1, data = test_data_anova_2)
 #&gt; 
@@ -317,7 +333,7 @@ of replicate samples.</p>
 #&gt; Residual standard error: 2.225 on 25 degrees of freedom
 #&gt; Multiple R-squared:  0.9979,	Adjusted R-squared:  0.9957 
 #&gt; F-statistic: 469.2 on 25 and 25 DF,  p-value: &lt; 2.2e-16
-#&gt; </div><div class='input'># }
+#&gt; </div><div class='input'><span class='co'># }</span>
 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -334,7 +350,7 @@ of replicate samples.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/logLik.mkinfit.html b/docs/dev/reference/logLik.mkinfit.html
index dbeeef60..66539dbd 100644
--- a/docs/dev/reference/logLik.mkinfit.html
+++ b/docs/dev/reference/logLik.mkinfit.html
@@ -193,10 +193,10 @@ and the fitted error model parameters.</p>
     <pre class="examples"><div class='input'>
   <span class='co'># \dontrun{</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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span><span class='op'>)</span>,
-    m1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>
+    parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span><span class='op'>)</span>,
+    m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>
   <span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>  <span class='va'>d_t</span> <span class='op'>&lt;-</span> <span class='va'>FOCUS_2006_D</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>  <span class='va'>d_t</span> <span class='op'>&lt;-</span> <span class='va'>FOCUS_2006_D</span>
   <span class='va'>f_nw</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>sfo_sfo</span>, <span class='va'>d_t</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='co'># no weighting (weights are unity)</span>
 </div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>  <span class='va'>f_obs</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>sfo_sfo</span>, <span class='va'>d_t</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>  <span class='va'>f_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>sfo_sfo</span>, <span class='va'>d_t</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
diff --git a/docs/dev/reference/logistic.solution.html b/docs/dev/reference/logistic.solution.html
index 86be11a7..950e8a8e 100644
--- a/docs/dev/reference/logistic.solution.html
+++ b/docs/dev/reference/logistic.solution.html
@@ -225,7 +225,7 @@ Version 1.1, 18 December 2014
          lty <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fl'>5</span>, col <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fl'>5</span><span class='op'>)</span>
 </div><div class='img'><img src='logistic.solution-1.png' alt='' width='700' height='433' /></div><div class='input'>
   <span class='co'># Fit with synthetic data</span>
-  <span class='va'>logistic</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"logistic"</span><span class='op'>)</span><span class='op'>)</span>
+  <span class='va'>logistic</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'>"logistic"</span><span class='op'>)</span><span class='op'>)</span>
 
   <span class='va'>sampling_times</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span>
   <span class='va'>parms_logistic</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>kmax <span class='op'>=</span> <span class='fl'>0.08</span>, k0 <span class='op'>=</span> <span class='fl'>0.0001</span>, r <span class='op'>=</span> <span class='fl'>0.2</span><span class='op'>)</span>
diff --git a/docs/dev/reference/lrtest.mkinfit.html b/docs/dev/reference/lrtest.mkinfit.html
index 712cfcfb..b76ebc87 100644
--- a/docs/dev/reference/lrtest.mkinfit.html
+++ b/docs/dev/reference/lrtest.mkinfit.html
@@ -76,7 +76,7 @@ and can be expressed by fixing the parameters of the other." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -124,7 +124,7 @@ and can be expressed by fixing the parameters of the other." />
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -143,7 +143,7 @@ and can be expressed by fixing the parameters of the other." />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Likelihood ratio test for mkinfit models</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/lrtest.mkinfit.R'><code>R/lrtest.mkinfit.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/lrtest.mkinfit.R'><code>R/lrtest.mkinfit.R</code></a></small>
     <div class="hidden name"><code>lrtest.mkinfit.Rd</code></div>
     </div>
 
@@ -156,10 +156,10 @@ and can be expressed by fixing the parameters of the other.</p>
     </div>
 
     <pre class="usage"><span class='co'># S3 method for mkinfit</span>
-<span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span>(<span class='no'>object</span>, <span class='kw'>object_2</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)
+<span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>object</span>, object_2 <span class='op'>=</span> <span class='cn'>NULL</span>, <span class='va'>...</span><span class='op'>)</span>
 
 <span class='co'># S3 method for mmkin</span>
-<span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span>(<span class='no'>object</span>, <span class='no'>...</span>)</pre>
+<span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -191,10 +191,11 @@ lower number of fitted parameters (null hypothesis).</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='co'># \dontrun{</span>
-<span class='no'>test_data</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>12</span>]]$<span class='no'>data</span>, <span class='no'>name</span> <span class='kw'>==</span> <span class='st'>"parent"</span>)
-<span class='no'>sfo_fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFO"</span>, <span class='no'>test_data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='no'>dfop_fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"DFOP"</span>, <span class='no'>test_data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span>(<span class='no'>dfop_fit</span>, <span class='no'>sfo_fit</span>)</div><div class='output co'>#&gt; Likelihood ratio test
+<span class='va'>test_data</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>synthetic_data_for_UBA_2014</span><span class='op'>[[</span><span class='fl'>12</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span>, <span class='va'>name</span> <span class='op'>==</span> <span class='st'>"parent"</span><span class='op'>)</span>
+<span class='va'>sfo_fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>test_data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='va'>dfop_fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='va'>test_data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>dfop_fit</span>, <span class='va'>sfo_fit</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Likelihood ratio test
 #&gt; 
 #&gt; Model 1: DFOP with error model const
 #&gt; Model 2: SFO with error model const
@@ -202,7 +203,8 @@ lower number of fitted parameters (null hypothesis).</p>
 #&gt; 1   5 -42.453                         
 #&gt; 2   3 -63.954 -2 43.002  4.594e-10 ***
 #&gt; ---
-#&gt; Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span>(<span class='no'>sfo_fit</span>, <span class='no'>dfop_fit</span>)</div><div class='output co'>#&gt; Likelihood ratio test
+#&gt; Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>sfo_fit</span>, <span class='va'>dfop_fit</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Likelihood ratio test
 #&gt; 
 #&gt; Model 1: DFOP with error model const
 #&gt; Model 2: SFO with error model const
@@ -217,7 +219,8 @@ lower number of fitted parameters (null hypothesis).</p>
 <span class='co'>#lrtest(dfop_fit, fixed_parms = c(k2 = 0))</span>
 
 <span class='co'># However, this equivalent syntax also works for static help pages</span>
-<span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span>(<span class='no'>dfop_fit</span>, <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>dfop_fit</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>))</div><div class='output co'>#&gt; Likelihood ratio test
+<span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>dfop_fit</span>, <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>dfop_fit</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Likelihood ratio test
 #&gt; 
 #&gt; Model 1: DFOP with error model tc
 #&gt; Model 2: DFOP with error model const
@@ -225,7 +228,8 @@ lower number of fitted parameters (null hypothesis).</p>
 #&gt; 1   6 -34.587                         
 #&gt; 2   5 -42.453 -1 15.731  7.302e-05 ***
 #&gt; ---
-#&gt; Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span>(<span class='no'>dfop_fit</span>, <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>dfop_fit</span>, <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k2</span> <span class='kw'>=</span> <span class='fl'>0</span>)))</div><div class='output co'>#&gt; Likelihood ratio test
+#&gt; Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>dfop_fit</span>, <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>dfop_fit</span>, fixed_parms <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k2 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Likelihood ratio test
 #&gt; 
 #&gt; Model 1: DFOP with error model const
 #&gt; Model 2: DFOP with error model const and fixed parameter(s) k2
@@ -233,7 +237,7 @@ lower number of fitted parameters (null hypothesis).</p>
 #&gt; 1   5 -42.453                         
 #&gt; 2   4 -57.340 -1 29.776  4.851e-08 ***
 #&gt; ---
-#&gt; Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'># }
+#&gt; Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='co'># }</span>
 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -250,7 +254,7 @@ lower number of fitted parameters (null hypothesis).</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/mccall81_245T.html b/docs/dev/reference/mccall81_245T.html
index 255c3568..c23bfda2 100644
--- a/docs/dev/reference/mccall81_245T.html
+++ b/docs/dev/reference/mccall81_245T.html
@@ -177,7 +177,7 @@
     <pre class="examples"><div class='input'>  <span class='va'>SFO_SFO_SFO</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>T245 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"phenol"</span><span class='op'>)</span>,
     phenol <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"anisole"</span><span class='op'>)</span>,
     anisole <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>  <span class='co'># \dontrun{</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>  <span class='co'># \dontrun{</span>
     <span class='va'>fit.1</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>mccall81_245T</span>, <span class='va'>soil</span> <span class='op'>==</span> <span class='st'>"Commerce"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>    <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span>
 </div><div class='output co'>#&gt;                         Estimate   se_notrans   t value       Pr(&gt;t)
@@ -211,7 +211,7 @@
     <span class='va'>SFO_SFO_SFO_2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>T245 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"phenol"</span><span class='op'>)</span>,
       phenol <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"anisole"</span>, sink <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>,
       anisole <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>    <span class='va'>fit.2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO_SFO_2</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>mccall81_245T</span>, <span class='va'>soil</span> <span class='op'>==</span> <span class='st'>"Commerce"</span><span class='op'>)</span>,
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>    <span class='va'>fit.2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO_SFO_2</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>mccall81_245T</span>, <span class='va'>soil</span> <span class='op'>==</span> <span class='st'>"Commerce"</span><span class='op'>)</span>,
       quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>    <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span>
 </div><div class='output co'>#&gt;                      Estimate   se_notrans   t value       Pr(&gt;t)        Lower
diff --git a/docs/dev/reference/mkin_long_to_wide.html b/docs/dev/reference/mkin_long_to_wide.html
index 143eb12a..28a37800 100644
--- a/docs/dev/reference/mkin_long_to_wide.html
+++ b/docs/dev/reference/mkin_long_to_wide.html
@@ -74,7 +74,7 @@ variable and several dependent variables as columns." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -122,7 +122,7 @@ variable and several dependent variables as columns." />
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -141,7 +141,7 @@ variable and several dependent variables as columns." />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Convert a dataframe from long to wide format</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mkin_long_to_wide.R'><code>R/mkin_long_to_wide.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkin_long_to_wide.R'><code>R/mkin_long_to_wide.R</code></a></small>
     <div class="hidden name"><code>mkin_long_to_wide.Rd</code></div>
     </div>
 
@@ -151,7 +151,7 @@ observed value, and converts it into a dataframe with one independent
 variable and several dependent variables as columns.</p>
     </div>
 
-    <pre class="usage"><span class='fu'>mkin_long_to_wide</span>(<span class='no'>long_data</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>, <span class='kw'>outtime</span> <span class='kw'>=</span> <span class='st'>"time"</span>)</pre>
+    <pre class="usage"><span class='fu'>mkin_long_to_wide</span><span class='op'>(</span><span class='va'>long_data</span>, time <span class='op'>=</span> <span class='st'>"time"</span>, outtime <span class='op'>=</span> <span class='st'>"time"</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -176,10 +176,14 @@ observed values called "value".</p></td>
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
     <p>Dataframe in wide format.</p>
+    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
+
+    <p>Johannes Ranke</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
-<span class='fu'>mkin_long_to_wide</span>(<span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#&gt;    time parent    m1
+<span class='fu'>mkin_long_to_wide</span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span><span class='op'>)</span>
+</div><div class='output co'>#&gt;    time parent    m1
 #&gt; 1     0  99.46  0.00
 #&gt; 2     0 102.04  0.00
 #&gt; 3     1  93.50  4.84
@@ -218,7 +222,7 @@ observed values called "value".</p></td>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/mkin_wide_to_long.html b/docs/dev/reference/mkin_wide_to_long.html
index 14419558..f085d162 100644
--- a/docs/dev/reference/mkin_wide_to_long.html
+++ b/docs/dev/reference/mkin_wide_to_long.html
@@ -74,7 +74,7 @@ mkinfit." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -122,7 +122,7 @@ mkinfit." />
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -141,7 +141,7 @@ mkinfit." />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Convert a dataframe with observations over time into long format</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mkin_wide_to_long.R'><code>R/mkin_wide_to_long.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkin_wide_to_long.R'><code>R/mkin_wide_to_long.R</code></a></small>
     <div class="hidden name"><code>mkin_wide_to_long.Rd</code></div>
     </div>
 
@@ -151,7 +151,7 @@ several dependent variable and converts it into the long form as required by
 <code><a href='mkinfit.html'>mkinfit</a></code>.</p>
     </div>
 
-    <pre class="usage"><span class='fu'>mkin_wide_to_long</span>(<span class='no'>wide_data</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"t"</span>)</pre>
+    <pre class="usage"><span class='fu'>mkin_wide_to_long</span><span class='op'>(</span><span class='va'>wide_data</span>, time <span class='op'>=</span> <span class='st'>"t"</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -171,11 +171,15 @@ column of observed values.</p></td>
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
     <p>Dataframe in long format as needed for <code><a href='mkinfit.html'>mkinfit</a></code>.</p>
+    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
+
+    <p>Johannes Ranke</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
-<span class='no'>wide</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>t</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>,<span class='fl'>2</span>,<span class='fl'>3</span>), <span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>,<span class='fl'>4</span>,<span class='fl'>7</span>), <span class='kw'>y</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>3</span>,<span class='fl'>4</span>,<span class='fl'>5</span>))
-<span class='fu'>mkin_wide_to_long</span>(<span class='no'>wide</span>)</div><div class='output co'>#&gt;   name time value
+<span class='va'>wide</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>t <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>1</span>,<span class='fl'>2</span>,<span class='fl'>3</span><span class='op'>)</span>, x <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>1</span>,<span class='fl'>4</span>,<span class='fl'>7</span><span class='op'>)</span>, y <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>3</span>,<span class='fl'>4</span>,<span class='fl'>5</span><span class='op'>)</span><span class='op'>)</span>
+<span class='fu'>mkin_wide_to_long</span><span class='op'>(</span><span class='va'>wide</span><span class='op'>)</span>
+</div><div class='output co'>#&gt;   name time value
 #&gt; 1    x    1     1
 #&gt; 2    x    2     4
 #&gt; 3    x    3     7
@@ -198,7 +202,7 @@ column of observed values.</p></td>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/mkinerrmin.html b/docs/dev/reference/mkinerrmin.html
index 9f58dfaa..1cff040d 100644
--- a/docs/dev/reference/mkinerrmin.html
+++ b/docs/dev/reference/mkinerrmin.html
@@ -73,7 +73,7 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -121,7 +121,7 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." />
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -140,7 +140,7 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Calculate the minimum error to assume in order to pass the variance test</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mkinerrmin.R'><code>R/mkinerrmin.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkinerrmin.R'><code>R/mkinerrmin.R</code></a></small>
     <div class="hidden name"><code>mkinerrmin.Rd</code></div>
     </div>
 
@@ -149,7 +149,7 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." />
 the chi-squared test as defined in the FOCUS kinetics report from 2006.</p>
     </div>
 
-    <pre class="usage"><span class='fu'>mkinerrmin</span>(<span class='no'>fit</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.05</span>)</pre>
+    <pre class="usage"><span class='fu'>mkinerrmin</span><span class='op'>(</span><span class='va'>fit</span>, alpha <span class='op'>=</span> <span class='fl'>0.05</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -189,18 +189,22 @@ Document Reference Sanco/10058/2005 version 2.0, 434 pp,
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
-<span class='no'>SFO_SFO</span> <span class='kw'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>),
-                  <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>),
-                  <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-<span class='no'>fit_FOCUS_D</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_D</span>), <span class='fl'>4</span>)</div><div class='output co'>#&gt;          err.min n.optim df
+<span class='va'>SFO_SFO</span> <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span><span class='op'>)</span>,
+                  m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>,
+                  use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
+<span class='va'>fit_FOCUS_D</span> <span class='op'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span><span class='op'>(</span><span class='fu'>mkinerrmin</span><span class='op'>(</span><span class='va'>fit_FOCUS_D</span><span class='op'>)</span>, <span class='fl'>4</span><span class='op'>)</span>
+</div><div class='output co'>#&gt;          err.min n.optim df
 #&gt; All data  0.0640       4 15
 #&gt; parent    0.0646       2  7
 #&gt; m1        0.0469       2  8</div><div class='input'><span class='co'># \dontrun{</span>
-  <span class='no'>fit_FOCUS_E</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_E</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-  <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_E</span>), <span class='fl'>4</span>)</div><div class='output co'>#&gt;          err.min n.optim df
+  <span class='va'>fit_FOCUS_E</span> <span class='op'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_E</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+  <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span><span class='op'>(</span><span class='fu'>mkinerrmin</span><span class='op'>(</span><span class='va'>fit_FOCUS_E</span><span class='op'>)</span>, <span class='fl'>4</span><span class='op'>)</span>
+</div><div class='output co'>#&gt;          err.min n.optim df
 #&gt; All data  0.1544       4 13
 #&gt; parent    0.1659       2  7
-#&gt; m1        0.1095       2  6</div><div class='input'># }
+#&gt; m1        0.1095       2  6</div><div class='input'><span class='co'># }</span>
 
 </div></pre>
   </div>
@@ -218,7 +222,7 @@ Document Reference Sanco/10058/2005 version 2.0, 434 pp,
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/mkinerrplot.html b/docs/dev/reference/mkinerrplot.html
index 48d20ca8..2324b968 100644
--- a/docs/dev/reference/mkinerrplot.html
+++ b/docs/dev/reference/mkinerrplot.html
@@ -242,8 +242,8 @@ lines of the mkinfit object.</p></div>
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
 <span class='co'># \dontrun{</span>
-<span class='va'>model</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>model</span>, <span class='va'>FOCUS_2006_D</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='va'>model</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'>"m1"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>model</span>, <span class='va'>FOCUS_2006_D</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinerrplot</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
 </div><div class='img'><img src='mkinerrplot-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
 
diff --git a/docs/dev/reference/mkinfit.html b/docs/dev/reference/mkinfit.html
index f5a913b2..73c09c1f 100644
--- a/docs/dev/reference/mkinfit.html
+++ b/docs/dev/reference/mkinfit.html
@@ -432,15 +432,15 @@ Degradation Data. <em>Environments</em> 6(12) 124
 <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; mkin version used for fitting:    0.9.50.4 
 #&gt; R version used for fitting:       4.0.3 
-#&gt; Date of fit:     Thu Nov 19 14:49:38 2020 
-#&gt; Date of summary: Thu Nov 19 14:49:38 2020 
+#&gt; Date of fit:     Mon Nov 30 15:48:34 2020 
+#&gt; Date of summary: Mon Nov 30 15:48:34 2020 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #&gt; 
 #&gt; Model predictions using solution type analytical 
 #&gt; 
-#&gt; Fitted using 222 model solutions performed in 0.045 s
+#&gt; Fitted using 222 model solutions performed in 0.046 s
 #&gt; 
 #&gt; Error model: Constant variance 
 #&gt; 
@@ -515,9 +515,9 @@ Degradation Data. <em>Environments</em> 6(12) 124
 <span class='va'>FOCUS_D</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>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 class='co'># Use mkinsub for convenience in model formulation. Pathway to sink included per default.</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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>,
-  m1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+  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>,
+  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>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
 <span class='co'># Fit the model quietly to the FOCUS example dataset D using defaults</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 class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
@@ -574,16 +574,16 @@ Degradation Data. <em>Environments</em> 6(12) 124
       solution_type <span class='op'>=</span> <span class='st'>"analytical"</span><span class='op'>)</span><span class='op'>)</span>
 <span class='op'>}</span>
 </div><div class='output co'>#&gt;               test relative elapsed
-#&gt; 3       analytical    1.000   0.534
-#&gt; 1 deSolve_compiled    1.908   1.019
-#&gt; 2            eigen    2.238   1.195</div><div class='input'><span class='co'># }</span>
+#&gt; 3       analytical    1.000   0.532
+#&gt; 1 deSolve_compiled    1.831   0.974
+#&gt; 2            eigen    2.235   1.189</div><div class='input'><span class='co'># }</span>
 
 <span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span>
 <span class='co'># \dontrun{</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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='st'>"m1"</span><span class='op'>)</span>,
-  m1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><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>
+  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>,
+  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>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><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 class='co'># Again, we get a warning and try a more sophisticated error model</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>
 </div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation did not converge:</span>
@@ -600,8 +600,8 @@ Degradation Data. <em>Environments</em> 6(12) 124
 <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>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>
 </div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#&gt; <span class='warning'>Warning: diag(.) had 0 or NA entries; non-finite result is doubtful</span></div><div class='output co'>#&gt; mkin version used for fitting:    0.9.50.4 
 #&gt; R version used for fitting:       4.0.3 
-#&gt; Date of fit:     Thu Nov 19 14:49:49 2020 
-#&gt; Date of summary: Thu Nov 19 14:49:49 2020 
+#&gt; Date of fit:     Mon Nov 30 15:48:45 2020 
+#&gt; Date of summary: Mon Nov 30 15:48:45 2020 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -610,7 +610,7 @@ Degradation Data. <em>Environments</em> 6(12) 124
 #&gt; 
 #&gt; Model predictions using solution type deSolve 
 #&gt; 
-#&gt; Fitted using 4273 model solutions performed in 3.1 s
+#&gt; Fitted using 4273 model solutions performed in 3.191 s
 #&gt; 
 #&gt; Error model: Two-component variance function 
 #&gt; 
diff --git a/docs/dev/reference/mkinmod.html b/docs/dev/reference/mkinmod.html
index 803be90d..9e37e664 100644
--- a/docs/dev/reference/mkinmod.html
+++ b/docs/dev/reference/mkinmod.html
@@ -162,9 +162,13 @@ components.</p>
     <pre class="usage"><span class='fu'>mkinmod</span><span class='op'>(</span>
   <span class='va'>...</span>,
   use_of_ff <span class='op'>=</span> <span class='st'>"max"</span>,
+  name <span class='op'>=</span> <span class='cn'>NULL</span>,
   speclist <span class='op'>=</span> <span class='cn'>NULL</span>,
   quiet <span class='op'>=</span> <span class='cn'>FALSE</span>,
-  verbose <span class='op'>=</span> <span class='cn'>FALSE</span>
+  verbose <span class='op'>=</span> <span class='cn'>FALSE</span>,
+  dll_dir <span class='op'>=</span> <span class='cn'>NULL</span>,
+  unload <span class='op'>=</span> <span class='cn'>FALSE</span>,
+  overwrite <span class='op'>=</span> <span class='cn'>FALSE</span>
 <span class='op'>)</span>
 
