Fully rebuild docs, rerun tests and check

author: Johannes Ranke <jranke@uni-bremen.de> 2021-02-15 17:36:12 +0100
committer: Johannes Ranke <jranke@uni-bremen.de> 2021-02-15 17:36:12 +0100
commit: b9be19af5e3085216d0cd5af439332f631fa8b92 (patch)
tree: e10511f60e7f1713b781d5ea2acf885f3d1e6767 /docs
parent: 11c7f26dd6c532d977d9875f3c16952c7bba37ca (diff)
176 files changed, 983 insertions, 703 deletions
diff --git a/docs/dev/404.html b/docs/dev/404.html
index ea547a2a..f9e51aa3 100644
--- a/docs/dev/404.html
+++ b/docs/dev/404.html
@@ -71,7 +71,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://pkgdown.jrwb.de/mkin/index.html">mkin</a>
-        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.2.9000</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
diff --git a/docs/dev/articles/FOCUS_D.html b/docs/dev/articles/FOCUS_D.html
index dd86f677..a35a255a 100644
--- a/docs/dev/articles/FOCUS_D.html
+++ b/docs/dev/articles/FOCUS_D.html
@@ -32,7 +32,7 @@
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -81,7 +81,7 @@
 <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -95,14 +95,13 @@
 
       
 
-      </header><link href="FOCUS_D_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
-<script src="FOCUS_D_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
+      </header><script src="FOCUS_D_files/header-attrs-2.6/header-attrs.js"></script><script src="FOCUS_D_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Example evaluation of FOCUS Example Dataset D</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2020-11-30</h4>
+            <h4 class="date">Last change 31 January 2019 (rebuilt 2021-02-15)</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>
@@ -187,10 +186,10 @@
 <p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code> objects.</p>
 <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
 <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 
+<pre><code>## mkin version used for fitting:    1.0.3.9000 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Mon Nov 30 16:01:50 2020 
-## Date of summary: Mon Nov 30 16:01:50 2020 
+## Date of fit:     Mon Feb 15 17:13:36 2021 
+## Date of summary: Mon Feb 15 17:13:37 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -241,11 +240,11 @@
 ## 
 ## Parameter correlation:
 ##                   parent_0 log_k_parent   log_k_m1 f_parent_qlogis      sigma
-## parent_0         1.000e+00    5.174e-01 -1.688e-01      -5.471e-01 -1.171e-06
-## log_k_parent     5.174e-01    1.000e+00 -3.263e-01      -5.426e-01 -8.481e-07
-## log_k_m1        -1.688e-01   -3.263e-01  1.000e+00       7.478e-01  8.209e-07
+## parent_0         1.000e+00    5.174e-01 -1.688e-01      -5.471e-01 -1.172e-06
+## log_k_parent     5.174e-01    1.000e+00 -3.263e-01      -5.426e-01 -8.483e-07
+## log_k_m1        -1.688e-01   -3.263e-01  1.000e+00       7.478e-01  8.205e-07
 ## f_parent_qlogis -5.471e-01   -5.426e-01  7.478e-01       1.000e+00  1.305e-06
-## sigma           -1.171e-06   -8.481e-07  8.209e-07       1.305e-06  1.000e+00
+## sigma           -1.172e-06   -8.483e-07  8.205e-07       1.305e-06  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
diff --git a/docs/dev/articles/FOCUS_D_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/dev/articles/FOCUS_D_files/accessible-code-block-0.0.1/empty-anchor.js
new file mode 100644
index 00000000..ca349fd6
--- /dev/null
+++ b/docs/dev/articles/FOCUS_D_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});
diff --git a/docs/dev/articles/FOCUS_D_files/figure-html/plot-1.png b/docs/dev/articles/FOCUS_D_files/figure-html/plot-1.png
index 8ddca415..abf26715 100644
--- a/docs/dev/articles/FOCUS_D_files/figure-html/plot-1.png
+++ b/docs/dev/articles/FOCUS_D_files/figure-html/plot-1.png
diff --git a/docs/dev/articles/FOCUS_D_files/header-attrs-2.6/header-attrs.js b/docs/dev/articles/FOCUS_D_files/header-attrs-2.6/header-attrs.js
new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/dev/articles/FOCUS_D_files/header-attrs-2.6/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
diff --git a/docs/dev/articles/FOCUS_L.html b/docs/dev/articles/FOCUS_L.html
index 2695db5e..547ec630 100644
--- a/docs/dev/articles/FOCUS_L.html
+++ b/docs/dev/articles/FOCUS_L.html
@@ -32,7 +32,7 @@
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -81,7 +81,7 @@
 <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -95,14 +95,13 @@
 
       
 
-      </header><link href="FOCUS_L_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
-<script src="FOCUS_L_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