 <span class='co'># S3 method for mkinmod</span>
@@ -201,6 +205,10 @@ formation fractions is made, i.e. each pathway to a metabolite has its
 own rate constant.</p></td>
     </tr>
     <tr>
+      <th>name</th>
+      <td><p>A name for the model. Should be a valid R object name.</p></td>
+    </tr>
+    <tr>
       <th>speclist</th>
       <td><p>The specification of the observed variables and their
 submodel types and pathways can be given as a single list using this
@@ -216,6 +224,23 @@ argument. Default is NULL.</p></td>
 applicable to give detailed information about the C function being built.</p></td>
     </tr>
     <tr>
+      <th>dll_dir</th>
+      <td><p>Directory where an DLL object, if generated internally by
+<code><a href='https://rdrr.io/pkg/inline/man/cfunction.html'>inline::cfunction()</a></code>, should be saved.  The DLL will only be stored in a
+permanent location for use in future sessions, if 'dll_dir' and 'name'
+are specified.</p></td>
+    </tr>
+    <tr>
+      <th>unload</th>
+      <td><p>If a DLL from the target location in 'dll_dir' is already
+loaded, should that be unloaded first?</p></td>
+    </tr>
+    <tr>
+      <th>overwrite</th>
+      <td><p>If a file exists at the target DLL location in 'dll_dir',
+should this be overwritten?</p></td>
+    </tr>
+    <tr>
       <th>x</th>
       <td><p>An <code>mkinmod</code> object.</p></td>
     </tr>
@@ -299,18 +324,37 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
 <span class='va'>SFO_SFO</span> <span class='op'>&lt;-</span> <span class='fu'>mkinmod</span><span class='op'>(</span>
   parent <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>,
   m1 <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; &lt;mkinmod&gt; model generated with
+#&gt; Use of formation fractions $use_of_ff: max 
+#&gt; Specification $spec:
+#&gt; $parent
+#&gt; $type: SFO; $to: m1; $sink: TRUE
+#&gt; $m1
+#&gt; $type: SFO; $sink: TRUE
+#&gt; Coefficient matrix $coefmat available
+#&gt; Compiled model $cf available
+#&gt; Differential equations:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt; d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1</div><div class='input'>
 <span class='co'># \dontrun{</span>
-<span class='co'># Now supplying full names used for plotting</span>
+ <span class='va'>fit_sfo_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>
+ <span class='co'># Now supplying compound names used for plotting, and write to user defined location</span>
+ <span class='co'># We need to choose a path outside the session tempdir because this gets removed</span>
+ <span class='va'>DLL_dir</span> <span class='op'>&lt;-</span> <span class='st'>"~/.local/share/mkin"</span>
+ <span class='kw'>if</span> <span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/files2.html'>dir.exists</a></span><span class='op'>(</span><span class='va'>DLL_dir</span><span class='op'>)</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/files2.html'>dir.create</a></span><span class='op'>(</span><span class='va'>DLL_dir</span><span class='op'>)</span>
  <span class='va'>SFO_SFO.2</span> <span class='op'>&lt;-</span> <span class='fu'>mkinmod</span><span class='op'>(</span>
    parent <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, full_name <span class='op'>=</span> <span class='st'>"Test compound"</span><span class='op'>)</span>,
-   m1 <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, full_name <span class='op'>=</span> <span class='st'>"Metabolite M1"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-<span class='co'># The above model used to be specified like this, before the advent of mkinsub()</span>
-<span class='va'>SFO_SFO</span> <span class='op'>&lt;-</span> <span class='fu'>mkinmod</span><span class='op'>(</span>
-  parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span><span class='op'>)</span>,
-  m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+   m1 <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, full_name <span class='op'>=</span> <span class='st'>"Metabolite M1"</span><span class='op'>)</span>,
+   name <span class='op'>=</span> <span class='st'>"SFO_SFO"</span>, dll_dir <span class='op'>=</span> <span class='va'>DLL_dir</span>, unload <span class='op'>=</span> <span class='cn'>TRUE</span>, overwrite <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Copied DLL from /tmp/RtmpX9Xf3y/file6d622f3b7e08.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span></div><div class='input'><span class='co'># Now we can save the model and restore it in a new session</span>
+<span class='fu'><a href='https://rdrr.io/r/base/readRDS.html'>saveRDS</a></span><span class='op'>(</span><span class='va'>SFO_SFO.2</span>, file <span class='op'>=</span> <span class='st'>"~/SFO_SFO.rds"</span><span class='op'>)</span>
+<span class='co'># Terminate the R session here if you would like to check, and then do</span>
+<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://pkgdown.jrwb.de/mkin/'>mkin</a></span><span class='op'>)</span>
+<span class='va'>SFO_SFO.3</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/readRDS.html'>readRDS</a></span><span class='op'>(</span><span class='st'>"~/SFO_SFO.rds"</span><span class='op'>)</span>
+<span class='va'>fit_sfo_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.3</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>
 <span class='co'># Show details of creating the C function</span>
 <span class='va'>SFO_SFO</span> <span class='op'>&lt;-</span> <span class='fu'>mkinmod</span><span class='op'>(</span>
   parent <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>,
@@ -330,11 +374,11 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
 #&gt;  12: }
 #&gt;  13: 
 #&gt;  14: 
-#&gt;  15: void func ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) {
+#&gt;  15: void diffs ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) {
 #&gt;  16: 
 #&gt;  17: f[0] = - k_parent * y[0];
 #&gt;  18: f[1] = + f_parent_to_m1 * k_parent * y[0] - k_m1 * y[1];
-#&gt;  19: }</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+#&gt;  19: }</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
 <span class='co'># The symbolic solution which is available in this case is not</span>
 <span class='co'># made for human reading but for speed of computation</span>
 <span class='va'>SFO_SFO</span><span class='op'>$</span><span class='va'>deg_func</span>
@@ -353,7 +397,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
 #&gt;     })
 #&gt;     return(predicted)
 #&gt; }
-#&gt; &lt;environment: 0x55555c97f8d8&gt;</div><div class='input'>
+#&gt; &lt;environment: 0x55555c5b8d68&gt;</div><div class='input'>
 <span class='co'># If we have several parallel metabolites</span>
 <span class='co'># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span>
 <span class='va'>m_synth_DFOP_par</span> <span class='op'>&lt;-</span> <span class='fu'>mkinmod</span><span class='op'>(</span>
@@ -367,27 +411,6 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
   quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 <span class='co'># }</span>
 
-
-  <span class='va'>m_synth_SFO_lin</span> <span class='op'>&lt;-</span> <span class='fu'>mkinmod</span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"M1"</span><span class='op'>)</span>,
-                             M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"M2"</span><span class='op'>)</span>,
-                             M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-  <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>m_synth_SFO_lin</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; &lt;mkinmod&gt; model generated with
-#&gt; Use of formation fractions $use_of_ff: max 
-#&gt; Specification $spec:
-#&gt; $parent
-#&gt; $type: SFO; $to: M1; $sink: TRUE
-#&gt; $M1
-#&gt; $type: SFO; $to: M2; $sink: TRUE
-#&gt; $M2
-#&gt; $type: SFO; $sink: TRUE
-#&gt; Coefficient matrix $coefmat available
-#&gt; Compiled model $cf available
-#&gt; Differential equations:
-#&gt; d_parent/dt = - k_parent * parent
-#&gt; d_M1/dt = + f_parent_to_M1 * k_parent * parent - k_M1 * M1
-#&gt; d_M2/dt = + f_M1_to_M2 * k_M1 * M1 - k_M2 * M2</div><div class='input'>
 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
diff --git a/docs/dev/reference/mkinparplot.html b/docs/dev/reference/mkinparplot.html
index e237ecae..0a989ef9 100644
--- a/docs/dev/reference/mkinparplot.html
+++ b/docs/dev/reference/mkinparplot.html
@@ -172,10 +172,10 @@ effect, namely to produce a plot.</p>
     <pre class="examples"><div class='input'>
 <span class='co'># \dontrun{</span>
 <span class='va'>model</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>
-  T245 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"phenol"</span><span class='op'>)</span>, sink <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>,
-  phenol <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"anisole"</span><span class='op'>)</span><span class='op'>)</span>,
-  anisole <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>model</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>mccall81_245T</span>, <span class='va'>soil</span> <span class='op'>==</span> <span class='st'>"Commerce"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+  T245 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"phenol"</span><span class='op'>)</span>, sink <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>,
+  phenol <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"anisole"</span><span class='op'>)</span><span class='op'>)</span>,
+  anisole <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>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>model</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>mccall81_245T</span>, <span class='va'>soil</span> <span class='op'>==</span> <span class='st'>"Commerce"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinparplot</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
 </div><div class='img'><img src='mkinparplot-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
 </div></pre>
diff --git a/docs/dev/reference/mkinplot.html b/docs/dev/reference/mkinplot.html
index b36bcfc2..417c8c73 100644
--- a/docs/dev/reference/mkinplot.html
+++ b/docs/dev/reference/mkinplot.html
@@ -73,7 +73,7 @@ plot.mkinfit." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -121,7 +121,7 @@ plot.mkinfit." />
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -140,7 +140,7 @@ plot.mkinfit." />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Plot the observed data and the fitted model of an mkinfit object</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/plot.mkinfit.R'><code>R/plot.mkinfit.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/plot.mkinfit.R'><code>R/plot.mkinfit.R</code></a></small>
     <div class="hidden name"><code>mkinplot.Rd</code></div>
     </div>
 
@@ -149,7 +149,7 @@ plot.mkinfit." />
 <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p>
     </div>
 
-    <pre class="usage"><span class='fu'>mkinplot</span>(<span class='no'>fit</span>, <span class='no'>...</span>)</pre>
+    <pre class="usage"><span class='fu'>mkinplot</span><span class='op'>(</span><span class='va'>fit</span>, <span class='va'>...</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -167,6 +167,9 @@ plot.mkinfit." />
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
     <p>The function is called for its side effect.</p>
+    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
+
+    <p>Johannes Ranke</p>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -183,7 +186,7 @@ plot.mkinfit." />
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/mkinpredict.html b/docs/dev/reference/mkinpredict.html
index d3a86276..3221fc23 100644
--- a/docs/dev/reference/mkinpredict.html
+++ b/docs/dev/reference/mkinpredict.html
@@ -266,7 +266,7 @@ as these always return mapped output.</p></td>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
-<span class='va'>SFO</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
+<span class='va'>SFO</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>degradinol <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 class='co'># Compare solution types</span>
 <span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_degradinol <span class='op'>=</span> <span class='fl'>0.3</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, <span class='fl'>0</span><span class='op'>:</span><span class='fl'>20</span>,
       solution_type <span class='op'>=</span> <span class='st'>"analytical"</span><span class='op'>)</span>
@@ -388,7 +388,7 @@ as these always return mapped output.</p></td>
 <span class='co'># Comparison of the performance of solution types</span>
 <span class='va'>SFO_SFO</span> <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span><span class='op'>)</span>,
                   m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='kw'>if</span><span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='va'><a href='http://rbenchmark.googlecode.com'>rbenchmark</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='kw'>if</span><span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='va'><a href='http://rbenchmark.googlecode.com'>rbenchmark</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
   <span class='fu'><a href='https://rdrr.io/pkg/rbenchmark/man/benchmark.html'>benchmark</a></span><span class='op'>(</span>replications <span class='op'>=</span> <span class='fl'>10</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'>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>,
     eigen <span class='op'>=</span> <span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO_SFO</span>,
       <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.15</span>, f_parent_to_m1 <span class='op'>=</span> <span class='fl'>0.5</span>, k_m1 <span class='op'>=</span> <span class='fl'>0.01</span><span class='op'>)</span>,
@@ -408,10 +408,10 @@ as these always return mapped output.</p></td>
       solution_type <span class='op'>=</span> <span class='st'>"analytical"</span>, use_compiled <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>201</span>,<span class='op'>]</span><span class='op'>)</span>
 <span class='op'>}</span>
 </div><div class='output co'>#&gt;               test relative elapsed
-#&gt; 2 deSolve_compiled      1.0   0.005
 #&gt; 4       analytical      1.0   0.005
+#&gt; 2 deSolve_compiled      1.2   0.006
 #&gt; 1            eigen      4.0   0.020
-#&gt; 3          deSolve     44.6   0.223</div><div class='input'>
+#&gt; 3          deSolve     44.2   0.221</div><div class='input'>
 <span class='co'># \dontrun{</span>
   <span class='co'># Predict from a fitted model</span>
   <span class='va'>f</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
diff --git a/docs/dev/reference/mkinresplot.html b/docs/dev/reference/mkinresplot.html
index 38c52425..4b2f6bea 100644
--- a/docs/dev/reference/mkinresplot.html
+++ b/docs/dev/reference/mkinresplot.html
@@ -246,8 +246,8 @@ combining the plot of the fit and the residual plot.</p></div>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
-<span class='va'>model</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>model</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='va'>model</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'>"m1"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>model</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinresplot</span><span class='op'>(</span><span class='va'>fit</span>, <span class='st'>"m1"</span><span class='op'>)</span>
 </div><div class='img'><img src='mkinresplot-1.png' alt='' width='700' height='433' /></div><div class='input'>
 </div></pre>
diff --git a/docs/dev/reference/mkinsub.html b/docs/dev/reference/mkinsub.html
deleted file mode 100644
index 68fd6268..00000000
--- a/docs/dev/reference/mkinsub.html
+++ /dev/null
@@ -1,234 +0,0 @@
-<!-- Generated by pkgdown: do not edit by hand -->
-<!DOCTYPE html>
-<html lang="en">
-  <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Function to set up a kinetic submodel for one state variable — mkinsub • 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>
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="Function to set up a kinetic submodel for one state variable — mkinsub" />
-<meta property="og:description" content="This is a convenience function to set up the lists used as arguments for
-mkinmod." />
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-<!-- mathjax -->
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-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
-        <span class="sr-only">Toggle navigation</span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../reference/index.html">Functions and data</a>
-</li>
-<li class="dropdown">
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-    Articles
-     
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-    <li>
-      <a href="../articles/mkin.html">Introduction to mkin</a>
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-      <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/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>
-<li>
-  <a href="../news/index.html">News</a>
-</li>
-      </ul>
-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/jranke/mkin/">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
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-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
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-      </header>
-
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Function to set up a kinetic submodel for one state variable</h1>
-    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkinsub.R'><code>R/mkinsub.R</code></a></small>
-    <div class="hidden name"><code>mkinsub.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    <p>This is a convenience function to set up the lists used as arguments for
-<code><a href='mkinmod.html'>mkinmod</a></code>.</p>
-    </div>
-
-    <pre class="usage"><span class='fu'>mkinsub</span><span class='op'>(</span><span class='va'>submodel</span>, to <span class='op'>=</span> <span class='cn'>NULL</span>, sink <span class='op'>=</span> <span class='cn'>TRUE</span>, full_name <span class='op'>=</span> <span class='cn'>NA</span><span class='op'>)</span></pre>
-
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>submodel</th>
-      <td><p>Character vector of length one to specify the submodel type.
-See <code><a href='mkinmod.html'>mkinmod</a></code> for the list of allowed submodel names.</p></td>
-    </tr>
-    <tr>
-      <th>to</th>
-      <td><p>Vector of the names of the state variable to which a
-transformation shall be included in the model.</p></td>
-    </tr>
-    <tr>
-      <th>sink</th>
-      <td><p>Should a pathway to sink be included in the model in addition to
-the pathways to other state variables?</p></td>
-    </tr>
-    <tr>
-      <th>full_name</th>
-      <td><p>An optional name to be used e.g. for plotting fits
-performed with the model.  You can use non-ASCII characters here, but then
-your R code will not be portable, <em>i.e.</em> may produce unintended plot
-results on other operating systems or system configurations.</p></td>
-    </tr>
-    </table>
-
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>A list for use with <code><a href='mkinmod.html'>mkinmod</a></code>.</p>
-    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
-
-    <p>Johannes Ranke</p>
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'>
-<span class='co'># One parent compound, one metabolite, both single first order.</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='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span><span class='op'>)</span>,
-  m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-<span class='co'># The same model using mkinsub</span>
-<span class='va'>SFO_SFO.2</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'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>,
-  m1 <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-<span class='co'># \dontrun{</span>
-  <span class='co'># Now supplying full names</span>
-  <span class='va'>SFO_SFO.2</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'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, full_name <span class='op'>=</span> <span class='st'>"Test compound"</span><span class='op'>)</span>,
-    m1 <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, full_name <span class='op'>=</span> <span class='st'>"Metabolite M1"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='co'># }</span>
-</div></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-    <nav id="toc" data-toggle="toc" class="sticky-top">
-      <h2 data-toc-skip>Contents</h2>
-    </nav>
-  </div>
-</div>
-
-
-      <footer>
-      <div class="copyright">
-  <p>Developed by Johannes Ranke.</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
-</div>
-
-      </footer>
-   </div>
-
-  
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-
-  </body>
-</html>
-
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diff --git a/docs/dev/reference/mmkin.html b/docs/dev/reference/mmkin.html
index 4786b02e..651eb9a6 100644
--- a/docs/dev/reference/mmkin.html
+++ b/docs/dev/reference/mmkin.html
@@ -210,14 +210,14 @@ plotting.</p></div>
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
 <span class='co'># \dontrun{</span>
-<span class='va'>m_synth_SFO_lin</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"M1"</span><span class='op'>)</span>,
-                           M1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"M2"</span><span class='op'>)</span>,
-                           M2 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-<span class='va'>m_synth_FOMC_lin</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='st'>"M1"</span><span class='op'>)</span>,
-                            M1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"M2"</span><span class='op'>)</span>,
-                            M2 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+<span class='va'>m_synth_SFO_lin</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'>"M1"</span><span class='op'>)</span>,
+                           M1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"M2"</span><span class='op'>)</span>,
+                           M2 <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>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
+<span class='va'>m_synth_FOMC_lin</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'>"M1"</span><span class='op'>)</span>,
+                            M1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"M2"</span><span class='op'>)</span>,
+                            M2 <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>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
 <span class='va'>models</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>SFO_lin <span class='op'>=</span> <span class='va'>m_synth_SFO_lin</span>, FOMC_lin <span class='op'>=</span> <span class='va'>m_synth_FOMC_lin</span><span class='op'>)</span>
 <span class='va'>datasets</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>synthetic_data_for_UBA_2014</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>3</span><span class='op'>]</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>)</span>
 <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>datasets</span><span class='op'>)</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Dataset"</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>3</span><span class='op'>)</span>
@@ -227,9 +227,9 @@ plotting.</p></div>
 
 <span class='va'>time_default</span>
 </div><div class='output co'>#&gt;    user  system elapsed 
-#&gt;   4.664   0.433   1.317 </div><div class='input'><span class='va'>time_1</span>
+#&gt;   4.968   0.427   1.342 </div><div class='input'><span class='va'>time_1</span>
 </div><div class='output co'>#&gt;    user  system elapsed 
-#&gt;   5.326   0.001   5.330 </div><div class='input'>
+#&gt;   5.365   0.000   5.368 </div><div class='input'>
 <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span><span class='op'>]</span><span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; $ff
 #&gt;   parent_M1 parent_sink       M1_M2     M1_sink 
diff --git a/docs/dev/reference/nlme-2.png b/docs/dev/reference/nlme-2.png
index 7129c580..c0fb6dcf 100644
--- a/docs/dev/reference/nlme-2.png
+++ b/docs/dev/reference/nlme-2.png
diff --git a/docs/dev/reference/nlme.html b/docs/dev/reference/nlme.html
index e109b34e..b3e88428 100644
--- a/docs/dev/reference/nlme.html
+++ b/docs/dev/reference/nlme.html
@@ -186,7 +186,7 @@ nlme for the case of a single grouping variable ds.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='va'>sampling_times</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span>
-<span class='va'>m_SFO</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
+<span class='va'>m_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='op'>)</span><span class='op'>)</span>
 <span class='va'>d_SFO_1</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>m_SFO</span>,
   <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span>,
   <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>98</span><span class='op'>)</span>, <span class='va'>sampling_times</span><span class='op'>)</span>
@@ -254,9 +254,8 @@ nlme for the case of a single grouping variable ds.</p>
 <span class='co'>#</span>
 <span class='co'># The procedure is greatly simplified by the nlme.mmkin function</span>
 <span class='va'>f_nlme</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme</span><span class='op'>)</span>
-</div><div class='img'><img src='nlme-2.png' alt='' width='700' height='433' /></div><div class='input'>
-</div></pre>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme</span><span class='op'>)</span>
+</div><div class='img'><img src='nlme-2.png' alt='' width='700' height='433' /></div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">
diff --git a/docs/dev/reference/nlme.mmkin-1.png b/docs/dev/reference/nlme.mmkin-1.png
index 25bebeca..d760e8f9 100644
--- a/docs/dev/reference/nlme.mmkin-1.png
+++ b/docs/dev/reference/nlme.mmkin-1.png
diff --git a/docs/dev/reference/nlme.mmkin-2.png b/docs/dev/reference/nlme.mmkin-2.png
index c314c149..c7085b81 100644
--- a/docs/dev/reference/nlme.mmkin-2.png
+++ b/docs/dev/reference/nlme.mmkin-2.png
diff --git a/docs/dev/reference/nlme.mmkin-3.png b/docs/dev/reference/nlme.mmkin-3.png
index 46846067..a40b7cad 100644
--- a/docs/dev/reference/nlme.mmkin-3.png
+++ b/docs/dev/reference/nlme.mmkin-3.png
diff --git a/docs/dev/reference/nlme.mmkin-4.png b/docs/dev/reference/nlme.mmkin-4.png
deleted file mode 100644
index 6724163f..00000000
--- a/docs/dev/reference/nlme.mmkin-4.png
+++ /dev/null
diff --git a/docs/dev/reference/nlme.mmkin-5.png b/docs/dev/reference/nlme.mmkin-5.png
deleted file mode 100644
index 2c299b08..00000000
--- a/docs/dev/reference/nlme.mmkin-5.png
+++ /dev/null
diff --git a/docs/dev/reference/nlme.mmkin-6.png b/docs/dev/reference/nlme.mmkin-6.png
deleted file mode 100644
index 2bcb9cec..00000000
--- a/docs/dev/reference/nlme.mmkin-6.png
+++ /dev/null
diff --git a/docs/dev/reference/nlme.mmkin-7.png b/docs/dev/reference/nlme.mmkin-7.png
deleted file mode 100644
index 30e2d351..00000000
--- a/docs/dev/reference/nlme.mmkin-7.png
+++ /dev/null
diff --git a/docs/dev/reference/nlme.mmkin.html b/docs/dev/reference/nlme.mmkin.html
index 84990521..6d9f2007 100644
--- a/docs/dev/reference/nlme.mmkin.html
+++ b/docs/dev/reference/nlme.mmkin.html
@@ -193,8 +193,10 @@ mmkin model are used as fixed parameters</p></td>
     </tr>
     <tr>
       <th>random</th>
-      <td><p>If not specified, all fixed effects are complemented
-with uncorrelated random effects</p></td>
+      <td><p>If not specified, correlated random effects are set up
+for all optimised degradation model parameters using the log-Cholesky
+parameterization <a href='https://rdrr.io/pkg/nlme/man/pdLogChol.html'>nlme::pdLogChol</a> that is also the default of
+the generic <a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a> method.</p></td>
     </tr>
     <tr>
       <th>groups</th>
@@ -274,11 +276,14 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 <span class='va'>f</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>
 <span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://svn.r-project.org/R-packages/trunk/nlme/'>nlme</a></span><span class='op'>)</span>
 <span class='va'>f_nlme_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
-<span class='va'>f_nlme_dfop</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
-<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo</span>, <span class='va'>f_nlme_dfop</span><span class='op'>)</span>
-</div><div class='output co'>#&gt;             df      AIC
-#&gt; f_nlme_sfo   5 625.0539
-#&gt; f_nlme_dfop  9 495.1270</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='input'>
+<span class='co'># \dontrun{</span>
+
+  <span class='va'>f_nlme_dfop</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
+  <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo</span>, <span class='va'>f_nlme_dfop</span><span class='op'>)</span>
+</div><div class='output co'>#&gt;             Model df      AIC      BIC    logLik   Test  L.Ratio p-value
+#&gt; f_nlme_sfo      1  6 622.0677 637.0666 -305.0338                        
+#&gt; f_nlme_dfop     2 15 487.0134 524.5105 -228.5067 1 vs 2 153.0543  &lt;.0001</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Kinetic nonlinear mixed-effects model fit by maximum likelihood
 #&gt; 
 #&gt; Structural model:
@@ -289,48 +294,30 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 #&gt; Data:
 #&gt; 90 observations of 1 variable(s) grouped in 5 datasets
 #&gt; 
-#&gt; Log-likelihood: -238.5635
+#&gt; Log-likelihood: -228.5067
 #&gt; 
 #&gt; Fixed effects:
 #&gt;  list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) 
 #&gt; parent_0   log_k1   log_k2 g_qlogis 
-#&gt;  94.1702  -1.8002  -4.1474   0.0324 
+#&gt; 94.18273 -1.82135 -4.16872  0.08949 
 #&gt; 
 #&gt; Random effects:
 #&gt;  Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)
 #&gt;  Level: ds
-#&gt;  Structure: Diagonal
-#&gt;         parent_0 log_k1 log_k2 g_qlogis Residual
-#&gt; StdDev:    2.488 0.8447   1.33   0.4652    2.321
-#&gt; </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span>
-</div><div class='img'><img src='nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span>
+#&gt;  Structure: General positive-definite, Log-Cholesky parametrization
+#&gt;          StdDev    Corr                
+#&gt; parent_0 2.4656397 prnt_0 log_k1 log_k2
+#&gt; log_k1   0.7950788  0.240              
+#&gt; log_k2   1.2605419  0.150  0.984       
+#&gt; g_qlogis 0.5013272 -0.075  0.843  0.834
+#&gt; Residual 2.3308100                     
+#&gt; </div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span>
+</div><div class='img'><img src='nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'>  <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; $distimes
 #&gt;            DT50     DT90 DT50back  DT50_k1  DT50_k2
-#&gt; parent 10.79857 100.7937 30.34192 4.193937 43.85442
+#&gt; parent 10.57119 101.0652 30.42366 4.283776 44.80015
 #&gt; </div><div class='input'>
-<span class='co'># \dontrun{</span>
-  <span class='va'>f_nlme_2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span>, start <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent_0 <span class='op'>=</span> <span class='fl'>100</span>, log_k_parent <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span><span class='op'>)</span>
-  <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_nlme_2</span>, random <span class='op'>=</span> <span class='va'>parent_0</span> <span class='op'>~</span> <span class='fl'>1</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; Kinetic nonlinear mixed-effects model fit by maximum likelihood
-#&gt; 
-#&gt; Structural model:
-#&gt; d_parent/dt = - k_parent * parent
-#&gt; 
-#&gt; Data:
-#&gt;  observations of 0 variable(s) grouped in 0 datasets
-#&gt; 
-#&gt; Log-likelihood: -404.3729
-#&gt; 
-#&gt; Fixed effects:
-#&gt;  list(parent_0 ~ 1, log_k_parent ~ 1) 
-#&gt;     parent_0 log_k_parent 
-#&gt;       75.933       -3.556 
-#&gt; 
-#&gt; Random effects:
-#&gt;  Formula: parent_0 ~ 1 | ds
-#&gt;         parent_0 Residual
-#&gt; StdDev: 0.002417    21.63
-#&gt; </div><div class='input'>  <span class='va'>ds_2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>,
+  <span class='va'>ds_2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>,
    <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span>
   <span class='va'>m_sfo_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
     A1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"min"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
@@ -345,66 +332,42 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
     <span class='va'>ds_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 
   <span class='va'>f_nlme_sfo_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
-  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 2, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span>
 </div><div class='img'><img src='nlme.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'>
-  <span class='co'># With formation fractions</span>
-  <span class='va'>f_nlme_sfo_sfo_ff</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"SFO-SFO-ff"</span>, <span class='op'>]</span><span class='op'>)</span>
-  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo_ff</span><span class='op'>)</span>
-</div><div class='img'><img src='nlme.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'>
-  <span class='co'># For the following fit we need to increase pnlsMaxIter and the tolerance</span>
-  <span class='co'># to get convergence</span>
-  <span class='va'>f_nlme_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>,
-    control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>5e-4</span><span class='op'>)</span>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; 
-#&gt; **Iteration 1
-#&gt; LME step: Loglik: -404.9583, nlminb iterations: 1
-#&gt; reStruct  parameters:
-#&gt;        ds1        ds2        ds3        ds4        ds5        ds6 
-#&gt; -0.4114356  0.9798646  1.3524300  0.7293315  0.3354323  1.3647313 
-#&gt;  Beginning PNLS step: ..  completed fit_nlme() step.
-#&gt; PNLS step: RSS =  630.3633 
-#&gt;  fixed effects: 93.82269  -5.455993  -0.9601037  -1.862196  -4.199671  0.07824609  
-#&gt;  iterations: 120 
-#&gt; Convergence crit. (must all become &lt;= tolerance = 0.0005):
-#&gt;     fixed  reStruct 
-#&gt; 0.7897284 0.5822782 
-#&gt; 
-#&gt; **Iteration 2
-#&gt; LME step: Loglik: -407.7755, nlminb iterations: 11
-#&gt; reStruct  parameters:
-#&gt;         ds1         ds2         ds3         ds4         ds5         ds6 
-#&gt; -0.37122411  0.00305562  1.44336560  0.72467122  0.30160310  1.40762692 
-#&gt;  Beginning PNLS step: ..  completed fit_nlme() step.
-#&gt; PNLS step: RSS =  630.3637 
-#&gt;  fixed effects: 93.82269  -5.455992  -0.9601036  -1.862196  -4.199671  0.0782462  
-#&gt;  iterations: 120 
-#&gt; Convergence crit. (must all become &lt;= tolerance = 0.0005):
-#&gt;        fixed     reStruct 
-#&gt; 1.375673e-06 9.758294e-06 </div><div class='input'>
+  <span class='co'># With formation fractions this does not coverge with defaults</span>
+  <span class='co'># f_nlme_sfo_sfo_ff &lt;- nlme(f_2["SFO-SFO-ff", ])</span>
+  <span class='co'>#plot(f_nlme_sfo_sfo_ff)</span>
+
+  <span class='co'># With the log-Cholesky parameterization, this converges in 11</span>
+  <span class='co'># iterations and around 100 seconds, but without tweaking control</span>
+  <span class='co'># parameters (with pdDiag, increasing the tolerance and pnlsMaxIter was</span>
+  <span class='co'># necessary)</span>
+  <span class='va'>f_nlme_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 2, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 3, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 4, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='input'>
   <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span><span class='op'>)</span>
-</div><div class='img'><img src='nlme.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'>
+</div><div class='img'><img src='nlme.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'>
   <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span>
 </div><div class='output co'>#&gt;                 Model df       AIC       BIC    logLik   Test  L.Ratio p-value
-#&gt; f_nlme_dfop_sfo     1 13  843.8547  884.6201 -408.9274                        
-#&gt; f_nlme_sfo_sfo      2  9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3274  &lt;.0001</div><div class='input'>
+#&gt; f_nlme_dfop_sfo     1 28  811.7199  899.5222 -377.8599                        
+#&gt; f_nlme_sfo_sfo      2 15 1075.1934 1122.2304 -522.5967 1 vs 2 289.4736  &lt;.0001</div><div class='input'>
   <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; $ff
 #&gt; parent_sink   parent_A1     A1_sink 
-#&gt;   0.5912432   0.4087568   1.0000000 
+#&gt;   0.6512742   0.3487258   1.0000000 
 #&gt; 
 #&gt; $distimes
-#&gt;            DT50     DT90
-#&gt; parent 19.13518  63.5657
-#&gt; A1     66.02155 219.3189
+#&gt;             DT50      DT90
+#&gt; parent  18.03144  59.89916
+#&gt; A1     102.72949 341.25997
 #&gt; </div><div class='input'>  <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; $ff
 #&gt;   parent_A1 parent_sink 
-#&gt;   0.2768574   0.7231426 
+#&gt;   0.2762167   0.7237833 
 #&gt; 
 #&gt; $distimes
 #&gt;             DT50     DT90 DT50back  DT50_k1  DT50_k2
-#&gt; parent  11.07091 104.6320 31.49738 4.462384 46.20825
-#&gt; A1     162.30523 539.1663       NA       NA       NA
+#&gt; parent  11.15024 133.9652 40.32755 4.688015 62.16017
+#&gt; A1     235.83191 783.4167       NA       NA       NA
 #&gt; </div><div class='input'>
   <span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='fu'>findFunction</span><span class='op'>(</span><span class='st'>"varConstProp"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>&gt;</span> <span class='fl'>0</span><span class='op'>)</span> <span class='op'>{</span> <span class='co'># tc error model for nlme available</span>
     <span class='co'># Attempts to fit metabolite kinetics with the tc error model are possible,</span>
@@ -416,7 +379,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
     <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo</span>, <span class='va'>f_nlme_sfo_tc</span>, <span class='va'>f_nlme_dfop</span>, <span class='va'>f_nlme_dfop_tc</span><span class='op'>)</span>
     <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_tc</span><span class='op'>)</span>
   <span class='op'>}</span>
-</div><div class='output co'>#&gt; Kinetic nonlinear mixed-effects model fit by maximum likelihood
+</div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 14, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 2, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 5, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 6, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 7, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 8, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 9, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 10, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 11, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 12, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 14, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 15, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 16, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 17, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 18, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='output co'>#&gt; Kinetic nonlinear mixed-effects model fit by maximum likelihood
 #&gt; 
 #&gt; Structural model:
 #&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -426,31 +389,35 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 #&gt; Data:
 #&gt; 90 observations of 1 variable(s) grouped in 5 datasets
 #&gt; 
-#&gt; Log-likelihood: -238.4298
+#&gt; Log-likelihood: -228.3575
 #&gt; 
 #&gt; Fixed effects:
 #&gt;  list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) 
 #&gt; parent_0   log_k1   log_k2 g_qlogis 
-#&gt; 94.04775 -1.82340 -4.16715  0.05685 
+#&gt;  93.6695  -1.9187  -4.4253   0.2215 
 #&gt; 
 #&gt; Random effects:
 #&gt;  Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)
 #&gt;  Level: ds
-#&gt;  Structure: Diagonal
-#&gt;         parent_0 log_k1 log_k2 g_qlogis Residual
-#&gt; StdDev:    2.474   0.85  1.337   0.4659        1
+#&gt;  Structure: General positive-definite, Log-Cholesky parametrization
+#&gt;          StdDev    Corr                
+#&gt; parent_0 2.8574651 prnt_0 log_k1 log_k2
+#&gt; log_k1   0.9689083  0.506              
+#&gt; log_k2   1.5798002  0.446  0.997       
+#&gt; g_qlogis 0.5761569 -0.457  0.247  0.263
+#&gt; Residual 1.0000000                     
 #&gt; 
 #&gt; Variance function:
 #&gt;  Structure: Constant plus proportion of variance covariate
 #&gt;  Formula: ~fitted(.) 
 #&gt;  Parameter estimates:
-#&gt;      const       prop 
-#&gt; 2.23224114 0.01262341 </div><div class='input'>
+#&gt;     const      prop 
+#&gt; 2.0376990 0.0221686 </div><div class='input'>
   <span class='va'>f_2_obs</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>m_sfo_sfo</span>,
    <span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>m_dfop_sfo</span><span class='op'>)</span>,
     <span class='va'>ds_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span><span class='op'>)</span>
   <span class='va'>f_nlme_sfo_sfo_obs</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2_obs</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
-  <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo_obs</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo_obs</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Kinetic nonlinear mixed-effects model fit by maximum likelihood
 #&gt; 
 #&gt; Structural model:
@@ -460,29 +427,44 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 #&gt; Data:
 #&gt; 170 observations of 2 variable(s) grouped in 5 datasets
 #&gt; 
-#&gt; Log-likelihood: -472.976
+#&gt; Log-likelihood: -462.2203
 #&gt; 
 #&gt; Fixed effects:
 #&gt;  list(parent_0 ~ 1, log_k_parent_sink ~ 1, log_k_parent_A1 ~ 1,      log_k_A1_sink ~ 1) 
 #&gt;          parent_0 log_k_parent_sink   log_k_parent_A1     log_k_A1_sink 
-#&gt;            87.976            -3.670            -4.164            -4.645 
+#&gt;            88.682            -3.664            -4.164            -4.665 
 #&gt; 
 #&gt; Random effects:
 #&gt;  Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1, log_k_parent_A1 ~ 1,      log_k_A1_sink ~ 1)
 #&gt;  Level: ds
-#&gt;  Structure: Diagonal
-#&gt;         parent_0 log_k_parent_sink log_k_parent_A1 log_k_A1_sink Residual
-#&gt; StdDev:    3.992             1.777           1.055        0.4821    6.483
+#&gt;  Structure: General positive-definite, Log-Cholesky parametrization
+#&gt;                   StdDev    Corr                
+#&gt; parent_0          4.9153305 prnt_0 lg_k__ l___A1
+#&gt; log_k_parent_sink 1.8158570 0.956               
+#&gt; log_k_parent_A1   1.0514548 0.821  0.907        
+#&gt; log_k_A1_sink     0.4924122 0.035  0.315  0.533 
+#&gt; Residual          6.3987599                     
 #&gt; 
 #&gt; Variance function:
 #&gt;  Structure: Different standard deviations per stratum
 #&gt;  Formula: ~1 | name 
 #&gt;  Parameter estimates:
 #&gt;    parent        A1 
-#&gt; 1.0000000 0.2050003 </div><div class='input'>  <span class='co'># The same with DFOP-SFO does not converge, apparently the variances of</span>
-  <span class='co'># parent and A1 are too similar in this case, so that the model is</span>
-  <span class='co'># overparameterised</span>
-  <span class='co'>#f_nlme_dfop_sfo_obs &lt;- nlme(f_2_obs["DFOP-SFO", ], control = list(maxIter = 100))</span>
+#&gt; 1.0000000 0.2040647 </div><div class='input'>  <span class='va'>f_nlme_dfop_sfo_obs</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2_obs</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 2, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 3, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 4, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='input'>
+  <span class='va'>f_2_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>m_sfo_sfo</span>,
+   <span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>m_dfop_sfo</span><span class='op'>)</span>,
+    <span class='va'>ds_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
+  <span class='co'># f_nlme_sfo_sfo_tc &lt;- nlme(f_2_tc["SFO-SFO", ]) # stops with error message</span>
+  <span class='va'>f_nlme_dfop_sfo_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2_tc</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 2, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 3, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 4, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 6, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 7, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 8, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 9, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 11, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 12, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 15, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 25, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='input'>  <span class='co'># We get warnings about false convergence in the LME step in several iterations</span>
+  <span class='co'># but as the last such warning occurs in iteration 25 and we have 28 iterations</span>
+  <span class='co'># we can ignore these</span>
+  <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='va'>f_nlme_dfop_sfo_obs</span>, <span class='va'>f_nlme_dfop_sfo_tc</span><span class='op'>)</span>
+</div><div class='output co'>#&gt;                     Model df      AIC      BIC    logLik   Test L.Ratio p-value
+#&gt; f_nlme_dfop_sfo         1 28 811.7199 899.5222 -377.8599                       
+#&gt; f_nlme_dfop_sfo_obs     2 29 784.1304 875.0685 -363.0652 1 vs 2 29.5895  &lt;.0001
+#&gt; f_nlme_dfop_sfo_tc      3 29 791.9981 882.9362 -366.9990                       </div><div class='input'>
 <span class='co'># }</span>
 </div></pre>
   </div>
diff --git a/docs/dev/reference/nobs.mkinfit.html b/docs/dev/reference/nobs.mkinfit.html
index 06575d54..621eb622 100644
--- a/docs/dev/reference/nobs.mkinfit.html
+++ b/docs/dev/reference/nobs.mkinfit.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -120,7 +120,7 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -139,7 +139,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Number of observations on which an mkinfit object was fitted</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/nobs.mkinfit.R'><code>R/nobs.mkinfit.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/nobs.mkinfit.R'><code>R/nobs.mkinfit.R</code></a></small>
     <div class="hidden name"><code>nobs.mkinfit.Rd</code></div>
     </div>
 