+      </header><script src="FOCUS_L_files/header-attrs-2.6/header-attrs.js"></script><script src="FOCUS_L_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Example evaluation of FOCUS Laboratory Data L1 to L3</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2020-11-30</h4>
+            <h4 class="date">Last change 17 November 2016 (rebuilt 2021-02-15)</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>
@@ -128,10 +127,10 @@
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">m.L1.SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_L1_mkin</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/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 
+<pre><code>## mkin version used for fitting:    1.0.3.9000 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Mon Nov 30 16:01:52 2020 
-## Date of summary: Mon Nov 30 16:01:52 2020 
+## Date of fit:     Mon Feb 15 17:13:39 2021 
+## Date of summary: Mon Feb 15 17:13:39 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -234,17 +233,17 @@
 <pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre>
 <pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
 ## doubtful</code></pre>
-<pre><code>## mkin version used for fitting:    0.9.50.4 
+<pre><code>## mkin version used for fitting:    1.0.3.9000 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Mon Nov 30 16:01:53 2020 
-## Date of summary: Mon Nov 30 16:01:53 2020 
+## Date of fit:     Mon Feb 15 17:13:40 2021 
+## Date of summary: Mon Feb 15 17:13:40 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 380 model solutions performed in 0.087 s
+## Fitted using 369 model solutions performed in 0.084 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -272,22 +271,22 @@
 ## 
 ## Results:
 ## 
-##        AIC      BIC    logLik
-##   95.88778 99.44927 -43.94389
+##        AIC      BIC   logLik
+##   95.88781 99.44929 -43.9439
 ## 
 ## Optimised, transformed parameters with symmetric confidence intervals:
 ##           Estimate Std. Error  Lower  Upper
 ## parent_0     92.47     1.2820 89.720 95.220
-## log_alpha    16.92        NaN    NaN    NaN
-## log_beta     19.26        NaN    NaN    NaN
-## sigma         2.78     0.4501  1.814  3.745
+## log_alpha    13.78        NaN    NaN    NaN
+## log_beta     16.13        NaN    NaN    NaN
+## sigma         2.78     0.4598  1.794  3.766
 ## 
 ## Parameter correlation:
-##           parent_0 log_alpha log_beta    sigma
-## parent_0  1.000000       NaN      NaN 0.002218
-## log_alpha      NaN         1      NaN      NaN
-## log_beta       NaN       NaN        1      NaN
-## sigma     0.002218       NaN      NaN 1.000000
+##            parent_0 log_alpha log_beta     sigma
+## parent_0  1.0000000       NaN      NaN 0.0001671
+## log_alpha       NaN         1      NaN       NaN
+## log_beta        NaN       NaN        1       NaN
+## sigma     0.0001671       NaN      NaN 1.0000000
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -295,9 +294,9 @@
 ## for estimators of untransformed parameters.
 ##           Estimate t value Pr(&gt;t)  Lower  Upper
 ## parent_0 9.247e+01      NA     NA 89.720 95.220
-## alpha    2.223e+07      NA     NA     NA     NA
-## beta     2.325e+08      NA     NA     NA     NA
-## sigma    2.780e+00      NA     NA  1.814  3.745
+## alpha    9.658e+05      NA     NA     NA     NA
+## beta     1.010e+07      NA     NA     NA     NA
+## sigma    2.780e+00      NA     NA  1.794  3.766
 ## 
 ## FOCUS Chi2 error levels in percent:
 ##          err.min n.optim df
@@ -346,10 +345,10 @@
 <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p>
 <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
 <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 
+<pre><code>## mkin version used for fitting:    1.0.3.9000 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Mon Nov 30 16:01:54 2020 
-## Date of summary: Mon Nov 30 16:01:54 2020 
+## Date of fit:     Mon Feb 15 17:13:40 2021 
+## Date of summary: Mon Feb 15 17:13:40 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -391,10 +390,10 @@
 ## 
 ## Parameter correlation:
 ##             parent_0  log_alpha   log_beta      sigma
-## parent_0   1.000e+00 -1.151e-01 -2.085e-01 -7.436e-09
-## log_alpha -1.151e-01  1.000e+00  9.741e-01 -1.617e-07
-## log_beta  -2.085e-01  9.741e-01  1.000e+00 -1.386e-07
-## sigma     -7.436e-09 -1.617e-07 -1.386e-07  1.000e+00
+## parent_0   1.000e+00 -1.151e-01 -2.085e-01 -7.828e-09
+## log_alpha -1.151e-01  1.000e+00  9.741e-01 -1.602e-07
+## log_beta  -2.085e-01  9.741e-01  1.000e+00 -1.372e-07