@@ -148,7 +148,7 @@
     </div>
 
     <pre class="usage"><span class='co'># S3 method for mkinfit</span>
-<span class='fu'><a href='https://rdrr.io/r/stats/nobs.html'>nobs</a></span>(<span class='no'>object</span>, <span class='no'>...</span>)</pre>
+<span class='fu'><a href='https://rdrr.io/r/stats/nobs.html'>nobs</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -182,7 +182,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/plot.mixed.mmkin-2.png b/docs/dev/reference/plot.mixed.mmkin-2.png
index c0d67204..0821dcca 100644
--- a/docs/dev/reference/plot.mixed.mmkin-2.png
+++ b/docs/dev/reference/plot.mixed.mmkin-2.png
diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html
index 6ed7cbba..492e289c 100644
--- a/docs/dev/reference/plot.mixed.mmkin.html
+++ b/docs/dev/reference/plot.mixed.mmkin.html
@@ -264,8 +264,8 @@ corresponding model prediction lines for the different datasets.</p></td>
     <pre class="examples"><div class='input'><span class='va'>ds</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>,
  <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span>
 <span class='fu'><a href='https://rdrr.io/r/base/names.html'>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'>paste0</a></span><span class='op'>(</span><span class='st'>"ds "</span>, <span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>)</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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
-  A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='va'>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>,
+  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>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 <span class='co'># \dontrun{</span>
 <span class='va'>f</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>]</span>, standardized <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
@@ -273,14 +273,14 @@ corresponding model prediction lines for the different datasets.</p></td>
 <span class='co'># For this fit we need to increase pnlsMaxiter, and we increase the</span>
 <span class='co'># tolerance in order to speed up the fit for this example evaluation</span>
 <span class='va'>f_nlme</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span>, control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>1e-3</span><span class='op'>)</span><span class='op'>)</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 2, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme</span><span class='op'>)</span>
 </div><div class='img'><img src='plot.mixed.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'>
 <span class='va'>f_saem</span> <span class='op'>&lt;-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Thu Nov 19 14:51:14 2020"
+#&gt; [1] "Mon Nov 30 15:52:45 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Thu Nov 19 14:51:24 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem</span><span class='op'>)</span>
+#&gt; [1] "Mon Nov 30 15:52:54 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem</span><span class='op'>)</span>
 </div><div class='img'><img src='plot.mixed.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
 </div></pre>
   </div>
diff --git a/docs/dev/reference/plot.mkinfit.html b/docs/dev/reference/plot.mkinfit.html
index 3a05a02d..c7eda78f 100644
--- a/docs/dev/reference/plot.mkinfit.html
+++ b/docs/dev/reference/plot.mkinfit.html
@@ -340,9 +340,9 @@ latex is being used for the formatting of the chi2 error level, if
 <span class='co'># One parent compound, one metabolite, both single first order, path from</span>
 <span class='co'># parent to sink included</span>
 <span class='co'># \dontrun{</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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, full <span class='op'>=</span> <span class='st'>"Parent"</span><span class='op'>)</span>,
-                   m1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, full <span class='op'>=</span> <span class='st'>"Metabolite M1"</span> <span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</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'>"m1"</span>, full <span class='op'>=</span> <span class='st'>"Parent"</span><span class='op'>)</span>,
+                   m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, full <span class='op'>=</span> <span class='st'>"Metabolite M1"</span> <span class='op'>)</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</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>
 </div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
 </div><div class='img'><img src='plot.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_res</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
diff --git a/docs/dev/reference/plot.nafta.html b/docs/dev/reference/plot.nafta.html
index dab84955..9fc59f94 100644
--- a/docs/dev/reference/plot.nafta.html
+++ b/docs/dev/reference/plot.nafta.html
@@ -73,7 +73,7 @@ function (SFO, then IORE, then DFOP)." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -121,7 +121,7 @@ function (SFO, then IORE, then DFOP)." />
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -140,7 +140,7 @@ function (SFO, then IORE, then DFOP)." />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Plot the results of the three models used in the NAFTA scheme.</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/nafta.R'><code>R/nafta.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/nafta.R'><code>R/nafta.R</code></a></small>
     <div class="hidden name"><code>plot.nafta.Rd</code></div>
     </div>
 
@@ -150,7 +150,7 @@ function (SFO, then IORE, then DFOP).</p>
     </div>
 
     <pre class="usage"><span class='co'># S3 method for nafta</span>
-<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>x</span>, <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>main</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='no'>...</span>)</pre>
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>x</span>, legend <span class='op'>=</span> <span class='cn'>FALSE</span>, main <span class='op'>=</span> <span class='st'>"auto"</span>, <span class='va'>...</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -179,6 +179,9 @@ function (SFO, then IORE, then DFOP).</p>
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
     <p>Calls <code><a href='plot.mmkin.html'>plot.mmkin</a></code>.</p>
+    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
+
+    <p>Johannes Ranke</p>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -195,7 +198,7 @@ function (SFO, then IORE, then DFOP).</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/plot.nlme.mmkin-1.png b/docs/dev/reference/plot.nlme.mmkin-1.png
deleted file mode 100644
index 5cb33214..00000000
--- a/docs/dev/reference/plot.nlme.mmkin-1.png
+++ /dev/null
diff --git a/docs/dev/reference/plot.nlme.mmkin-2.png b/docs/dev/reference/plot.nlme.mmkin-2.png
deleted file mode 100644
index c0d67204..00000000
--- a/docs/dev/reference/plot.nlme.mmkin-2.png
+++ /dev/null
diff --git a/docs/dev/reference/plot.nlme.mmkin.html b/docs/dev/reference/plot.nlme.mmkin.html
deleted file mode 100644
index 8f5f85f7..00000000
--- a/docs/dev/reference/plot.nlme.mmkin.html
+++ /dev/null
@@ -1,302 +0,0 @@
-<!-- Generated by pkgdown: do not edit by hand -->
-<!DOCTYPE html>
-<html lang="en">
-  <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<script src="../bootstrap-toc.js"></script>
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-<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" />
-
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-
-<!-- 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>
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-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
-        <span class="sr-only">Toggle navigation</span>
-        <span class="icon-bar"></span>
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-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
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-    </div>
-
-    <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="../articles/mkin.html">Introduction to mkin</a>
-    </li>
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-      <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/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>
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-    <div class="page-header">
-    <h1>Plot a fitted nonlinear mixed model obtained via an mmkin row object</h1>
-    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/plot.nlme.mmkin.R'><code>R/plot.nlme.mmkin.R</code></a></small>
-    <div class="hidden name"><code>plot.nlme.mmkin.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    <p>Plot a fitted nonlinear mixed model obtained via an mmkin row object</p>
-    </div>
-
-    <pre class="usage"><span class='co'># S3 method for nlme.mmkin</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span>
-  <span class='va'>x</span>,
-  i <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin</span><span class='op'>)</span>,
-  obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>,
-  standardized <span class='op'>=</span> <span class='cn'>TRUE</span>,
-  xlab <span class='op'>=</span> <span class='st'>"Time"</span>,
-  xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span>,
-  resplot <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"predicted"</span>, <span class='st'>"time"</span><span class='op'>)</span>,
-  ymax <span class='op'>=</span> <span class='st'>"auto"</span>,
-  maxabs <span class='op'>=</span> <span class='st'>"auto"</span>,
-  ncol.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>8</span>, <span class='fl'>3</span>, <span class='fl'>4</span><span class='op'>)</span><span class='op'>)</span>,
-  nrow.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>ceiling</a></span><span class='op'>(</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ncol.legend</span><span class='op'>)</span>,
-  rel.height.legend <span class='op'>=</span> <span class='fl'>0.03</span> <span class='op'>+</span> <span class='fl'>0.08</span> <span class='op'>*</span> <span class='va'>nrow.legend</span>,
-  rel.height.bottom <span class='op'>=</span> <span class='fl'>1.1</span>,
-  pch_ds <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span>,
-  col_ds <span class='op'>=</span> <span class='va'>pch_ds</span> <span class='op'>+</span> <span class='fl'>1</span>,
-  lty_ds <span class='op'>=</span> <span class='va'>col_ds</span>,
-  frame <span class='op'>=</span> <span class='cn'>TRUE</span>
-<span class='op'>)</span></pre>
-
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>An object of class <code><a href='nlme.mmkin.html'>nlme.mmkin</a></code></p></td>
-    </tr>
-    <tr>
-      <th>i</th>
-      <td><p>A numeric index to select datasets for which to plot the nlme fit,
-in case plots get too large</p></td>
-    </tr>
-    <tr>
-      <th>obs_vars</th>
-      <td><p>A character vector of names of the observed variables for
-which the data and the model should be plotted. Defauls to all observed
-variables in the model.</p></td>
-    </tr>
-    <tr>
-      <th>standardized</th>
-      <td><p>Should the residuals be standardized? Only takes effect if
-<code>resplot = "time"</code>.</p></td>
-    </tr>
-    <tr>
-      <th>xlab</th>
-      <td><p>Label for the x axis.</p></td>
-    </tr>
-    <tr>
-      <th>xlim</th>
-      <td><p>Plot range in x direction.</p></td>
-    </tr>
-    <tr>
-      <th>resplot</th>
-      <td><p>Should the residuals plotted against time or against
-predicted values?</p></td>
-    </tr>
-    <tr>
-      <th>ymax</th>
-      <td><p>Vector of maximum y axis values</p></td>
-    </tr>
-    <tr>
-      <th>maxabs</th>
-      <td><p>Maximum absolute value of the residuals. This is used for the
-scaling of the y axis and defaults to "auto".</p></td>
-    </tr>
-    <tr>
-      <th>ncol.legend</th>
-      <td><p>Number of columns to use in the legend</p></td>
-    </tr>
-    <tr>
-      <th>nrow.legend</th>
-      <td><p>Number of rows to use in the legend</p></td>
-    </tr>
-    <tr>
-      <th>rel.height.legend</th>
-      <td><p>The relative height of the legend shown on top</p></td>
-    </tr>
-    <tr>
-      <th>rel.height.bottom</th>
-      <td><p>The relative height of the bottom plot row</p></td>
-    </tr>
-    <tr>
-      <th>pch_ds</th>
-      <td><p>Symbols to be used for plotting the data.</p></td>
-    </tr>
-    <tr>
-      <th>col_ds</th>
-      <td><p>Colors used for plotting the observed data and the
-corresponding model prediction lines for the different datasets.</p></td>
-    </tr>
-    <tr>
-      <th>lty_ds</th>
-      <td><p>Line types to be used for the model predictions.</p></td>
-    </tr>
-    <tr>
-      <th>frame</th>
-      <td><p>Should a frame be drawn around the plots?</p></td>
-    </tr>
-    </table>
-
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>The function is called for its side effect.</p>
-    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
-
-    <p>Johannes Ranke</p>
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='va'>ds</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>,
- <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span>
-<span class='fu'><a href='https://rdrr.io/r/base/names.html'>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'>paste0</a></span><span class='op'>(</span><span class='st'>"ds "</span>, <span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>)</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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
-  A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-<span class='co'># \dontrun{</span>
-<span class='va'>f</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>]</span>, standardized <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='img'><img src='plot.nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'>
-<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://svn.r-project.org/R-packages/trunk/nlme/'>nlme</a></span><span class='op'>)</span>
-<span class='co'># For this fit we need to increase pnlsMaxiter, and we increase the</span>
-<span class='co'># tolerance in order to speed up the fit for this example evaluation</span>
-<span class='va'>f_nlme</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span>, control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>1e-3</span><span class='op'>)</span><span class='op'>)</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme</span><span class='op'>)</span>
-</div><div class='img'><img src='plot.nlme.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
-</div></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-    <nav id="toc" data-toggle="toc" class="sticky-top">
-      <h2 data-toc-skip>Contents</h2>
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-    <h1>Plot an saem fitted nonlinear mixed model obtained via an mmkin row object</h1>
-    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/plot.saem.mmkin.R'><code>R/plot.saem.mmkin.R</code></a></small>
-    <div class="hidden name"><code>plot.saem.mmkin.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    <p>Plot an saem fitted nonlinear mixed model obtained via an mmkin row object</p>
-    </div>
-
-    <pre class="usage"><span class='co'># S3 method for saem.mmkin</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span>
-  <span class='va'>x</span>,
-  i <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin</span><span class='op'>)</span>,
-  obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>,
-  standardized <span class='op'>=</span> <span class='cn'>TRUE</span>,
-  xlab <span class='op'>=</span> <span class='st'>"Time"</span>,
-  xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span>,
-  resplot <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"predicted"</span>, <span class='st'>"time"</span><span class='op'>)</span>,
-  ymax <span class='op'>=</span> <span class='st'>"auto"</span>,
-  maxabs <span class='op'>=</span> <span class='st'>"auto"</span>,
-  ncol.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>8</span>, <span class='fl'>3</span>, <span class='fl'>4</span><span class='op'>)</span><span class='op'>)</span>,
-  nrow.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>ceiling</a></span><span class='op'>(</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ncol.legend</span><span class='op'>)</span>,
-  rel.height.legend <span class='op'>=</span> <span class='fl'>0.03</span> <span class='op'>+</span> <span class='fl'>0.08</span> <span class='op'>*</span> <span class='va'>nrow.legend</span>,
-  rel.height.bottom <span class='op'>=</span> <span class='fl'>1.1</span>,
-  pch_ds <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span>,
-  col_ds <span class='op'>=</span> <span class='va'>pch_ds</span> <span class='op'>+</span> <span class='fl'>1</span>,
-  lty_ds <span class='op'>=</span> <span class='va'>col_ds</span>,
-  frame <span class='op'>=</span> <span class='cn'>TRUE</span>,
-  <span class='va'>...</span>
-<span class='op'>)</span></pre>
-
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>An object of class <code><a href='saem.html'>saem.mmkin</a></code></p></td>
-    </tr>
-    <tr>
-      <th>i</th>
-      <td><p>A numeric index to select datasets for which to plot the saem fit,
-in case plots get too large</p></td>
-    </tr>
-    <tr>
-      <th>obs_vars</th>
-      <td><p>A character vector of names of the observed variables for
-which the data and the model should be plotted. Defauls to all observed
-variables in the model.</p></td>
-    </tr>
-    <tr>
-      <th>standardized</th>
-      <td><p>Should the residuals be standardized? Only takes effect if
-<code>resplot = "time"</code>.</p></td>
-    </tr>
-    <tr>
-      <th>xlab</th>
-      <td><p>Label for the x axis.</p></td>
-    </tr>
-    <tr>
-      <th>xlim</th>
-      <td><p>Plot range in x direction.</p></td>
-    </tr>
-    <tr>
-      <th>resplot</th>
-      <td><p>Should the residuals plotted against time or against
-predicted values?</p></td>
-    </tr>
-    <tr>
-      <th>ymax</th>
-      <td><p>Vector of maximum y axis values</p></td>
-    </tr>
-    <tr>
-      <th>maxabs</th>
-      <td><p>Maximum absolute value of the residuals. This is used for the
-scaling of the y axis and defaults to "auto".</p></td>
-    </tr>
-    <tr>
-      <th>ncol.legend</th>
-      <td><p>Number of columns to use in the legend</p></td>
-    </tr>
-    <tr>
-      <th>nrow.legend</th>
-      <td><p>Number of rows to use in the legend</p></td>
-    </tr>
-    <tr>
-      <th>rel.height.legend</th>
-      <td><p>The relative height of the legend shown on top</p></td>
-    </tr>
-    <tr>
-      <th>rel.height.bottom</th>
-      <td><p>The relative height of the bottom plot row</p></td>
-    </tr>
-    <tr>
-      <th>pch_ds</th>
-      <td><p>Symbols to be used for plotting the data.</p></td>
-    </tr>
-    <tr>
-      <th>col_ds</th>
-      <td><p>Colors used for plotting the observed data and the
-corresponding model prediction lines for the different datasets.</p></td>
-    </tr>
-    <tr>
-      <th>lty_ds</th>
-      <td><p>Line types to be used for the model predictions.</p></td>
-    </tr>
-    <tr>
-      <th>frame</th>
-      <td><p>Should a frame be drawn around the plots?</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></code>.</p></td>
-    </tr>
-    </table>
-
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>The function is called for its side effect.</p>
-    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
-
-    <p>Johannes Ranke</p>
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='va'>ds</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>,
- <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span>
-<span class='fu'><a href='https://rdrr.io/r/base/names.html'>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'>paste0</a></span><span class='op'>(</span><span class='st'>"ds "</span>, <span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>)</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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
-  A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-<span class='co'># \dontrun{</span>
-<span class='va'>f</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>]</span>, standardized <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='img'><img src='plot.saem.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'>
-<span class='va'>f_saem</span> <span class='op'>&lt;-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov  9 14:21:22 2020"
-#&gt; ....
-#&gt;     Minimisation finished
-#&gt; [1] "Mon Nov  9 14:21:31 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem</span><span class='op'>)</span>
-</div><div class='img'><img src='plot.saem.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
-</div></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-    <nav id="toc" data-toggle="toc" class="sticky-top">
-      <h2 data-toc-skip>Contents</h2>
-    </nav>
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-</div>
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-      <div class="copyright">
-  <p>Developed by Johannes Ranke.</p>
-</div>
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-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
-</div>
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-   </div>
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-</html>
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diff --git a/docs/dev/reference/plot_mixed-1.png b/docs/dev/reference/plot_mixed-1.png
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--- a/docs/dev/reference/plot_mixed.html
+++ /dev/null
@@ -1,336 +0,0 @@
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-    <h1>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</h1>
-    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/plot_mixed.R'><code>R/plot_mixed.R</code></a></small>
-    <div class="hidden name"><code>plot_mixed.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    <p>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</p>
-    </div>
-
-    <pre class="usage"><span class='co'># S3 method for saem.mmkin</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span>
-  <span class='va'>x</span>,
-  i <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin</span><span class='op'>)</span>,
-  obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>,
-  standardized <span class='op'>=</span> <span class='cn'>TRUE</span>,
-  xlab <span class='op'>=</span> <span class='st'>"Time"</span>,
-  xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span>,
-  resplot <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"predicted"</span>, <span class='st'>"time"</span><span class='op'>)</span>,
-  ymax <span class='op'>=</span> <span class='st'>"auto"</span>,
-  maxabs <span class='op'>=</span> <span class='st'>"auto"</span>,
-  ncol.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>8</span>, <span class='fl'>3</span>, <span class='fl'>4</span><span class='op'>)</span><span class='op'>)</span>,
-  nrow.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>ceiling</a></span><span class='op'>(</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ncol.legend</span><span class='op'>)</span>,
-  rel.height.legend <span class='op'>=</span> <span class='fl'>0.03</span> <span class='op'>+</span> <span class='fl'>0.08</span> <span class='op'>*</span> <span class='va'>nrow.legend</span>,
-  rel.height.bottom <span class='op'>=</span> <span class='fl'>1.1</span>,
-  pch_ds <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span>,
-  col_ds <span class='op'>=</span> <span class='va'>pch_ds</span> <span class='op'>+</span> <span class='fl'>1</span>,
-  lty_ds <span class='op'>=</span> <span class='va'>col_ds</span>,
-  frame <span class='op'>=</span> <span class='cn'>TRUE</span>,
-  <span class='va'>...</span>
-<span class='op'>)</span>
-
-<span class='co'># S3 method for nlme.mmkin</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span>
-  <span class='va'>x</span>,
-  i <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin</span><span class='op'>)</span>,
-  obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>,
-  standardized <span class='op'>=</span> <span class='cn'>TRUE</span>,
-  xlab <span class='op'>=</span> <span class='st'>"Time"</span>,
-  xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</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='va'>time</span><span class='op'>)</span>,
-  resplot <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"predicted"</span>, <span class='st'>"time"</span><span class='op'>)</span>,
-  ymax <span class='op'>=</span> <span class='st'>"auto"</span>,
-  maxabs <span class='op'>=</span> <span class='st'>"auto"</span>,
-  ncol.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>8</span>, <span class='fl'>3</span>, <span class='fl'>4</span><span class='op'>)</span><span class='op'>)</span>,
-  nrow.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>ceiling</a></span><span class='op'>(</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ncol.legend</span><span class='op'>)</span>,
-  rel.height.legend <span class='op'>=</span> <span class='fl'>0.03</span> <span class='op'>+</span> <span class='fl'>0.08</span> <span class='op'>*</span> <span class='va'>nrow.legend</span>,
-  rel.height.bottom <span class='op'>=</span> <span class='fl'>1.1</span>,
-  pch_ds <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span>,
-  col_ds <span class='op'>=</span> <span class='va'>pch_ds</span> <span class='op'>+</span> <span class='fl'>1</span>,
-  lty_ds <span class='op'>=</span> <span class='va'>col_ds</span>,
-  frame <span class='op'>=</span> <span class='cn'>TRUE</span>,
-  <span class='va'>...</span>
-<span class='op'>)</span></pre>
-
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>An object of class <a href='saem.html'>saem.mmkin</a> or <a href='nlme.mmkin.html'>nlme.mmkin</a></p></td>
-    </tr>
-    <tr>
-      <th>i</th>
-      <td><p>A numeric index to select datasets for which to plot the individual predictions,
-in case plots get too large</p></td>
-    </tr>
-    <tr>
-      <th>obs_vars</th>
-      <td><p>A character vector of names of the observed variables for
-which the data and the model should be plotted. Defauls to all observed
-variables in the model.</p></td>
-    </tr>
-    <tr>
-      <th>standardized</th>
-      <td><p>Should the residuals be standardized? Only takes effect if
-<code>resplot = "time"</code>.</p></td>
-    </tr>
-    <tr>
-      <th>xlab</th>
-      <td><p>Label for the x axis.</p></td>
-    </tr>
-    <tr>
-      <th>xlim</th>
-      <td><p>Plot range in x direction.</p></td>
-    </tr>
-    <tr>
-      <th>resplot</th>
-      <td><p>Should the residuals plotted against time or against
-predicted values?</p></td>
-    </tr>
-    <tr>
-      <th>ymax</th>
-      <td><p>Vector of maximum y axis values</p></td>
-    </tr>
-    <tr>
-      <th>maxabs</th>
-      <td><p>Maximum absolute value of the residuals. This is used for the
-scaling of the y axis and defaults to "auto".</p></td>
-    </tr>
-    <tr>
-      <th>ncol.legend</th>
-      <td><p>Number of columns to use in the legend</p></td>
-    </tr>
-    <tr>
-      <th>nrow.legend</th>
-      <td><p>Number of rows to use in the legend</p></td>
-    </tr>
-    <tr>
-      <th>rel.height.legend</th>
-      <td><p>The relative height of the legend shown on top</p></td>
-    </tr>
-    <tr>
-      <th>rel.height.bottom</th>
-      <td><p>The relative height of the bottom plot row</p></td>
-    </tr>
-    <tr>
-      <th>pch_ds</th>
-      <td><p>Symbols to be used for plotting the data.</p></td>
-    </tr>
-    <tr>
-      <th>col_ds</th>
-      <td><p>Colors used for plotting the observed data and the
-corresponding model prediction lines for the different datasets.</p></td>
-    </tr>
-    <tr>
-      <th>lty_ds</th>
-      <td><p>Line types to be used for the model predictions.</p></td>
-    </tr>
-    <tr>
-      <th>frame</th>
-      <td><p>Should a frame be drawn around the plots?</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></code>.</p></td>
-    </tr>
-    </table>
-
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>The functions are called for their side effect.</p>
-    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
-
-    <p>Johannes Ranke</p>
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='va'>ds</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>,
- <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span>
-<span class='fu'><a href='https://rdrr.io/r/base/names.html'>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'>paste0</a></span><span class='op'>(</span><span class='st'>"ds "</span>, <span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>)</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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
-  A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-<span class='co'># \dontrun{</span>
-<span class='va'>f</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>]</span>, standardized <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='img'><img src='plot_mixed-1.png' alt='' width='700' height='433' /></div><div class='input'>
-<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://svn.r-project.org/R-packages/trunk/nlme/'>nlme</a></span><span class='op'>)</span>
-<span class='co'># For this fit we need to increase pnlsMaxiter, and we increase the</span>
-<span class='co'># tolerance in order to speed up the fit for this example evaluation</span>
-<span class='va'>f_nlme</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span>, control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>1e-3</span><span class='op'>)</span><span class='op'>)</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme</span><span class='op'>)</span>
-</div><div class='img'><img src='plot_mixed-2.png' alt='' width='700' height='433' /></div><div class='input'>
-<span class='va'>f_saem</span> <span class='op'>&lt;-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov  9 16:07:05 2020"
-#&gt; ....
-#&gt;     Minimisation finished
-#&gt; [1] "Mon Nov  9 16:07:14 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem</span><span class='op'>)</span>
-</div><div class='img'><img src='plot_mixed-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
-</div></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-    <nav id="toc" data-toggle="toc" class="sticky-top">
-      <h2 data-toc-skip>Contents</h2>
-    </nav>
-  </div>
-</div>
-
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-      <div class="copyright">
-  <p>Developed by Johannes Ranke.</p>
-</div>
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-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
-</div>
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diff --git a/docs/dev/reference/print.mkinds.html b/docs/dev/reference/print.mkinds.html
deleted file mode 100644
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-      <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
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-      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
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-      <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
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-      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
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-      <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
-    </li>
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-    <h1>Print mkinds objects</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mkinds.R'><code>R/mkinds.R</code></a></small>
-    <div class="hidden name"><code>print.mkinds.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    <p>Print mkinds objects</p>
-    </div>
-
-    <pre class="usage"><span class='co'># S3 method for mkinds</span>
-<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
-
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>An <code><a href='mkinds.html'>mkinds</a></code> object.</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Not used.</p></td>
-    </tr>
-    </table>
-
-
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diff --git a/docs/dev/reference/print.mkinmod.html b/docs/dev/reference/print.mkinmod.html
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-    <h1>Print mkinmod objects</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mkinmod.R'><code>R/mkinmod.R</code></a></small>
-    <div class="hidden name"><code>print.mkinmod.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    <p>Print mkinmod objects in a way that the user finds his way to get to its
-components.</p>
-    </div>
-
-    <pre class="usage"><span class='co'># S3 method for mkinmod</span>
-<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
-
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>An <code><a href='mkinmod.html'>mkinmod</a></code> object.</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Not used.</p></td>
-    </tr>
-    </table>
-
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'>
-  <span class='no'>m_synth_SFO_lin</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M1"</span>),
-                             <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M2"</span>),
-                             <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-  <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>m_synth_SFO_lin</span>)</div><div class='output co'>#&gt; &lt;mkinmod&gt; model generated with
-#&gt; Use of formation fractions $use_of_ff: max 
-#&gt; Specification $spec:
-#&gt; $parent
-#&gt; $type: SFO; $to: M1; $sink: TRUE
-#&gt; $M1
-#&gt; $type: SFO; $to: M2; $sink: TRUE
-#&gt; $M2
-#&gt; $type: SFO; $sink: TRUE
-#&gt; Coefficient matrix $coefmat available
-#&gt; Compiled model $cf available
-#&gt; Differential equations:
-#&gt; d_parent/dt = - k_parent * parent
-#&gt; d_M1/dt = + f_parent_to_M1 * k_parent * parent - k_M1 * M1
-#&gt; d_M2/dt = + f_M1_to_M2 * k_M1 * M1 - k_M2 * M2</div><div class='input'>
-</div></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-    <nav id="toc" data-toggle="toc" class="sticky-top">
-      <h2 data-toc-skip>Contents</h2>
-    </nav>
-  </div>
-</div>
-
-
-      <footer>
-      <div class="copyright">
-  <p>Developed by Johannes Ranke.</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
-</div>
-
-      </footer>
-   </div>
-
-  
-
-
-  </body>
-</html>
-
-
diff --git a/docs/dev/reference/residuals.mkinfit.html b/docs/dev/reference/residuals.mkinfit.html
index 89552630..95114dae 100644
--- a/docs/dev/reference/residuals.mkinfit.html
+++ b/docs/dev/reference/residuals.mkinfit.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -120,7 +120,7 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -139,7 +139,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Extract residuals from an mkinfit model</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/residuals.mkinfit.R'><code>R/residuals.mkinfit.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/residuals.mkinfit.R'><code>R/residuals.mkinfit.R</code></a></small>
     <div class="hidden name"><code>residuals.mkinfit.Rd</code></div>
     </div>
 
@@ -148,7 +148,7 @@
     </div>
 
     <pre class="usage"><span class='co'># S3 method for mkinfit</span>
-<span class='fu'><a href='https://rdrr.io/r/stats/residuals.html'>residuals</a></span>(<span class='no'>object</span>, <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
+<span class='fu'><a href='https://rdrr.io/r/stats/residuals.html'>residuals</a></span><span class='op'>(</span><span class='va'>object</span>, standardized <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -170,10 +170,12 @@ standard deviation obtained from the fitted error model?</p></td>
 
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"DFOP"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'><a href='https://rdrr.io/r/stats/residuals.html'>residuals</a></span>(<span class='no'>f</span>)</div><div class='output co'>#&gt; [1]  0.09726306 -0.13912135 -0.15351176  0.73388319 -0.08657030 -0.93204730
-#&gt; [7] -0.03269102  1.45347805 -0.88423710</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/residuals.html'>residuals</a></span>(<span class='no'>f</span>, <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; [1]  0.13969820 -0.19981894 -0.22048777  1.05407086 -0.12434027 -1.33869248
-#&gt; [7] -0.04695387  2.08761953 -1.27002305</div></pre>
+    <pre class="examples"><div class='input'><span class='va'>f</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/stats/residuals.html'>residuals</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; [1]  0.09726374 -0.13912142 -0.15351210  0.73388322 -0.08657004 -0.93204702
+#&gt; [7] -0.03269080  1.45347823 -0.88423697</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/residuals.html'>residuals</a></span><span class='op'>(</span><span class='va'>f</span>, standardized <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; [1]  0.13969917 -0.19981904 -0.22048826  1.05407091 -0.12433989 -1.33869208
+#&gt; [7] -0.04695354  2.08761977 -1.27002287</div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">
@@ -189,7 +191,7 @@ standard deviation obtained from the fitted error model?</p></td>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html
index 948e1378..e4ebf5d9 100644
--- a/docs/dev/reference/saem.html
+++ b/docs/dev/reference/saem.html
@@ -247,27 +247,27 @@ using <a href='mmkin.html'>mmkin</a>.</p>
   state.ini <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, fixed_initials <span class='op'>=</span> <span class='st'>"parent"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 <span class='va'>f_saem_p0_fixed</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_p0_fixed</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Thu Nov 19 14:51:31 2020"
+#&gt; [1] "Mon Nov 30 15:53:02 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Thu Nov 19 14:51:33 2020"</div><div class='input'>
+#&gt; [1] "Mon Nov 30 15:53:04 2020"</div><div class='input'>
 <span class='va'>f_mmkin_parent</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 <span class='va'>f_saem_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Thu Nov 19 14:51:34 2020"
+#&gt; [1] "Mon Nov 30 15:53:05 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Thu Nov 19 14:51:36 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Mon Nov 30 15:53:07 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Thu Nov 19 14:51:36 2020"
+#&gt; [1] "Mon Nov 30 15:53:07 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Thu Nov 19 14:51:38 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Mon Nov 30 15:53:09 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Thu Nov 19 14:51:39 2020"
+#&gt; [1] "Mon Nov 30 15:53:10 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Thu Nov 19 14:51:42 2020"</div><div class='input'>
+#&gt; [1] "Mon Nov 30 15:53:13 2020"</div><div class='input'>
 <span class='co'># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span>
 <span class='co'># functions from saemix</span>
 <span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'>saemix</span><span class='op'>)</span>
@@ -313,20 +313,20 @@ using <a href='mmkin.html'>mmkin</a>.</p>
 <span class='va'>f_mmkin_parent_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_mmkin_parent</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
 <span class='va'>f_saem_fomc_tc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_tc</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Thu Nov 19 14:51:44 2020"
+#&gt; [1] "Mon Nov 30 15:53:15 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Thu Nov 19 14:51:49 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
+#&gt; [1] "Mon Nov 30 15:53:20 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Likelihoods computed by importance sampling </div><div class='output co'>#&gt;        AIC      BIC
 #&gt; 1 467.7096 464.9757
 #&gt; 2 469.5208 466.3963</div><div class='input'>
-<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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
-  A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
-  A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
-  A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># The following fit uses analytical solutions for SFO-SFO and DFOP-SFO,</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>,
+  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>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><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>,
+  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>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><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>,
+  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>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='co'># The following fit uses analytical solutions for SFO-SFO and DFOP-SFO,</span>
 <span class='co'># and compiled ODEs for FOMC that are much slower</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'>list</a></span><span class='op'>(</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>,
@@ -336,15 +336,15 @@ using <a href='mmkin.html'>mmkin</a>.</p>
 <span class='co'># solutions written for mkin this took around four minutes</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>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Thu Nov 19 14:51:52 2020"
+#&gt; [1] "Mon Nov 30 15:53:23 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Thu Nov 19 14:51:57 2020"</div><div class='input'><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>
+#&gt; [1] "Mon Nov 30 15:53:28 2020"</div><div class='input'><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>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Thu Nov 19 14:51:57 2020"
+#&gt; [1] "Mon Nov 30 15:53:29 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Thu Nov 19 14:52:06 2020"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span>
+#&gt; [1] "Mon Nov 30 15:53:38 2020"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span>
 <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Kinetic nonlinear mixed-effects model fit by SAEM
 #&gt; Structural model:
@@ -387,8 +387,8 @@ using <a href='mmkin.html'>mmkin</a>.</p>
 </div><div class='output co'>#&gt; saemix version used for fitting:      3.1.9000 
 #&gt; mkin version used for pre-fitting:  0.9.50.4 
 #&gt; R version used for fitting:         4.0.3 
-#&gt; Date of fit:     Thu Nov 19 14:52:07 2020 
-#&gt; Date of summary: Thu Nov 19 14:52:07 2020 
+#&gt; Date of fit:     Mon Nov 30 15:53:38 2020 
+#&gt; Date of summary: Mon Nov 30 15:53:39 2020 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -403,7 +403,7 @@ using <a href='mmkin.html'>mmkin</a>.</p>
 #&gt; 
 #&gt; Model predictions using solution type analytical 
 #&gt; 
-#&gt; Fitted in 10.034 s using 300, 100 iterations
+#&gt; Fitted in 9.963 s using 300, 100 iterations
 #&gt; 
 #&gt; Variance model: Constant variance 
 #&gt; 
@@ -647,7 +647,7 @@ using <a href='mmkin.html'>mmkin</a>.</p>
 <span class='co'># analytical solution. Using 10 cores it is slower instead of faster</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</span><span class='op'>[</span><span class='st'>"FOMC-SFO"</span>, <span class='op'>]</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Thu Nov 19 14:52:08 2020"
+#&gt; [1] "Mon Nov 30 15:53:39 2020"
 #&gt; DLSODA-  At current T (=R1), MXSTEP (=I1) steps   
 #&gt;       taken on this call before reaching TOUT     
 #&gt; In above message, I1 = 5000
@@ -667,7 +667,7 @@ using <a href='mmkin.html'>mmkin</a>.</p>
 #&gt;  
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Thu Nov 19 14:59:05 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>)</span>
+#&gt; [1] "Mon Nov 30 16:00:45 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>)</span>
 </div><div class='img'><img src='saem-6.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
 </div></pre>
   </div>
diff --git a/docs/dev/reference/saemix-1.png b/docs/dev/reference/saemix-1.png
deleted file mode 100644
index e5e01249..00000000
--- a/docs/dev/reference/saemix-1.png
+++ /dev/null
diff --git a/docs/dev/reference/saemix-10.png b/docs/dev/reference/saemix-10.png
deleted file mode 100644
index 19aa6cfb..00000000
--- a/docs/dev/reference/saemix-10.png
+++ /dev/null
diff --git a/docs/dev/reference/saemix-11.png b/docs/dev/reference/saemix-11.png
deleted file mode 100644
index 454b9be0..00000000
--- a/docs/dev/reference/saemix-11.png
+++ /dev/null
diff --git a/docs/dev/reference/saemix-12.png b/docs/dev/reference/saemix-12.png
deleted file mode 100644
index c8b0fd71..00000000
--- a/docs/dev/reference/saemix-12.png
+++ /dev/null
diff --git a/docs/dev/reference/saemix-13.png b/docs/dev/reference/saemix-13.png
deleted file mode 100644
index e3538cb6..00000000
--- a/docs/dev/reference/saemix-13.png
+++ /dev/null
diff --git a/docs/dev/reference/saemix-2.png b/docs/dev/reference/saemix-2.png
deleted file mode 100644
index 4bc3d0bc..00000000
--- a/docs/dev/reference/saemix-2.png
+++ /dev/null
diff --git a/docs/dev/reference/saemix-3.png b/docs/dev/reference/saemix-3.png
deleted file mode 100644
index be6b0acb..00000000
--- a/docs/dev/reference/saemix-3.png
+++ /dev/null
diff --git a/docs/dev/reference/saemix-4.png b/docs/dev/reference/saemix-4.png
deleted file mode 100644
index fa4db812..00000000
--- a/docs/dev/reference/saemix-4.png
+++ /dev/null
diff --git a/docs/dev/reference/saemix-5.png b/docs/dev/reference/saemix-5.png
deleted file mode 100644
index 2b7b8f46..00000000
--- a/docs/dev/reference/saemix-5.png
+++ /dev/null
diff --git a/docs/dev/reference/saemix-6.png b/docs/dev/reference/saemix-6.png
deleted file mode 100644
index af14b43b..00000000
--- a/docs/dev/reference/saemix-6.png
+++ /dev/null
diff --git a/docs/dev/reference/saemix-7.png b/docs/dev/reference/saemix-7.png
deleted file mode 100644
index e3538cb6..00000000
--- a/docs/dev/reference/saemix-7.png
+++ /dev/null
diff --git a/docs/dev/reference/saemix-8.png b/docs/dev/reference/saemix-8.png
deleted file mode 100644
index 35cc6c6e..00000000
--- a/docs/dev/reference/saemix-8.png
+++ /dev/null
diff --git a/docs/dev/reference/saemix-9.png b/docs/dev/reference/saemix-9.png
deleted file mode 100644
index e3538cb6..00000000
--- a/docs/dev/reference/saemix-9.png
+++ /dev/null
diff --git a/docs/dev/reference/schaefer07_complex_case-1.png b/docs/dev/reference/schaefer07_complex_case-1.png
index 7cf7484d..16e657dd 100644
--- a/docs/dev/reference/schaefer07_complex_case-1.png
+++ b/docs/dev/reference/schaefer07_complex_case-1.png
diff --git a/docs/dev/reference/schaefer07_complex_case.html b/docs/dev/reference/schaefer07_complex_case.html
index 308db2db..83555b99 100644
--- a/docs/dev/reference/schaefer07_complex_case.html
+++ b/docs/dev/reference/schaefer07_complex_case.html
@@ -74,7 +74,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -122,7 +122,7 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -151,12 +151,12 @@
   The results from the fitting are also included.</p>
     </div>
 
-    <pre class="usage"><span class='no'>schaefer07_complex_case</span></pre>
+    <pre class="usage"><span class='va'>schaefer07_complex_case</span></pre>
 
 
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
-    <p>The data set is a data frame with 8 observations on the following 6 variables.</p><dl'>
+    <p>The data set is a data frame with 8 observations on the following 6 variables.</p><dl>
     <dt><code>time</code></dt><dd><p>a numeric vector</p></dd>
     <dt><code>parent</code></dt><dd><p>a numeric vector</p></dd>
     <dt><code>A1</code></dt><dd><p>a numeric vector</p></dd>
@@ -173,28 +173,32 @@
   Symposium Pesticide Chemistry, Piacenza, 2007, p. 916-923.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='no'>data</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span>(<span class='no'>schaefer07_complex_case</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>)
-<span class='no'>model</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
-  <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"A1"</span>, <span class='st'>"B1"</span>, <span class='st'>"C1"</span>), <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
-  <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A2"</span>),
-  <span class='kw'>B1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
-  <span class='kw'>C1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
-  <span class='kw'>A2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>  <span class='co'># \dontrun{</span>
-    <span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-    <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='schaefer07_complex_case-1.png' alt='' width='700' height='433' /></div><div class='input'>    <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
+    <pre class="examples"><div class='input'><span class='va'>data</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span><span class='op'>(</span><span class='va'>schaefer07_complex_case</span>, time <span class='op'>=</span> <span class='st'>"time"</span><span class='op'>)</span>
+<span class='va'>model</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='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"A1"</span>, <span class='st'>"B1"</span>, <span class='st'>"C1"</span><span class='op'>)</span>, sink <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>,
+  A1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"A2"</span><span class='op'>)</span>,
+  B1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>,
+  C1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>,
+  A2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>  <span class='co'># \dontrun{</span>
+    <span class='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>model</span>, <span class='va'>data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+    <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
+</div><div class='img'><img src='schaefer07_complex_case-1.png' alt='' width='700' height='433' /></div><div class='input'>    <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; $ff
 #&gt;   parent_A1   parent_B1   parent_C1 parent_sink       A1_A2     A1_sink 
-#&gt;   0.3809619   0.1954667   0.4235714   0.0000000   0.4479609   0.5520391 
+#&gt;   0.3809620   0.1954665   0.4235715   0.0000000   0.4479662   0.5520338 
 #&gt; 
 #&gt; $distimes
 #&gt;            DT50      DT90
 #&gt; parent 13.95078  46.34350
-#&gt; A1     49.75343 165.27733
-#&gt; B1     37.26907 123.80517
+#&gt; A1     49.75343 165.27731
+#&gt; B1     37.26912 123.80533
 #&gt; C1     11.23131  37.30959
-#&gt; A2     28.50638  94.69614
+#&gt; A2     28.50569  94.69386
 #&gt; </div><div class='input'>  <span class='co'># }</span>
  <span class='co'># Compare with the results obtained in the original publication</span>
- <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>schaefer07_complex_results</span>)</div><div class='output co'>#&gt;         compound          parameter  KinGUI ModelMaker deviation
+ <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>schaefer07_complex_results</span><span class='op'>)</span>
+</div><div class='output co'>#&gt;         compound          parameter  KinGUI ModelMaker deviation
 #&gt; 1         parent   degradation rate  0.0496     0.0506       2.0
 #&gt; 2         parent               DT50 13.9900    13.6900       2.2
 #&gt; 3  metabolite A1 formation fraction  0.3803     0.3696       2.9
@@ -224,7 +228,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/summary.mkinfit.html b/docs/dev/reference/summary.mkinfit.html
index cd183cbc..f314dfa8 100644
--- a/docs/dev/reference/summary.mkinfit.html
+++ b/docs/dev/reference/summary.mkinfit.html
@@ -235,18 +235,18 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
-  <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>, <span class='va'>FOCUS_2006_A</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span>
+  <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>, <span class='va'>FOCUS_2006_A</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; mkin version used for fitting:    0.9.50.4 
 #&gt; R version used for fitting:       4.0.3 
-#&gt; Date of fit:     Thu Nov 19 14:59:41 2020 
-#&gt; Date of summary: Thu Nov 19 14:59:41 2020 
+#&gt; Date of fit:     Mon Nov 30 16:01:20 2020 
+#&gt; Date of summary: Mon Nov 30 16:01:20 2020 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - k_parent * parent
 #&gt; 
 #&gt; Model predictions using solution type analytical 
 #&gt; 
-#&gt; Fitted using 131 model solutions performed in 0.033 s
+#&gt; Fitted using 131 model solutions performed in 0.028 s
 #&gt; 
 #&gt; Error model: Constant variance 
 #&gt; 
diff --git a/docs/dev/reference/summary.nlme.mmkin.html b/docs/dev/reference/summary.nlme.mmkin.html
index d016796e..2aeadc46 100644
--- a/docs/dev/reference/summary.nlme.mmkin.html
+++ b/docs/dev/reference/summary.nlme.mmkin.html
@@ -239,7 +239,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p>
 <span class='va'>k_in_pop</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span> <span class='op'>/</span> <span class='va'>dt50_sfo_in_pop</span>
 <span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span><span class='op'>(</span><span class='fl'>1234</span><span class='op'>)</span>
 <span class='va'>k_in</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Lognormal.html'>rlnorm</a></span><span class='op'>(</span><span class='fl'>5</span>, <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='va'>k_in_pop</span><span class='op'>)</span>, <span class='fl'>0.5</span><span class='op'>)</span>
-<span class='va'>SFO</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
+<span class='va'>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='op'>)</span><span class='op'>)</span>
 