+## sigma     -7.828e-09 -1.602e-07 -1.372e-07  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -427,10 +426,10 @@
 <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p>
 <div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
 <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 
+<pre><code>## mkin version used for fitting:    1.0.3.9000 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Mon Nov 30 16:01:54 2020 
-## Date of summary: Mon Nov 30 16:01:54 2020 
+## Date of fit:     Mon Feb 15 17:13:41 2021 
+## Date of summary: Mon Feb 15 17:13:41 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -439,7 +438,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 581 model solutions performed in 0.136 s
+## Fitted using 581 model solutions performed in 0.134 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -470,18 +469,18 @@
 ## Optimised, transformed parameters with symmetric confidence intervals:
 ##          Estimate Std. Error      Lower     Upper
 ## parent_0   93.950  9.998e-01    91.5900   96.3100
-## log_k1      3.117  1.929e+03 -4558.0000 4564.0000
+## log_k1      3.112  1.842e+03 -4353.0000 4359.0000
 ## log_k2     -1.088  6.285e-02    -1.2370   -0.9394
 ## g_qlogis   -0.399  9.946e-02    -0.6342   -0.1638
 ## sigma       1.414  2.886e-01     0.7314    2.0960
 ## 
 ## Parameter correlation:
-##           parent_0     log_k1     log_k2   g_qlogis      sigma
-## parent_0 1.000e+00  6.459e-07  9.147e-11  2.665e-01  8.413e-11
-## log_k1   6.459e-07  1.000e+00  1.061e-04 -2.087e-04 -9.802e-06
-## log_k2   9.147e-11  1.061e-04  1.000e+00 -7.903e-01 -2.429e-09
-## g_qlogis 2.665e-01 -2.087e-04 -7.903e-01  1.000e+00  4.049e-09
-## sigma    8.413e-11 -9.802e-06 -2.429e-09  4.049e-09  1.000e+00
+##            parent_0     log_k1     log_k2   g_qlogis      sigma
+## parent_0  1.000e+00  6.783e-07 -3.390e-10  2.665e-01 -2.967e-10
+## log_k1    6.783e-07  1.000e+00  1.116e-04 -2.196e-04 -1.031e-05
+## log_k2   -3.390e-10  1.116e-04  1.000e+00 -7.903e-01  2.917e-09
+## g_qlogis  2.665e-01 -2.196e-04 -7.903e-01  1.000e+00 -4.408e-09
+## sigma    -2.967e-10 -1.031e-05  2.917e-09 -4.408e-09  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -489,7 +488,7 @@
 ## for estimators of untransformed parameters.
 ##          Estimate   t value    Pr(&gt;t)   Lower   Upper
 ## parent_0  93.9500 9.397e+01 2.036e-12 91.5900 96.3100
-## k1        22.5800 5.303e-04 4.998e-01  0.0000     Inf
+## k1        22.4800 5.553e-04 4.998e-01  0.0000     Inf
 ## k2         0.3369 1.591e+01 4.697e-07  0.2904  0.3909
 ## g          0.4016 1.680e+01 3.238e-07  0.3466  0.4591
 ## sigma      1.4140 4.899e+00 8.776e-04  0.7314  2.0960
@@ -501,7 +500,7 @@
 ## 
 ## Estimated disappearance times:
 ##          DT50  DT90 DT50back DT50_k1 DT50_k2
-## parent 0.5335 5.311    1.599  0.0307   2.058</code></pre>
+## parent 0.5335 5.311    1.599 0.03084   2.058</code></pre>
 <p>Here, the DFOP model is clearly the best-fit model for dataset L2 based on the chi^2 error level criterion. However, the failure to calculate the covariance matrix indicates that the parameter estimates correlate excessively. Therefore, the FOMC model may be preferred for this dataset.</p>
 </div>
 </div>
@@ -533,10 +532,10 @@
 <p>We can extract the summary and plot for <em>e.g.</em> the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.</p>
 <div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
 <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 
+<pre><code>## mkin version used for fitting:    1.0.3.9000 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Mon Nov 30 16:01:55 2020 
-## Date of summary: Mon Nov 30 16:01:55 2020 
+## Date of fit:     Mon Feb 15 17:13:41 2021 
+## Date of summary: Mon Feb 15 17:13:42 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -545,7 +544,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 376 model solutions performed in 0.081 s
+## Fitted using 376 model solutions performed in 0.082 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -583,11 +582,11 @@
 ## 
 ## Parameter correlation:
 ##            parent_0     log_k1     log_k2   g_qlogis      sigma
-## parent_0  1.000e+00  1.732e-01  2.282e-02  4.009e-01 -9.671e-08
-## log_k1    1.732e-01  1.000e+00  4.945e-01 -5.809e-01  7.148e-07
+## parent_0  1.000e+00  1.732e-01  2.282e-02  4.009e-01 -9.664e-08
+## log_k1    1.732e-01  1.000e+00  4.945e-01 -5.809e-01  7.147e-07
 ## log_k2    2.282e-02  4.945e-01  1.000e+00 -6.812e-01  1.022e-06
-## g_qlogis  4.009e-01 -5.809e-01 -6.812e-01  1.000e+00 -7.929e-07