 <span class='va'>pred_sfo</span> <span class='op'>&lt;-</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>k</span><span class='op'>)</span> <span class='op'>{</span>
   <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>SFO</span>,
@@ -251,6 +251,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p>
 <span class='va'>ds_sfo_mean</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>k_in</span>, <span class='va'>pred_sfo</span><span class='op'>)</span>
 <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>ds_sfo_mean</span><span class='op'>)</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"ds"</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>5</span><span class='op'>)</span>
 
+<span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span><span class='op'>(</span><span class='fl'>12345</span><span class='op'>)</span>
 <span class='va'>ds_sfo_syn</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>ds_sfo_mean</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'>{</span>
   <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>ds</span>,
     sdfunc <span class='op'>=</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>sqrt</a></span><span class='op'>(</span><span class='fl'>1</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>+</span> <span class='va'>value</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>*</span> <span class='fl'>0.07</span><span class='op'>^</span><span class='fl'>2</span><span class='op'>)</span>,
@@ -260,13 +261,14 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p>
 <span class='co'># Evaluate using mmkin and nlme</span>
 <span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://svn.r-project.org/R-packages/trunk/nlme/'>nlme</a></span><span class='op'>)</span>
 <span class='va'>f_mmkin</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>ds_sfo_syn</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>
-<span class='va'>f_nlme</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 3, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_nlme</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation did not converge:</span>
+#&gt; <span class='warning'>iteration limit reached without convergence (10)</span></div><div class='input'><span class='va'>f_nlme</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_nlme</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; nlme version used for fitting:      3.1.150.1 
 #&gt; mkin version used for pre-fitting:  0.9.50.4 
 #&gt; R version used for fitting:         4.0.3 
-#&gt; Date of fit:     Thu Nov 19 14:59:43 2020 
-#&gt; Date of summary: Thu Nov 19 14:59:43 2020 
+#&gt; Date of fit:     Mon Nov 30 16:01:23 2020 
+#&gt; Date of summary: Mon Nov 30 16:01:23 2020 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - k_parent * parent
@@ -276,146 +278,148 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p>
 #&gt; 
 #&gt; Model predictions using solution type analytical 
 #&gt; 
-#&gt; Fitted in 0.681 s using 5 iterations
+#&gt; Fitted in 0.996 s using 6 iterations
 #&gt; 
 #&gt; Variance model: Two-component variance function 
 #&gt; 
 #&gt; Mean of starting values for individual parameters:
 #&gt;     parent_0 log_k_parent 
-#&gt;    97.849556    -4.455036 
+#&gt;   101.568773    -4.454103 
 #&gt; 
 #&gt; Fixed degradation parameter values:
 #&gt; None
 #&gt; 
 #&gt; Results:
 #&gt; 
-#&gt;       AIC      BIC   logLik
-#&gt;   555.792 570.7908 -271.896
+#&gt;        AIC      BIC    logLik
+#&gt;   586.4159 603.9145 -286.2079
 #&gt; 
 #&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt;               lower   est.   upper
-#&gt; parent_0     94.701 97.763 100.826
-#&gt; log_k_parent -5.008 -4.462  -3.916
+#&gt;               lower    est.   upper
+#&gt; parent_0     99.360 101.593 103.825
+#&gt; log_k_parent -4.979  -4.451  -3.924
 #&gt; 
 #&gt; Correlation: 
 #&gt;              prnt_0
-#&gt; log_k_parent 0.024 
+#&gt; log_k_parent 0.155 
 #&gt; 
 #&gt; Random effects:
 #&gt;  Formula: list(parent_0 ~ 1, log_k_parent ~ 1)
 #&gt;  Level: ds
-#&gt;  Structure: Diagonal
-#&gt;         parent_0 log_k_parent Residual
-#&gt; StdDev:    2.898       0.6119        1
+#&gt;  Structure: General positive-definite, Log-Cholesky parametrization
+#&gt;              StdDev    Corr  
+#&gt; parent_0     0.2624248 prnt_0
+#&gt; log_k_parent 0.5907146 0.999 
+#&gt; Residual     1.0000000       
 #&gt; 
 #&gt; Variance function:
 #&gt;  Structure: Constant plus proportion of variance covariate
 #&gt;  Formula: ~fitted(.) 
 #&gt;  Parameter estimates:
-#&gt;      const       prop 
-#&gt; 1.55075176 0.05680853 
+#&gt;       const        prop 
+#&gt; 6.56706e-24 7.89583e-02 
 #&gt; 
 #&gt; Backtransformed parameters with asymmetric confidence intervals:
-#&gt;              lower     est.     upper
-#&gt; parent_0 94.701336 97.76345 100.82556
-#&gt; k_parent  0.006687  0.01154   0.01992
+#&gt;              lower      est.     upper
+#&gt; parent_0 99.360213 101.59280 103.82539
+#&gt; k_parent  0.006883   0.01166   0.01976
 #&gt; 
 #&gt; Estimated disappearance times:
 #&gt;         DT50  DT90
-#&gt; parent 60.05 199.5
+#&gt; parent 59.44 197.4
 #&gt; 
 #&gt; Data:
-#&gt;    ds   name time observed predicted residual   std standardized
-#&gt;  ds 1 parent    0    103.6     97.42  6.17540 5.748     1.074413
-#&gt;  ds 1 parent    0     95.9     97.42 -1.52460 5.748    -0.265253
-#&gt;  ds 1 parent    1     95.4     96.72 -1.31719 5.709    -0.230721
-#&gt;  ds 1 parent    1     95.3     96.72 -1.41719 5.709    -0.248237
-#&gt;  ds 1 parent    3     91.6     95.32 -3.71774 5.633    -0.660046
-#&gt;  ds 1 parent    3     94.5     95.32 -0.81774 5.633    -0.145181
-#&gt;  ds 1 parent    7     88.1     92.58 -4.47930 5.483    -0.816920
-#&gt;  ds 1 parent    7     89.6     92.58 -2.97930 5.483    -0.543355
-#&gt;  ds 1 parent   14     90.3     87.97  2.32502 5.233     0.444318
-#&gt;  ds 1 parent   14     96.0     87.97  8.02502 5.233     1.533602
-#&gt;  ds 1 parent   28     80.2     79.44  0.75809 4.772     0.158862
-#&gt;  ds 1 parent   28     77.9     79.44 -1.54191 4.772    -0.323118
-#&gt;  ds 1 parent   60     59.3     62.92 -3.61742 3.896    -0.928458
-#&gt;  ds 1 parent   60     59.6     62.92 -3.31742 3.896    -0.851459
-#&gt;  ds 1 parent   90     59.4     50.56  8.83825 3.264     2.707613
-#&gt;  ds 1 parent   90     51.0     50.56  0.43825 3.264     0.134260
-#&gt;  ds 1 parent  120     38.8     40.63 -1.83247 2.781    -0.658968
-#&gt;  ds 1 parent  120     38.9     40.63 -1.73247 2.781    -0.623007
-#&gt;  ds 2 parent    0    103.2     97.17  6.02995 5.734     1.051655
-#&gt;  ds 2 parent    0     95.1     97.17 -2.07005 5.734    -0.361027
-#&gt;  ds 2 parent    1     88.3     95.59 -7.28901 5.647    -1.290694
-#&gt;  ds 2 parent    1    102.4     95.59  6.81099 5.647     1.206048
-#&gt;  ds 2 parent    3     88.4     92.50 -4.10371 5.479    -0.748984
-#&gt;  ds 2 parent    3     95.2     92.50  2.69629 5.479     0.492110
-#&gt;  ds 2 parent    7     83.5     86.63 -3.12863 5.160    -0.606349
-#&gt;  ds 2 parent    7     96.4     86.63  9.77137 5.160     1.893751
-#&gt;  ds 2 parent   14     77.3     77.23  0.06920 4.653     0.014871
-#&gt;  ds 2 parent   14     76.0     77.23 -1.23080 4.653    -0.264497
-#&gt;  ds 2 parent   28     61.7     61.38  0.31692 3.816     0.083043
-#&gt;  ds 2 parent   28     56.5     61.38 -4.88308 3.816    -1.279513
-#&gt;  ds 2 parent   60     35.1     36.31 -1.21343 2.581    -0.470178
-#&gt;  ds 2 parent   60     32.2     36.31 -4.11343 2.581    -1.593868
-#&gt;  ds 2 parent   90     21.2     22.20 -0.99906 1.999    -0.499832
-#&gt;  ds 2 parent   90     23.3     22.20  1.10094 1.999     0.550800
-#&gt;  ds 2 parent  120     14.1     13.57  0.52931 1.732     0.305638
-#&gt;  ds 2 parent  120     16.9     13.57  3.32931 1.732     1.922443
-#&gt;  ds 3 parent    0     92.4     94.12 -1.71979 5.567    -0.308917
-#&gt;  ds 3 parent    0     94.0     94.12 -0.11979 5.567    -0.021517
-#&gt;  ds 3 parent    1     95.7     91.97  3.72634 5.450     0.683712
-#&gt;  ds 3 parent    1     90.8     91.97 -1.17366 5.450    -0.215343
-#&gt;  ds 3 parent    3     86.7     87.83 -1.12709 5.225    -0.215720
-#&gt;  ds 3 parent    3     85.8     87.83 -2.02709 5.225    -0.387976
-#&gt;  ds 3 parent    7     77.1     80.09 -2.98635 4.807    -0.621300
-#&gt;  ds 3 parent    7     81.5     80.09  1.41365 4.807     0.294104
-#&gt;  ds 3 parent   14     69.1     68.15  0.95467 4.170     0.228922
-#&gt;  ds 3 parent   14     62.4     68.15 -5.74533 4.170    -1.377682
-#&gt;  ds 3 parent   28     49.1     49.34 -0.23911 3.203    -0.074644
-#&gt;  ds 3 parent   28     47.2     49.34 -2.13911 3.203    -0.667787
-#&gt;  ds 3 parent   60     21.9     23.58 -1.68477 2.049    -0.822090
-#&gt;  ds 3 parent   60     23.6     23.58  0.01523 2.049     0.007431
-#&gt;  ds 3 parent   90     12.4     11.81  0.59388 1.690     0.351500
-#&gt;  ds 3 parent   90     13.8     11.81  1.99388 1.690     1.180112
-#&gt;  ds 3 parent  120      4.9      5.91 -1.00993 1.587    -0.636506
-#&gt;  ds 3 parent  120      7.5      5.91  1.59007 1.587     1.002137
-#&gt;  ds 4 parent    0     91.8    101.72 -9.92097 5.983    -1.658171
-#&gt;  ds 4 parent    0    104.6    101.72  2.87903 5.983     0.481194
-#&gt;  ds 4 parent    1    117.5    101.27 16.23017 5.958     2.723944
-#&gt;  ds 4 parent    1     99.3    101.27 -1.96983 5.958    -0.330602
-#&gt;  ds 4 parent    3     94.0    100.37 -6.37355 5.909    -1.078583
-#&gt;  ds 4 parent    3     98.7    100.37 -1.67355 5.909    -0.283212
-#&gt;  ds 4 parent    7    109.2     98.60 10.59529 5.812     1.822915
-#&gt;  ds 4 parent    7     89.2     98.60 -9.40471 5.812    -1.618075
-#&gt;  ds 4 parent   14    103.3     95.58  7.71609 5.647     1.366386
-#&gt;  ds 4 parent   14    103.0     95.58  7.41609 5.647     1.313261
-#&gt;  ds 4 parent   28     90.8     89.82  0.98290 5.333     0.184310
-#&gt;  ds 4 parent   28     88.7     89.82 -1.11710 5.333    -0.209477
-#&gt;  ds 4 parent   60     74.8     77.91 -3.10870 4.690    -0.662879
-#&gt;  ds 4 parent   60     75.3     77.91 -2.60870 4.690    -0.556262
-#&gt;  ds 4 parent   90     71.1     68.18  2.91738 4.172     0.699234
-#&gt;  ds 4 parent   90     78.0     68.18  9.81738 4.172     2.353017
-#&gt;  ds 4 parent  120     59.1     59.67 -0.57073 3.728    -0.153107
-#&gt;  ds 4 parent  120     53.8     59.67 -5.87073 3.728    -1.574902
-#&gt;  ds 5 parent    0     94.9     98.38 -3.48183 5.800    -0.600307
-#&gt;  ds 5 parent    0    101.8     98.38  3.41817 5.800     0.589332
-#&gt;  ds 5 parent    1     96.1     96.75 -0.65141 5.711    -0.114065
-#&gt;  ds 5 parent    1     97.1     96.75  0.34859 5.711     0.061040
-#&gt;  ds 5 parent    3     93.8     93.57  0.22881 5.537     0.041323
-#&gt;  ds 5 parent    3     85.8     93.57 -7.77119 5.537    -1.403444
-#&gt;  ds 5 parent    7     87.6     87.52  0.07909 5.208     0.015186
-#&gt;  ds 5 parent    7     94.0     87.52  6.47909 5.208     1.244026
-#&gt;  ds 5 parent   14     82.5     77.86  4.64101 4.687     0.990182
-#&gt;  ds 5 parent   14     81.7     77.86  3.84101 4.687     0.819498
-#&gt;  ds 5 parent   28     60.0     61.62 -1.61729 3.829    -0.422433
-#&gt;  ds 5 parent   28     61.0     61.62 -0.61729 3.829    -0.161236
-#&gt;  ds 5 parent   60     32.5     36.10 -3.59608 2.571    -1.398750
-#&gt;  ds 5 parent   60     35.5     36.10 -0.59608 2.571    -0.231854
-#&gt;  ds 5 parent   90     21.8     21.86 -0.06415 1.987    -0.032287
-#&gt;  ds 5 parent   90     24.4     21.86  2.53585 1.987     1.276317
-#&gt;  ds 5 parent  120     14.1     13.24  0.85643 1.724     0.496877
-#&gt;  ds 5 parent  120     12.1     13.24 -1.14357 1.724    -0.663473</div><div class='input'>
+#&gt;    ds   name time observed predicted  residual    std standardized
+#&gt;  ds 1 parent    0    104.1   101.417   2.68283 8.0077     0.335030
+#&gt;  ds 1 parent    0    105.0   101.417   3.58283 8.0077     0.447422
+#&gt;  ds 1 parent    1     98.5   100.624  -2.12400 7.9451    -0.267334
+#&gt;  ds 1 parent    1     96.1   100.624  -4.52400 7.9451    -0.569407
+#&gt;  ds 1 parent    3    101.9    99.056   2.84379 7.8213     0.363595
+#&gt;  ds 1 parent    3     85.2    99.056 -13.85621 7.8213    -1.771597
+#&gt;  ds 1 parent    7     99.1    95.994   3.10646 7.5795     0.409850
+#&gt;  ds 1 parent    7     93.0    95.994  -2.99354 7.5795    -0.394953
+#&gt;  ds 1 parent   14     88.1    90.860  -2.75997 7.1741    -0.384710
+#&gt;  ds 1 parent   14     84.1    90.860  -6.75997 7.1741    -0.942268
+#&gt;  ds 1 parent   28     80.2    81.402  -1.20174 6.4273    -0.186973
+#&gt;  ds 1 parent   28     91.3    81.402   9.89826 6.4273     1.540024
+#&gt;  ds 1 parent   60     65.1    63.316   1.78361 4.9994     0.356767
+#&gt;  ds 1 parent   60     65.8    63.316   2.48361 4.9994     0.496785
+#&gt;  ds 1 parent   90     47.8    50.029  -2.22862 3.9502    -0.564182
+#&gt;  ds 1 parent   90     53.5    50.029   3.47138 3.9502     0.878792
+#&gt;  ds 1 parent  120     37.6    39.529  -1.92946 3.1212    -0.618182
+#&gt;  ds 1 parent  120     39.3    39.529  -0.22946 3.1212    -0.073516
+#&gt;  ds 2 parent    0    107.9   101.711   6.18875 8.0309     0.770613
+#&gt;  ds 2 parent    0    102.1   101.711   0.38875 8.0309     0.048406
+#&gt;  ds 2 parent    1    103.8   100.174   3.62597 7.9096     0.458428
+#&gt;  ds 2 parent    1    108.6   100.174   8.42597 7.9096     1.065287
+#&gt;  ds 2 parent    3     91.0    97.169  -6.16895 7.6723    -0.804055
+#&gt;  ds 2 parent    3     84.9    97.169 -12.26895 7.6723    -1.599124
+#&gt;  ds 2 parent    7     79.3    91.427 -12.12652 7.2189    -1.679833
+#&gt;  ds 2 parent    7    100.9    91.427   9.47348 7.2189     1.312320
+#&gt;  ds 2 parent   14     77.3    82.182  -4.88174 6.4889    -0.752318
+#&gt;  ds 2 parent   14     83.5    82.182   1.31826 6.4889     0.203155
+#&gt;  ds 2 parent   28     66.8    66.402   0.39792 5.2430     0.075895
+#&gt;  ds 2 parent   28     63.3    66.402  -3.10208 5.2430    -0.591662
+#&gt;  ds 2 parent   60     40.8    40.789   0.01138 3.2206     0.003532
+#&gt;  ds 2 parent   60     44.8    40.789   4.01138 3.2206     1.245537
+#&gt;  ds 2 parent   90     27.8    25.830   1.97002 2.0395     0.965937
+#&gt;  ds 2 parent   90     27.0    25.830   1.17002 2.0395     0.573682
+#&gt;  ds 2 parent  120     15.2    16.357  -1.15721 1.2915    -0.895991
+#&gt;  ds 2 parent  120     15.5    16.357  -0.85721 1.2915    -0.663710
+#&gt;  ds 3 parent    0     97.7   101.907  -4.20726 8.0464    -0.522873
+#&gt;  ds 3 parent    0     88.2   101.907 -13.70726 8.0464    -1.703521
+#&gt;  ds 3 parent    1    109.9    99.522  10.37805 7.8581     1.320685
+#&gt;  ds 3 parent    1     97.8    99.522  -1.72195 7.8581    -0.219130
+#&gt;  ds 3 parent    3    100.5    94.918   5.58248 7.4945     0.744875
+#&gt;  ds 3 parent    3     77.4    94.918 -17.51752 7.4945    -2.337375
+#&gt;  ds 3 parent    7     78.3    86.338  -8.03788 6.8171    -1.179077
+#&gt;  ds 3 parent    7     90.3    86.338   3.96212 6.8171     0.581204
+#&gt;  ds 3 parent   14     76.0    73.147   2.85281 5.7756     0.493944
+#&gt;  ds 3 parent   14     79.1    73.147   5.95281 5.7756     1.030687
+#&gt;  ds 3 parent   28     46.0    52.504  -6.50373 4.1456    -1.568826
+#&gt;  ds 3 parent   28     53.4    52.504   0.89627 4.1456     0.216197
+#&gt;  ds 3 parent   60     25.1    24.605   0.49461 1.9428     0.254586
+#&gt;  ds 3 parent   60     21.4    24.605  -3.20539 1.9428    -1.649882
+#&gt;  ds 3 parent   90     11.0    12.090  -1.09046 0.9546    -1.142271
+#&gt;  ds 3 parent   90     14.2    12.090   2.10954 0.9546     2.209770
+#&gt;  ds 3 parent  120      5.8     5.941  -0.14094 0.4691    -0.300464
+#&gt;  ds 3 parent  120      6.1     5.941   0.15906 0.4691     0.339077
+#&gt;  ds 4 parent    0     95.3   101.177  -5.87672 7.9887    -0.735625
+#&gt;  ds 4 parent    0    102.0   101.177   0.82328 7.9887     0.103056
+#&gt;  ds 4 parent    1    104.4   100.716   3.68438 7.9523     0.463307
+#&gt;  ds 4 parent    1    105.4   100.716   4.68438 7.9523     0.589057
+#&gt;  ds 4 parent    3    113.7    99.800  13.90026 7.8800     1.763989
+#&gt;  ds 4 parent    3     82.3    99.800 -17.49974 7.8800    -2.220774
+#&gt;  ds 4 parent    7     98.1    97.993   0.10713 7.7374     0.013846
+#&gt;  ds 4 parent    7     87.8    97.993 -10.19287 7.7374    -1.317359
+#&gt;  ds 4 parent   14     97.9    94.909   2.99079 7.4939     0.399098
+#&gt;  ds 4 parent   14    104.8    94.909   9.89079 7.4939     1.319851
+#&gt;  ds 4 parent   28     85.0    89.030  -4.02995 7.0297    -0.573279
+#&gt;  ds 4 parent   28     77.2    89.030 -11.82995 7.0297    -1.682864
+#&gt;  ds 4 parent   60     82.2    76.923   5.27690 6.0737     0.868808
+#&gt;  ds 4 parent   60     86.1    76.923   9.17690 6.0737     1.510919
+#&gt;  ds 4 parent   90     70.5    67.073   3.42743 5.2959     0.647182
+#&gt;  ds 4 parent   90     61.7    67.073  -5.37257 5.2959    -1.014470
+#&gt;  ds 4 parent  120     60.0    58.483   1.51654 4.6178     0.328416
+#&gt;  ds 4 parent  120     56.4    58.483  -2.08346 4.6178    -0.451184
+#&gt;  ds 5 parent    0     92.6   101.752  -9.15161 8.0341    -1.139091
+#&gt;  ds 5 parent    0    116.5   101.752  14.74839 8.0341     1.835716
+#&gt;  ds 5 parent    1    108.0   100.069   7.93112 7.9013     1.003778
+#&gt;  ds 5 parent    1    104.9   100.069   4.83112 7.9013     0.611436
+#&gt;  ds 5 parent    3    100.5    96.786   3.71355 7.6421     0.485934
+#&gt;  ds 5 parent    3     89.5    96.786  -7.28645 7.6421    -0.953462
+#&gt;  ds 5 parent    7     91.7    90.541   1.15895 7.1490     0.162114
+#&gt;  ds 5 parent    7     95.1    90.541   4.55895 7.1490     0.637707
+#&gt;  ds 5 parent   14     82.2    80.566   1.63437 6.3613     0.256923
+#&gt;  ds 5 parent   14     84.5    80.566   3.93437 6.3613     0.618483
+#&gt;  ds 5 parent   28     60.5    63.791  -3.29084 5.0368    -0.653357
+#&gt;  ds 5 parent   28     72.8    63.791   9.00916 5.0368     1.788662
+#&gt;  ds 5 parent   60     38.3    37.412   0.88840 2.9540     0.300748
+#&gt;  ds 5 parent   60     40.7    37.412   3.28840 2.9540     1.113217
+#&gt;  ds 5 parent   90     22.5    22.685  -0.18500 1.7912    -0.103287
+#&gt;  ds 5 parent   90     20.8    22.685  -1.88500 1.7912    -1.052387
+#&gt;  ds 5 parent  120     13.4    13.755  -0.35534 1.0861    -0.327173
+#&gt;  ds 5 parent  120     13.8    13.755   0.04466 1.0861     0.041118</div><div class='input'>
 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
diff --git a/docs/dev/reference/summary.saem.mmkin-1.png b/docs/dev/reference/summary.saem.mmkin-1.png
deleted file mode 100644
index e3538cb6..00000000
--- a/docs/dev/reference/summary.saem.mmkin-1.png
+++ /dev/null
diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html
index b7804247..1a82f7ef 100644
--- a/docs/dev/reference/summary.saem.mmkin.html
+++ b/docs/dev/reference/summary.saem.mmkin.html
@@ -223,8 +223,8 @@ saemix authors for the parts inherited from saemix.</p>
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='co'># Generate five datasets following DFOP-SFO kinetics</span>
 <span class='va'>sampling_times</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span>
-<span class='va'>dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='st'>"m1"</span><span class='op'>)</span>,
- m1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='va'>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'>"m1"</span><span class='op'>)</span>,
+ m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 <span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span><span class='op'>(</span><span class='fl'>1234</span><span class='op'>)</span>
 <span class='va'>k1_in</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Lognormal.html'>rlnorm</a></span><span class='op'>(</span><span class='fl'>5</span>, <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>0.1</span><span class='op'>)</span>, <span class='fl'>0.3</span><span class='op'>)</span>
 <span class='va'>k2_in</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Lognormal.html'>rlnorm</a></span><span class='op'>(</span><span class='fl'>5</span>, <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>0.02</span><span class='op'>)</span>, <span class='fl'>0.3</span><span class='op'>)</span>
@@ -260,15 +260,15 @@ saemix authors for the parts inherited from saemix.</p>
   quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, cores <span class='op'>=</span> <span class='fl'>5</span><span class='op'>)</span>
 <span class='va'>f_saem_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f_mmkin_dfop_sfo</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Thu Nov 19 14:59:46 2020"
+#&gt; [1] "Mon Nov 30 16:01:26 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Thu Nov 19 15:00:00 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+#&gt; [1] "Mon Nov 30 16:01:39 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; saemix version used for fitting:      3.1.9000 
 #&gt; mkin version used for pre-fitting:  0.9.50.4 
 #&gt; R version used for fitting:         4.0.3 
-#&gt; Date of fit:     Thu Nov 19 15:00:01 2020 
-#&gt; Date of summary: Thu Nov 19 15:00:01 2020 
+#&gt; Date of fit:     Mon Nov 30 16:01:40 2020 
+#&gt; Date of summary: Mon Nov 30 16:01:40 2020 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -283,7 +283,7 @@ saemix authors for the parts inherited from saemix.</p>
 #&gt; 
 #&gt; Model predictions using solution type analytical 
 #&gt; 
-#&gt; Fitted in 15.23 s using 300, 100 iterations
+#&gt; Fitted in 14.5 s using 300, 100 iterations
 #&gt; 
 #&gt; Variance model: Two-component variance function 
 #&gt; 
diff --git a/docs/dev/reference/synthetic_data_for_UBA_2014-1.png b/docs/dev/reference/synthetic_data_for_UBA_2014-1.png
index 02976ced..351b21aa 100644
--- a/docs/dev/reference/synthetic_data_for_UBA_2014-1.png
+++ b/docs/dev/reference/synthetic_data_for_UBA_2014-1.png
diff --git a/docs/dev/reference/synthetic_data_for_UBA_2014.html b/docs/dev/reference/synthetic_data_for_UBA_2014.html
index da4af114..1edc7c1e 100644
--- a/docs/dev/reference/synthetic_data_for_UBA_2014.html
+++ b/docs/dev/reference/synthetic_data_for_UBA_2014.html
@@ -87,7 +87,7 @@ Compare also the code in the example section to see the degradation models." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -135,7 +135,7 @@ Compare also the code in the example section to see the degradation models." />
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -177,13 +177,13 @@ Compare also the code in the example section to see the degradation models." />
 <p>Compare also the code in the example section to see the degradation models.</p>
     </div>
 
-    <pre class="usage"><span class='no'>synthetic_data_for_UBA_2014</span></pre>
+    <pre class="usage"><span class='va'>synthetic_data_for_UBA_2014</span></pre>
 
 
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
     <p>A list containing twelve datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>,
-  each containing, among others, the following components</p><dl'>
+  each containing, among others, the following components</p><dl>
     <dt><code>title</code></dt><dd><p>The name of the dataset, e.g. <code>SFO_lin_a</code></p></dd>
     <dt><code>data</code></dt><dd><p>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></p></dd>
   
@@ -199,55 +199,59 @@ Compare also the code in the example section to see the degradation models." />
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='co'># \dontrun{</span>
 <span class='co'># The data have been generated using the following kinetic models</span>
-<span class='no'>m_synth_SFO_lin</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M1"</span>),
-                           <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M2"</span>),
-                           <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-
-<span class='no'>m_synth_SFO_par</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>),
-                                         <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
-                           <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
-                           <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-<span class='no'>m_synth_DFOP_lin</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"DFOP"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M1"</span>),
-                            <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M2"</span>),
-                            <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-<span class='no'>m_synth_DFOP_par</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"DFOP"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>),
-                                          <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
-                            <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
-                            <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+<span class='va'>m_synth_SFO_lin</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='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"M1"</span><span class='op'>)</span>,
+                           M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"M2"</span><span class='op'>)</span>,
+                           M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
+
+<span class='va'>m_synth_SFO_par</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='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span>,
+                                         sink <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>,
+                           M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>,
+                           M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
+<span class='va'>m_synth_DFOP_lin</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='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"DFOP"</span>, to <span class='op'>=</span> <span class='st'>"M1"</span><span class='op'>)</span>,
+                            M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"M2"</span><span class='op'>)</span>,
+                            M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
+<span class='va'>m_synth_DFOP_par</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='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"DFOP"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span>,
+                                          sink <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>,
+                            M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>,
+                            M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
 <span class='co'># The model predictions without intentional error were generated as follows</span>
-<span class='no'>sampling_times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span>)
-
-<span class='no'>d_synth_SFO_lin</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>m_synth_SFO_lin</span>,
-                               <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.7</span>, <span class='kw'>f_parent_to_M1</span> <span class='kw'>=</span> <span class='fl'>0.8</span>,
-                                 <span class='kw'>k_M1</span> <span class='kw'>=</span> <span class='fl'>0.3</span>, <span class='kw'>f_M1_to_M2</span> <span class='kw'>=</span> <span class='fl'>0.7</span>,
-                                 <span class='kw'>k_M2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>),
-                               <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fl'>0</span>),
-                               <span class='no'>sampling_times</span>)
-
-<span class='no'>d_synth_DFOP_lin</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>m_synth_DFOP_lin</span>,
-                                <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k1</span> <span class='kw'>=</span> <span class='fl'>0.2</span>, <span class='kw'>k2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>, <span class='kw'>g</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
-                                  <span class='kw'>f_parent_to_M1</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>k_M1</span> <span class='kw'>=</span> <span class='fl'>0.3</span>,
-                                  <span class='kw'>f_M1_to_M2</span> <span class='kw'>=</span> <span class='fl'>0.7</span>, <span class='kw'>k_M2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>),
-                                 <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fl'>0</span>),
-                                 <span class='no'>sampling_times</span>)
-
-<span class='no'>d_synth_SFO_par</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>m_synth_SFO_par</span>,
-                               <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.2</span>,
-                                 <span class='kw'>f_parent_to_M1</span> <span class='kw'>=</span> <span class='fl'>0.8</span>, <span class='kw'>k_M1</span> <span class='kw'>=</span> <span class='fl'>0.01</span>,
-                                 <span class='kw'>f_parent_to_M2</span> <span class='kw'>=</span> <span class='fl'>0.2</span>, <span class='kw'>k_M2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>),
-                                 <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fl'>0</span>),
-                                 <span class='no'>sampling_times</span>)
-
-<span class='no'>d_synth_DFOP_par</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>m_synth_DFOP_par</span>,
-                               <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k1</span> <span class='kw'>=</span> <span class='fl'>0.3</span>, <span class='kw'>k2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>, <span class='kw'>g</span> <span class='kw'>=</span> <span class='fl'>0.7</span>,
-                                 <span class='kw'>f_parent_to_M1</span> <span class='kw'>=</span> <span class='fl'>0.6</span>, <span class='kw'>k_M1</span> <span class='kw'>=</span> <span class='fl'>0.04</span>,
-                                 <span class='kw'>f_parent_to_M2</span> <span class='kw'>=</span> <span class='fl'>0.4</span>, <span class='kw'>k_M2</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
-                                 <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fl'>0</span>),
-                                 <span class='no'>sampling_times</span>)
+<span class='va'>sampling_times</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span>
+
+<span class='va'>d_synth_SFO_lin</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>m_synth_SFO_lin</span>,
+                               <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.7</span>, f_parent_to_M1 <span class='op'>=</span> <span class='fl'>0.8</span>,
+                                 k_M1 <span class='op'>=</span> <span class='fl'>0.3</span>, f_M1_to_M2 <span class='op'>=</span> <span class='fl'>0.7</span>,
+                                 k_M2 <span class='op'>=</span> <span class='fl'>0.02</span><span class='op'>)</span>,
+                               <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, M1 <span class='op'>=</span> <span class='fl'>0</span>, M2 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>,
+                               <span class='va'>sampling_times</span><span class='op'>)</span>
+
+<span class='va'>d_synth_DFOP_lin</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>m_synth_DFOP_lin</span>,
+                                <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k1 <span class='op'>=</span> <span class='fl'>0.2</span>, k2 <span class='op'>=</span> <span class='fl'>0.02</span>, g <span class='op'>=</span> <span class='fl'>0.5</span>,
+                                  f_parent_to_M1 <span class='op'>=</span> <span class='fl'>0.5</span>, k_M1 <span class='op'>=</span> <span class='fl'>0.3</span>,
+                                  f_M1_to_M2 <span class='op'>=</span> <span class='fl'>0.7</span>, k_M2 <span class='op'>=</span> <span class='fl'>0.02</span><span class='op'>)</span>,
+                                 <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, M1 <span class='op'>=</span> <span class='fl'>0</span>, M2 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>,
+                                 <span class='va'>sampling_times</span><span class='op'>)</span>
+
+<span class='va'>d_synth_SFO_par</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>m_synth_SFO_par</span>,
+                               <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.2</span>,
+                                 f_parent_to_M1 <span class='op'>=</span> <span class='fl'>0.8</span>, k_M1 <span class='op'>=</span> <span class='fl'>0.01</span>,
+                                 f_parent_to_M2 <span class='op'>=</span> <span class='fl'>0.2</span>, k_M2 <span class='op'>=</span> <span class='fl'>0.02</span><span class='op'>)</span>,
+                                 <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, M1 <span class='op'>=</span> <span class='fl'>0</span>, M2 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>,
+                                 <span class='va'>sampling_times</span><span class='op'>)</span>
+
+<span class='va'>d_synth_DFOP_par</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>m_synth_DFOP_par</span>,
+                               <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k1 <span class='op'>=</span> <span class='fl'>0.3</span>, k2 <span class='op'>=</span> <span class='fl'>0.02</span>, g <span class='op'>=</span> <span class='fl'>0.7</span>,
+                                 f_parent_to_M1 <span class='op'>=</span> <span class='fl'>0.6</span>, k_M1 <span class='op'>=</span> <span class='fl'>0.04</span>,
+                                 f_parent_to_M2 <span class='op'>=</span> <span class='fl'>0.4</span>, k_M2 <span class='op'>=</span> <span class='fl'>0.01</span><span class='op'>)</span>,
+                                 <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, M1 <span class='op'>=</span> <span class='fl'>0</span>, M2 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>,
+                                 <span class='va'>sampling_times</span><span class='op'>)</span>
 
 <span class='co'># Construct names for datasets with errors</span>
-<span class='no'>d_synth_names</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='st'>"d_synth_"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"SFO_lin"</span>, <span class='st'>"SFO_par"</span>,
-                                     <span class='st'>"DFOP_lin"</span>, <span class='st'>"DFOP_par"</span>))
+<span class='va'>d_synth_names</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='st'>"d_synth_"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO_lin"</span>, <span class='st'>"SFO_par"</span>,
+                                     <span class='st'>"DFOP_lin"</span>, <span class='st'>"DFOP_par"</span><span class='op'>)</span><span class='op'>)</span>
 
 <span class='co'># Original function used or adding errors. The add_err function now published</span>
 <span class='co'># with this package is a slightly generalised version where the names of</span>
@@ -268,33 +272,35 @@ Compare also the code in the example section to see the degradation models." />
 
 <span class='co'># The following is the simplified version of the two-component model of Rocke</span>
 <span class='co'># and Lorenzato (1995)</span>
-<span class='no'>sdfunc_twocomp</span> <span class='kw'>=</span> <span class='kw'>function</span>(<span class='no'>value</span>, <span class='no'>sd_low</span>, <span class='no'>rsd_high</span>) {
-  <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>sqrt</a></span>(<span class='no'>sd_low</span>^<span class='fl'>2</span> + <span class='no'>value</span>^<span class='fl'>2</span> * <span class='no'>rsd_high</span>^<span class='fl'>2</span>)
-}
+<span class='va'>sdfunc_twocomp</span> <span class='op'>=</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span>, <span class='va'>sd_low</span>, <span class='va'>rsd_high</span><span class='op'>)</span> <span class='op'>{</span>
+  <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>sqrt</a></span><span class='op'>(</span><span class='va'>sd_low</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>+</span> <span class='va'>value</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>*</span> <span class='va'>rsd_high</span><span class='op'>^</span><span class='fl'>2</span><span class='op'>)</span>
+<span class='op'>}</span>
 
 <span class='co'># Add the errors.</span>
-<span class='kw'>for</span> (<span class='no'>d_synth_name</span> <span class='kw'>in</span> <span class='no'>d_synth_names</span>)
-{
-  <span class='no'>d_synth</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/get.html'>get</a></span>(<span class='no'>d_synth_name</span>)
-  <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='no'>d_synth_name</span>, <span class='st'>"_a"</span>), <span class='fu'><a href='add_err.html'>add_err</a></span>(<span class='no'>d_synth</span>, <span class='kw'>function</span>(<span class='no'>value</span>) <span class='fl'>3</span>))
-  <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='no'>d_synth_name</span>, <span class='st'>"_b"</span>), <span class='fu'><a href='add_err.html'>add_err</a></span>(<span class='no'>d_synth</span>, <span class='kw'>function</span>(<span class='no'>value</span>) <span class='fl'>7</span>))
-  <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='no'>d_synth_name</span>, <span class='st'>"_c"</span>), <span class='fu'><a href='add_err.html'>add_err</a></span>(<span class='no'>d_synth</span>,
-                           <span class='kw'>function</span>(<span class='no'>value</span>) <span class='fu'>sdfunc_twocomp</span>(<span class='no'>value</span>, <span class='fl'>0.5</span>, <span class='fl'>0.07</span>)))
+<span class='kw'>for</span> <span class='op'>(</span><span class='va'>d_synth_name</span> <span class='kw'>in</span> <span class='va'>d_synth_names</span><span class='op'>)</span>
+<span class='op'>{</span>
+  <span class='va'>d_synth</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/get.html'>get</a></span><span class='op'>(</span><span class='va'>d_synth_name</span><span class='op'>)</span>
+  <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>d_synth_name</span>, <span class='st'>"_a"</span><span class='op'>)</span>, <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>d_synth</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fl'>3</span><span class='op'>)</span><span class='op'>)</span>
+  <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>d_synth_name</span>, <span class='st'>"_b"</span><span class='op'>)</span>, <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>d_synth</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fl'>7</span><span class='op'>)</span><span class='op'>)</span>
+  <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>d_synth_name</span>, <span class='st'>"_c"</span><span class='op'>)</span>, <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>d_synth</span>,
+                           <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fu'>sdfunc_twocomp</span><span class='op'>(</span><span class='va'>value</span>, <span class='fl'>0.5</span>, <span class='fl'>0.07</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>
 
-}
+<span class='op'>}</span>
 
-<span class='no'>d_synth_err_names</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(
-  <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='no'>d_synth_names</span>, <span class='kw'>each</span> <span class='kw'>=</span> <span class='fl'>3</span>), <span class='no'>letters</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"_"</span>)
-)
+<span class='va'>d_synth_err_names</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>
+  <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span><span class='op'>(</span><span class='va'>d_synth_names</span>, each <span class='op'>=</span> <span class='fl'>3</span><span class='op'>)</span>, <span class='va'>letters</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>3</span><span class='op'>]</span>, sep <span class='op'>=</span> <span class='st'>"_"</span><span class='op'>)</span>
+<span class='op'>)</span>
 