-## sigma    -9.671e-08  7.148e-07  1.022e-06 -7.929e-07  1.000e+00
+## g_qlogis  4.009e-01 -5.809e-01 -6.812e-01  1.000e+00 -7.926e-07
+## sigma    -9.664e-08  7.147e-07  1.022e-06 -7.926e-07  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -646,10 +645,10 @@
 <p>The <span class="math inline">\(\chi^2\)</span> error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the <span class="math inline">\(\chi^2\)</span> test passes is slightly lower for the FOMC model. However, the difference appears negligible.</p>
 <div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
 <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 
+<pre><code>## mkin version used for fitting:    1.0.3.9000 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Mon Nov 30 16:01:55 2020 
-## Date of summary: Mon Nov 30 16:01:55 2020 
+## Date of fit:     Mon Feb 15 17:13:42 2021 
+## Date of summary: Mon Feb 15 17:13:42 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -711,17 +710,17 @@
 ## parent  106  352</code></pre>
 <div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
 <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 
+<pre><code>## mkin version used for fitting:    1.0.3.9000 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Mon Nov 30 16:01:55 2020 
-## Date of summary: Mon Nov 30 16:01:56 2020 
+## Date of fit:     Mon Feb 15 17:13:42 2021 
+## Date of summary: Mon Feb 15 17:13:42 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 224 model solutions performed in 0.045 s
+## Fitted using 224 model solutions performed in 0.046 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -756,10 +755,10 @@
 ## 
 ## Parameter correlation:
 ##             parent_0  log_alpha   log_beta      sigma
-## parent_0   1.000e+00 -4.696e-01 -5.543e-01 -2.456e-07
-## log_alpha -4.696e-01  1.000e+00  9.889e-01  2.169e-08
-## log_beta  -5.543e-01  9.889e-01  1.000e+00  4.910e-08
-## sigma     -2.456e-07  2.169e-08  4.910e-08  1.000e+00
+## parent_0   1.000e+00 -4.696e-01 -5.543e-01 -2.468e-07
+## log_alpha -4.696e-01  1.000e+00  9.889e-01  2.478e-08
+## log_beta  -5.543e-01  9.889e-01  1.000e+00  5.211e-08
+## sigma     -2.468e-07  2.478e-08  5.211e-08  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -783,7 +782,7 @@
 <div id="references" class="section level1 unnumbered">
 <h1 class="hasAnchor">
 <a href="#references" class="anchor"></a>References</h1>
-<div id="refs" class="references">
+<div id="refs" class="references hanging-indent">
 <div id="ref-ranke2014">
 <p>Ranke, Johannes. 2014. “Prüfung und Validierung von Modellierungssoftware als Alternative zu ModelMaker 4.0.” Umweltbundesamt Projektnummer 27452.</p>
 </div>
diff --git a/docs/dev/articles/FOCUS_L_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/dev/articles/FOCUS_L_files/accessible-code-block-0.0.1/empty-anchor.js
new file mode 100644
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--- /dev/null
+++ b/docs/dev/articles/FOCUS_L_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});
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index 36e862f6..b3aa8334 100644
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index f644c299..570f0026 100644
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+++ b/docs/dev/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png
diff --git a/docs/dev/articles/FOCUS_L_files/header-attrs-2.6/header-attrs.js b/docs/dev/articles/FOCUS_L_files/header-attrs-2.6/header-attrs.js
new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/dev/articles/FOCUS_L_files/header-attrs-2.6/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html
index 57d0c0eb..17ee4a69 100644
--- a/docs/dev/articles/index.html
+++ b/docs/dev/articles/index.html
@@ -71,7 +71,7 @@
       </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">1.0.2.9000</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
diff --git a/docs/dev/articles/mkin.html b/docs/dev/articles/mkin.html
index 2de8b9f0..fed85a33 100644
--- a/docs/dev/articles/mkin.html
+++ b/docs/dev/articles/mkin.html
@@ -32,7 +32,7 @@
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -81,7 +81,7 @@
 <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -95,14 +95,13 @@
 
       
 
-      </header><link href="mkin_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
-<script src="mkin_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
+      </header><script src="mkin_files/header-attrs-2.6/header-attrs.js"></script><script src="mkin_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Introduction to mkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2020-11-30</h4>
+            <h4 class="date">Last change 15 February 2021 (rebuilt 2021-02-15)</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>
@@ -150,28 +149,34 @@
 <div id="background" class="section level1">
 <h1 class="hasAnchor">
 <a href="#background" class="anchor"></a>Background</h1>
-<p>Many approaches are possible regarding the evaluation of chemical degradation data.</p>
-<p>The <code>mkin</code> package <span class="citation">(Ranke 2019)</span> implements the approach recommended in the kinetics report provided by the FOrum for Co-ordination of pesticide fate models and their USe <span class="citation">(FOCUS Work Group on Degradation Kinetics 2006, 2014)</span> for simple decline data series, data series with transformation products, commonly termed metabolites, and for data series for more than one compartment. It is also possible to include back reactions, so equilibrium reactions and equilibrium partitioning can be specified, although this oftentimes leads to an overparameterisation of the model.</p>
+<p>The <code>mkin</code> package <span class="citation">(Ranke 2021)</span> implements the approach to degradation kinetics recommended in the kinetics report provided by the FOrum for Co-ordination of pesticide fate models and their USe <span class="citation">(FOCUS Work Group on Degradation Kinetics 2006, 2014)</span>. It covers data series describing the decline of one compound, data series with transformation products (commonly termed metabolites) and data series for more than one compartment. It is possible to include back reactions. Therefore, equilibrium reactions and equilibrium partitioning can be specified, although this often leads to an overparameterisation of the model.</p>
 <p>When the first <code>mkin</code> code was published in 2010, the most commonly used tools for fitting more complex kinetic degradation models to experimental data were KinGUI <span class="citation">(Schäfer et al. 2007)</span>, a MATLAB based tool with a graphical user interface that was specifically tailored to the task and included some output as proposed by the FOCUS Kinetics Workgroup, and ModelMaker, a general purpose compartment based tool providing infrastructure for fitting dynamic simulation models based on differential equations to data.</p>
-<p>The code was first uploaded to the BerliOS platform. When this was taken down, the version control history was imported into the R-Forge site (see <em>e.g.</em> <a href="https://cgit.jrwb.de/mkin/commit/?id=30cbb4092f6d2d3beff5800603374a0d009ad770">the initial commit on 11 May 2010</a>), where the code is still occasionally updated.</p>
-<p>At that time, the R package <code>FME</code> (Flexible Modelling Environment) <span class="citation">(Soetaert and Petzoldt 2010)</span> was already available, and provided a good basis for developing a package specifically tailored to the task. The remaining challenge was to make it as easy as possible for the users (including the author of this vignette) to specify the system of differential equations and to include the output requested by the FOCUS guidance, such as the relative standard deviation that has to be assumed for the residuals, such that the <span class="math inline">\(\chi^2\)</span> goodness-of-fit test as defined by the FOCUS kinetics workgroup would pass using an significance level <span class="math inline">\(\alpha\)</span> of 0.05. This relative error, expressed as a percentage, is often termed <span class="math inline">\(\chi^2\)</span> error level or similar.</p>
-<p>Also, <code>mkin</code> introduced using analytical solutions for parent only kinetics for improved optimization speed. Later, Eigenvalue based solutions were introduced to <code>mkin</code> for the case of linear differential equations (<em>i.e.</em> where the FOMC or DFOP models were not used for the parent compound), greatly improving the optimization speed for these cases. This, however, has become somehow obsolete, as the use of compiled code described below gives even smaller execution times.</p>
+<p>The ‘mkin’ code was first uploaded to the BerliOS development platform. When this was taken down, the version control history was imported into the R-Forge site (see <em>e.g.</em> <a href="https://cgit.jrwb.de/mkin/commit/?id=30cbb4092f6d2d3beff5800603374a0d009ad770">the initial commit on 11 May 2010</a>), where the code is still being updated.</p>