 <span class='co'># This is just one example of an evaluation using the kinetic model used for</span>
 <span class='co'># the generation of the data</span>
-  <span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_SFO_lin</span>, <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>,
-                 <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-  <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='synthetic_data_for_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting:    0.9.50.3 
-#&gt; R version used for fitting:       4.0.0 
-#&gt; Date of fit:     Wed May 27 06:02:14 2020 
-#&gt; Date of summary: Wed May 27 06:02:14 2020 
+  <span class='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_synth_SFO_lin</span>, <span class='va'>synthetic_data_for_UBA_2014</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span>,
+                 quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</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>
+</div><div class='img'><img src='synthetic_data_for_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; mkin version used for fitting:    0.9.50.4 
+#&gt; R version used for fitting:       4.0.3 
+#&gt; Date of fit:     Mon Nov 30 16:01:42 2020 
+#&gt; Date of summary: Mon Nov 30 16:01:42 2020 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - k_parent * parent
@@ -303,7 +309,7 @@ Compare also the code in the example section to see the degradation models." />
 #&gt; 
 #&gt; Model predictions using solution type deSolve 
 #&gt; 
-#&gt; Fitted using 817 model solutions performed in 0.623 s
+#&gt; Fitted using 822 model solutions performed in 0.652 s
 #&gt; 
 #&gt; Error model: Constant variance 
 #&gt; 
@@ -319,13 +325,13 @@ Compare also the code in the example section to see the degradation models." />
 #&gt; f_M1_to_M2       0.5000 deparm
 #&gt; 
 #&gt; Starting values for the transformed parameters actually optimised:
-#&gt;                     value lower upper
-#&gt; parent_0       101.350000  -Inf   Inf
-#&gt; log_k_parent    -2.302585  -Inf   Inf
-#&gt; log_k_M1        -2.301586  -Inf   Inf
-#&gt; log_k_M2        -2.300587  -Inf   Inf
-#&gt; f_parent_ilr_1   0.000000  -Inf   Inf
-#&gt; f_M1_ilr_1       0.000000  -Inf   Inf
+#&gt;                      value lower upper
+#&gt; parent_0        101.350000  -Inf   Inf
+#&gt; log_k_parent     -2.302585  -Inf   Inf
+#&gt; log_k_M1         -2.301586  -Inf   Inf
+#&gt; log_k_M2         -2.300587  -Inf   Inf
+#&gt; f_parent_qlogis   0.000000  -Inf   Inf
+#&gt; f_M1_qlogis       0.000000  -Inf   Inf
 #&gt; 
 #&gt; Fixed parameter values:
 #&gt;      value  type
@@ -338,32 +344,32 @@ Compare also the code in the example section to see the degradation models." />
 #&gt;   188.7274 200.3723 -87.36368
 #&gt; 
 #&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt;                Estimate Std. Error   Lower    Upper
-#&gt; parent_0       102.1000    1.57000 98.8600 105.3000
-#&gt; log_k_parent    -0.3020    0.03885 -0.3812  -0.2229
-#&gt; log_k_M1        -1.2070    0.07123 -1.3520  -1.0620
-#&gt; log_k_M2        -3.9010    0.06571 -4.0350  -3.7670
-#&gt; f_parent_ilr_1   0.8492    0.16640  0.5103   1.1880
-#&gt; f_M1_ilr_1       0.6780    0.17600  0.3196   1.0360
-#&gt; sigma            2.2730    0.25740  1.7490   2.7970
+#&gt;                 Estimate Std. Error   Lower    Upper
+#&gt; parent_0        102.1000    1.57000 98.8600 105.3000
+#&gt; log_k_parent     -0.3020    0.03885 -0.3812  -0.2229
+#&gt; log_k_M1         -1.2070    0.07123 -1.3520  -1.0620
+#&gt; log_k_M2         -3.9010    0.06571 -4.0350  -3.7670
+#&gt; f_parent_qlogis   1.2010    0.23530  0.7216   1.6800
+#&gt; f_M1_qlogis       0.9589    0.24890  0.4520   1.4660
+#&gt; sigma             2.2730    0.25740  1.7490   2.7970
 #&gt; 
 #&gt; Parameter correlation:
-#&gt;                  parent_0 log_k_parent   log_k_M1   log_k_M2 f_parent_ilr_1
-#&gt; parent_0        1.000e+00    3.933e-01 -1.605e-01  2.819e-02     -4.624e-01
-#&gt; log_k_parent    3.933e-01    1.000e+00 -4.082e-01  7.166e-02     -5.682e-01
-#&gt; log_k_M1       -1.605e-01   -4.082e-01  1.000e+00 -3.929e-01      7.478e-01
-#&gt; log_k_M2        2.819e-02    7.166e-02 -3.929e-01  1.000e+00     -2.658e-01
-#&gt; f_parent_ilr_1 -4.624e-01   -5.682e-01  7.478e-01 -2.658e-01      1.000e+00
-#&gt; f_M1_ilr_1      1.614e-01    4.102e-01 -8.109e-01  5.419e-01     -8.605e-01
-#&gt; sigma          -1.384e-07   -2.581e-07  9.499e-08  1.518e-07      1.236e-07
-#&gt;                f_M1_ilr_1      sigma
-#&gt; parent_0        1.614e-01 -1.384e-07
-#&gt; log_k_parent    4.102e-01 -2.581e-07
-#&gt; log_k_M1       -8.109e-01  9.499e-08
-#&gt; log_k_M2        5.419e-01  1.518e-07
-#&gt; f_parent_ilr_1 -8.605e-01  1.236e-07
-#&gt; f_M1_ilr_1      1.000e+00  8.795e-09
-#&gt; sigma           8.795e-09  1.000e+00
+#&gt;                   parent_0 log_k_parent   log_k_M1   log_k_M2 f_parent_qlogis
+#&gt; parent_0         1.000e+00    3.933e-01 -1.605e-01  2.819e-02      -4.624e-01
+#&gt; log_k_parent     3.933e-01    1.000e+00 -4.082e-01  7.166e-02      -5.682e-01
+#&gt; log_k_M1        -1.605e-01   -4.082e-01  1.000e+00 -3.929e-01       7.478e-01
+#&gt; log_k_M2         2.819e-02    7.166e-02 -3.929e-01  1.000e+00      -2.658e-01
+#&gt; f_parent_qlogis -4.624e-01   -5.682e-01  7.478e-01 -2.658e-01       1.000e+00
+#&gt; f_M1_qlogis      1.614e-01    4.102e-01 -8.109e-01  5.419e-01      -8.605e-01
+#&gt; sigma           -7.941e-08   -9.143e-09 -1.268e-08  5.947e-08       5.657e-08
+#&gt;                 f_M1_qlogis      sigma
+#&gt; parent_0          1.614e-01 -7.941e-08
+#&gt; log_k_parent      4.102e-01 -9.143e-09
+#&gt; log_k_M1         -8.109e-01 -1.268e-08
+#&gt; log_k_M2          5.419e-01  5.947e-08
+#&gt; f_parent_qlogis  -8.605e-01  5.657e-08
+#&gt; f_M1_qlogis       1.000e+00 -2.382e-10
+#&gt; sigma            -2.382e-10  1.000e+00
 #&gt; 
 #&gt; Backtransformed parameters:
 #&gt; Confidence intervals for internally transformed parameters are asymmetric.
@@ -410,8 +416,8 @@ Compare also the code in the example section to see the degradation models." />
 #&gt;     7   parent      0.3  5.772e-01 -0.27717
 #&gt;    14   parent      3.5  3.264e-03  3.49674
 #&gt;    28   parent      3.2  1.045e-07  3.20000
-#&gt;    90   parent      0.6  9.535e-10  0.60000
-#&gt;   120   parent      3.5 -5.941e-10  3.50000
+#&gt;    90   parent      0.6  9.532e-10  0.60000
+#&gt;   120   parent      3.5 -5.940e-10  3.50000
 #&gt;     1       M1     36.4  3.479e+01  1.61088
 #&gt;     1       M1     37.4  3.479e+01  2.61088
 #&gt;     3       M1     34.3  3.937e+01 -5.07027
@@ -421,9 +427,9 @@ Compare also the code in the example section to see the degradation models." />
 #&gt;    14       M1      5.8  1.995e+00  3.80469
 #&gt;    14       M1      1.2  1.995e+00 -0.79531
 #&gt;    60       M1      0.5  2.111e-06  0.50000
-#&gt;    90       M1      3.2 -9.676e-10  3.20000
-#&gt;   120       M1      1.5  7.671e-10  1.50000
-#&gt;   120       M1      0.6  7.671e-10  0.60000
+#&gt;    90       M1      3.2 -9.671e-10  3.20000
+#&gt;   120       M1      1.5  7.670e-10  1.50000
+#&gt;   120       M1      0.6  7.670e-10  0.60000
 #&gt;     1       M2      4.8  4.455e+00  0.34517
 #&gt;     3       M2     20.9  2.153e+01 -0.62527
 #&gt;     3       M2     19.3  2.153e+01 -2.22527
@@ -438,7 +444,7 @@ Compare also the code in the example section to see the degradation models." />
 #&gt;    90       M2     10.6  1.013e+01  0.47130
 #&gt;    90       M2     10.8  1.013e+01  0.67130
 #&gt;   120       M2      9.8  5.521e+00  4.27893
-#&gt;   120       M2      3.3  5.521e+00 -2.22107</div><div class='input'># }
+#&gt;   120       M2      3.3  5.521e+00 -2.22107</div><div class='input'><span class='co'># }</span>
 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -455,7 +461,7 @@ Compare also the code in the example section to see the degradation models." />
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/test_data_from_UBA_2014-1.png b/docs/dev/reference/test_data_from_UBA_2014-1.png
index 431181cf..9e0afad2 100644
--- a/docs/dev/reference/test_data_from_UBA_2014-1.png
+++ b/docs/dev/reference/test_data_from_UBA_2014-1.png
diff --git a/docs/dev/reference/test_data_from_UBA_2014-2.png b/docs/dev/reference/test_data_from_UBA_2014-2.png
index 4a064163..e889efde 100644
--- a/docs/dev/reference/test_data_from_UBA_2014-2.png
+++ b/docs/dev/reference/test_data_from_UBA_2014-2.png
diff --git a/docs/dev/reference/test_data_from_UBA_2014.html b/docs/dev/reference/test_data_from_UBA_2014.html
index 291e3959..89ec3480 100644
--- a/docs/dev/reference/test_data_from_UBA_2014.html
+++ b/docs/dev/reference/test_data_from_UBA_2014.html
@@ -73,7 +73,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -121,7 +121,7 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -149,13 +149,13 @@
  software packages (Ranke, 2014).</p>
     </div>
 
-    <pre class="usage"><span class='no'>test_data_from_UBA_2014</span></pre>
+    <pre class="usage"><span class='va'>test_data_from_UBA_2014</span></pre>
 
 
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
     <p>A list containing three datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>.
-  Each dataset has, among others, the following components</p><dl'>
+  Each dataset has, among others, the following components</p><dl>
     <dt><code>title</code></dt><dd><p>The name of the dataset, e.g. <code>UBA_2014_WS_river</code></p></dd>
     <dt><code>data</code></dt><dd><p>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></p></dd>
   
@@ -174,52 +174,62 @@
   <span class='co'># generally considered deprecated due to the frequent occurrence of such</span>
   <span class='co'># large parameter correlations, among other reasons (e.g. the adequacy of the</span>
   <span class='co'># model).</span>
-  <span class='no'>m_ws</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent_w</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_s"</span>),
-                  <span class='kw'>parent_s</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_w"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>  <span class='no'>f_river</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_ws</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>  <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_river</span>)</div><div class='img'><img src='test_data_from_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'>
-  <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f_river</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt;                           Estimate se_notrans t value Pr(&gt;t) Lower Upper
-#&gt; parent_w_0             95.91998116         NA      NA     NA    NA    NA
+  <span class='va'>m_ws</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent_w <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'>"parent_s"</span><span class='op'>)</span>,
+                  parent_s <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'>"parent_w"</span><span class='op'>)</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>  <span class='va'>f_river</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_ws</span>, <span class='va'>test_data_from_UBA_2014</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>  <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>f_river</span><span class='op'>)</span>
+</div><div class='img'><img src='test_data_from_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'>
+  <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_river</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt;                           Estimate se_notrans t value Pr(&gt;t) Lower Upper
+#&gt; parent_w_0             95.91998118         NA      NA     NA    NA    NA
 #&gt; k_parent_w              0.41145375         NA      NA     NA    NA    NA
 #&gt; k_parent_s              0.04663944         NA      NA     NA    NA    NA
 #&gt; f_parent_w_to_parent_s  0.12467894         NA      NA     NA    NA    NA
 #&gt; f_parent_s_to_parent_w  0.50000000         NA      NA     NA    NA    NA
-#&gt; sigma                   3.13612618         NA      NA     NA    NA    NA</div><div class='input'>  <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_river</span>)</div><div class='output co'>#&gt;            err.min n.optim df
+#&gt; sigma                   3.13612618         NA      NA     NA    NA    NA</div><div class='input'>  <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span><span class='op'>(</span><span class='va'>f_river</span><span class='op'>)</span>
+</div><div class='output co'>#&gt;            err.min n.optim df
 #&gt; All data 0.1090929       5  6
 #&gt; parent_w 0.0817436       3  3
 #&gt; parent_s 0.1619965       2  3</div><div class='input'>
   <span class='co'># This is the evaluation used for the validation of software packages</span>
   <span class='co'># in the expertise from 2014</span>
-  <span class='no'>m_soil</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)),
-                    <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M3"</span>),
-                    <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M3"</span>),
-                    <span class='kw'>M3</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>),
-                    <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-  <span class='no'>f_soil</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_soil</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>3</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>  <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_soil</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='test_data_from_UBA_2014-2.png' alt='' width='700' height='433' /></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt;                   Estimate  se_notrans    t value       Pr(&gt;t)        Lower
-#&gt; parent_0       76.55425584 0.859186419 89.1008681 1.113862e-26 74.755958720
-#&gt; k_parent        0.12081956 0.004601919 26.2541703 1.077361e-16  0.111561576
-#&gt; k_M1            0.84258629 0.806165149  1.0451783 1.545282e-01  0.113778910
-#&gt; k_M2            0.04210878 0.017083049  2.4649452 1.170195e-02  0.018013823
-#&gt; k_M3            0.01122919 0.007245870  1.5497364 6.885076e-02  0.002909418
-#&gt; f_parent_to_M1  0.32240193 0.240785518  1.3389590 9.819221e-02           NA
-#&gt; f_parent_to_M2  0.16099854 0.033691991  4.7785404 6.531224e-05           NA
-#&gt; f_M1_to_M3      0.27921506 0.269425582  1.0363346 1.565282e-01  0.022977955
-#&gt; f_M2_to_M3      0.55641331 0.595121774  0.9349571 1.807710e-01  0.008002320
+  <span class='va'>m_soil</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='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span><span class='op'>)</span>,
+                    M1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"M3"</span><span class='op'>)</span>,
+                    M2 <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'>"M3"</span><span class='op'>)</span>,
+                    M3 <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>,
+                    use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
+  <span class='va'>f_soil</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_soil</span>, <span class='va'>test_data_from_UBA_2014</span><span class='op'>[[</span><span class='fl'>3</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>  <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>f_soil</span>, lpos <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span><span class='op'>)</span><span class='op'>)</span>
+</div><div class='img'><img src='test_data_from_UBA_2014-2.png' alt='' width='700' height='433' /></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_soil</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span>
+</div><div class='output co'>#&gt;                   Estimate  se_notrans    t value       Pr(&gt;t)        Lower
+#&gt; parent_0       76.55425649 0.859186399 89.1008710 1.113861e-26 74.755959406
+#&gt; k_parent        0.12081956 0.004601918 26.2541722 1.077359e-16  0.111561575
+#&gt; k_M1            0.84258614 0.806159820  1.0451850 1.545267e-01  0.113779670
+#&gt; k_M2            0.04210880 0.017083035  2.4649483 1.170188e-02  0.018013857
+#&gt; k_M3            0.01122918 0.007245855  1.5497385 6.885052e-02  0.002909431
+#&gt; f_parent_to_M1  0.32240200 0.240783909  1.3389682 9.819073e-02           NA
+#&gt; f_parent_to_M2  0.16099855 0.033691953  4.7785463 6.531137e-05           NA
+#&gt; f_M1_to_M3      0.27921507 0.269423745  1.0363417 1.565266e-01  0.022978220
+#&gt; f_M2_to_M3      0.55641253 0.595119954  0.9349586 1.807707e-01  0.008002509
 #&gt; sigma           1.14005399 0.149696423  7.6157731 1.727024e-07  0.826735778
 #&gt;                      Upper
-#&gt; parent_0       78.35255297
+#&gt; parent_0       78.35255357
 #&gt; k_parent        0.13084582
-#&gt; k_M1            6.23974738
-#&gt; k_M2            0.09843271
-#&gt; k_M3            0.04334017
+#&gt; k_M1            6.23970352
+#&gt; k_M2            0.09843260
+#&gt; k_M3            0.04333992
 #&gt; f_parent_to_M1          NA
 #&gt; f_parent_to_M2          NA
-#&gt; f_M1_to_M3      0.86450905
-#&gt; f_M2_to_M3      0.99489911
-#&gt; sigma           1.45337221</div><div class='input'>  <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_soil</span>)</div><div class='output co'>#&gt;             err.min n.optim df
+#&gt; f_M1_to_M3      0.86450768
+#&gt; f_M2_to_M3      0.99489895
+#&gt; sigma           1.45337221</div><div class='input'>  <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span><span class='op'>(</span><span class='va'>f_soil</span><span class='op'>)</span>
+</div><div class='output co'>#&gt;             err.min n.optim df
 #&gt; All data 0.09649963       9 20
 #&gt; parent   0.04721283       2  6
 #&gt; M1       0.26551208       2  5
 #&gt; M2       0.20327575       2  5
-#&gt; M3       0.05196550       3  4</div><div class='input'>  # }
+#&gt; M3       0.05196550       3  4</div><div class='input'>  <span class='co'># }</span>
 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -236,7 +246,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/transform_odeparms.html b/docs/dev/reference/transform_odeparms.html
index 0845d478..46b66073 100644
--- a/docs/dev/reference/transform_odeparms.html
+++ b/docs/dev/reference/transform_odeparms.html
@@ -232,7 +232,7 @@ This is no problem for the internal use in <a href='mkinfit.html'>mkinfit</a>.</
 <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='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span>, sink <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
   m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
 <span class='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='va'>fit.s</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
 <span class='co'># Transformed and backtransformed parameters</span>
@@ -252,7 +252,7 @@ This is no problem for the internal use in <a href='mkinfit.html'>mkinfit</a>.</
 <span class='co'># \dontrun{</span>
 <span class='co'># Compare to the version without transforming rate parameters</span>
 <span class='va'>fit.2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_D</span>, transform_rates <span class='op'>=</span> <span class='cn'>FALSE</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; <span class='error'>Error in if (cost &lt; cost.current) {    assign("cost.current", cost, inherits = TRUE)    if (!quiet)         cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"),             " at call ", calls, ": ", signif(cost.current, 6),             "\n", sep = "")}: missing value where TRUE/FALSE needed</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0.002 0 0.003</span></div><div class='input'><span class='va'>fit.2.s</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; <span class='error'>Error in if (cost &lt; cost.current) {    assign("cost.current", cost, inherits = TRUE)    if (!quiet)         cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"),             " at call ", calls, ": ", signif(cost.current, 6),             "\n", sep = "")}: missing value where TRUE/FALSE needed</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0.006 0 0.005</span></div><div class='input'><span class='va'>fit.2.s</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; <span class='error'>Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'summary': object 'fit.2' not found</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; <span class='error'>Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'print': object 'fit.2.s' not found</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; <span class='error'>Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'print': object 'fit.2.s' not found</span></div><div class='input'><span class='co'># }</span>
@@ -272,7 +272,7 @@ This is no problem for the internal use in <a href='mkinfit.html'>mkinfit</a>.</
   parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span>, sink <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
   m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>,
   use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
 <span class='va'>fit.ff</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.ff</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='va'>fit.ff.s</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.ff</span><span class='op'>)</span>
 <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.ff.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span>
@@ -297,7 +297,7 @@ This is no problem for the internal use in <a href='mkinfit.html'>mkinfit</a>.</
   parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span>, sink <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>,
   m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>,
   use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
 
 <span class='va'>fit.ff.2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.ff.2</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='va'>fit.ff.2.s</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.ff.2</span><span class='op'>)</span>
diff --git a/docs/dev/reference/update.mkinfit-1.png b/docs/dev/reference/update.mkinfit-1.png
index 4cbefa56..7d2f1bdb 100644
--- a/docs/dev/reference/update.mkinfit-1.png
+++ b/docs/dev/reference/update.mkinfit-1.png
diff --git a/docs/dev/reference/update.mkinfit-2.png b/docs/dev/reference/update.mkinfit-2.png
index f432f6f8..8dcabcdc 100644
--- a/docs/dev/reference/update.mkinfit-2.png
+++ b/docs/dev/reference/update.mkinfit-2.png
diff --git a/docs/dev/reference/update.mkinfit.html b/docs/dev/reference/update.mkinfit.html
index d6363edf..10a93373 100644
--- a/docs/dev/reference/update.mkinfit.html
+++ b/docs/dev/reference/update.mkinfit.html
@@ -75,7 +75,7 @@ override these starting values." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -123,7 +123,7 @@ override these starting values." />
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -142,7 +142,7 @@ override these starting values." />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Update an mkinfit model with different arguments</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/update.mkinfit.R'><code>R/update.mkinfit.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/update.mkinfit.R'><code>R/update.mkinfit.R</code></a></small>
     <div class="hidden name"><code>update.mkinfit.Rd</code></div>
     </div>
 
@@ -154,7 +154,7 @@ override these starting values.</p>
     </div>
 
     <pre class="usage"><span class='co'># S3 method for mkinfit</span>
-<span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>object</span>, <span class='no'>...</span>, <span class='kw'>evaluate</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+<span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span>, evaluate <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -178,11 +178,15 @@ remove arguments given in the original call</p></td>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='co'># \dontrun{</span>
-<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFO"</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt;      parent_0 k_parent_sink         sigma 
-#&gt;   99.44423886    0.09793574    3.39632469 </div><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_err</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='update.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='no'>fit_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>fit</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>)
-<span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit_2</span>)</div><div class='output co'>#&gt;      parent_0 k_parent_sink     sigma_low      rsd_high 
-#&gt;  1.008549e+02  1.005665e-01  3.752222e-03  6.763434e-02 </div><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_err</a></span>(<span class='no'>fit_2</span>)</div><div class='img'><img src='update.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'># }
+<span class='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/subset.html'>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>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='fu'><a href='parms.html'>parms</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
+</div><div class='output co'>#&gt;    parent_0    k_parent       sigma 
+#&gt; 99.44423885  0.09793574  3.39632469 </div><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_err</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
+</div><div class='img'><img src='update.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='va'>fit_2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>fit</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
+<span class='fu'><a href='parms.html'>parms</a></span><span class='op'>(</span><span class='va'>fit_2</span><span class='op'>)</span>
+</div><div class='output co'>#&gt;     parent_0     k_parent    sigma_low     rsd_high 
+#&gt; 1.008549e+02 1.005665e-01 3.752222e-03 6.763434e-02 </div><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_err</a></span><span class='op'>(</span><span class='va'>fit_2</span><span class='op'>)</span>
+</div><div class='img'><img src='update.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -199,7 +203,7 @@ remove arguments given in the original call</p></td>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/man/nlme.mmkin.Rd b/man/nlme.mmkin.Rd
index 0a9f6913..7a72a19a 100644
--- a/man/nlme.mmkin.Rd
+++ b/man/nlme.mmkin.Rd
@@ -35,8 +35,10 @@
 \item{fixed}{Ignored, all degradation parameters fitted in the
 mmkin model are used as fixed parameters}
 
-\item{random}{If not specified, all fixed effects are complemented
-with uncorrelated random effects}
+\item{random}{If not specified, correlated random effects are set up
+for all optimised degradation model parameters using the log-Cholesky
+parameterization \link[nlme:pdLogChol]{nlme::pdLogChol} that is also the default of
+the generic \link{nlme} method.}
 
 \item{groups}{See the documentation of nlme}
 
diff --git a/vignettes/web_only/mkin_benchmarks.rda b/vignettes/web_only/mkin_benchmarks.rda
index 576e7110..4cd33ca1 100644
--- a/vignettes/web_only/mkin_benchmarks.rda
+++ b/vignettes/web_only/mkin_benchmarks.rda
author	Johannes Ranke <jranke@uni-bremen.de>	2020-11-30 16:05:10 +0100
committer	Johannes Ranke <jranke@uni-bremen.de>	2020-11-30 16:05:10 +0100
commit	524a8bba89b95840b4e9215c403947a8bb76d7b2 (patch)
tree	f28717d46b0ac95bd56d4b84ee4fb770364b91ba
parent	78884beed74c18c99521b9ceeaa643e13cf94c06 (diff)