+<p>At that time, the R package <code>FME</code> (Flexible Modelling Environment) <span class="citation">(Soetaert and Petzoldt 2010)</span> was already available, and provided a good basis for developing a package specifically tailored to the task. The remaining challenge was to make it as easy as possible for the users (including the author of this vignette) to specify the system of differential equations and to include the output requested by the FOCUS guidance, such as the <span class="math inline">\(\chi^2\)</span> error level as defined in this guidance.</p>
+<p>Also, <code>mkin</code> introduced using analytical solutions for parent only kinetics for improved optimization speed. Later, Eigenvalue based solutions were introduced to <code>mkin</code> for the case of linear differential equations (<em>i.e.</em> where the FOMC or DFOP models were not used for the parent compound), greatly improving the optimization speed for these cases. This, has become somehow obsolete, as the use of compiled code described below gives even faster execution times.</p>
 <p>The possibility to specify back-reactions and a biphasic model (SFORB) for metabolites were present in <code>mkin</code> from the very beginning.</p>
 <div id="derived-software-tools" class="section level2">
 <h2 class="hasAnchor">
 <a href="#derived-software-tools" class="anchor"></a>Derived software tools</h2>
-<p>Soon after the publication of <code>mkin</code>, two derived tools were published, namely KinGUII (available from Bayer Crop Science) and CAKE (commissioned to Tessella by Syngenta), which added a graphical user interface (GUI), and added fitting by iteratively reweighted least squares (IRLS) and characterisation of likely parameter distributions by Markov Chain Monte Carlo (MCMC) sampling.</p>
-<p>CAKE focuses on a smooth use experience, sacrificing some flexibility in the model definition, originally allowing only two primary metabolites in parallel. The current version 3.3 of CAKE release in March 2016 uses a basic scheme for up to six metabolites in a flexible arrangement, but does not support back-reactions (non-instantaneous equilibria) or biphasic kinetics for metabolites.</p>
+<p>Soon after the publication of <code>mkin</code>, two derived tools were published, namely KinGUII (developed at Bayer Crop Science) and CAKE (commissioned to Tessella by Syngenta), which added a graphical user interface (GUI), and added fitting by iteratively reweighted least squares (IRLS) and characterisation of likely parameter distributions by Markov Chain Monte Carlo (MCMC) sampling.</p>
+<p>CAKE focuses on a smooth use experience, sacrificing some flexibility in the model definition, originally allowing only two primary metabolites in parallel. The current version 3.4 of CAKE released in May 2020 uses a scheme for up to six metabolites in a flexible arrangement and supports biphasic modelling of metabolites, but does not support back-reactions (non-instantaneous equilibria).</p>
 <p>KinGUI offers an even more flexible widget for specifying complex kinetic models. Back-reactions (non-instantaneous equilibria) were supported early on, but until 2014, only simple first-order models could be specified for transformation products. Starting with KinGUII version 2.1, biphasic modelling of metabolites was also available in KinGUII.</p>
 <p>A further graphical user interface (GUI) that has recently been brought to a decent degree of maturity is the browser based GUI named <code>gmkin</code>. Please see its <a href="https://pkgdown.jrwb.de/gmkin/">documentation page</a> and <a href="https://pkgdown.jrwb.de/gmkin/articles/gmkin_manual.html">manual</a> for further information.</p>
 <p>A comparison of scope, usability and numerical results obtained with these tools has been recently been published by <span class="citation">Ranke, Wöltjen, and Meinecke (2018)</span>.</p>
 </div>
-<div id="recent-developments" class="section level2">
-<h2 class="hasAnchor">
-<a href="#recent-developments" class="anchor"></a>Recent developments</h2>
-<p>Currently (July 2019), the main features available in <code>mkin</code> which are not present in KinGUII or CAKE, are the speed increase by using compiled code when a compiler is present, parallel model fitting on multicore machines using the <code>mmkin</code> function, and the estimation of parameter confidence intervals based on transformed parameters.</p>
-<p>In addition, the possibility to use two alternative error models to constant variance have been integrated. The variance by variable error model introduced by <span class="citation">Gao et al. (2011)</span> has been available via an iteratively reweighted least squares (IRLS) procedure since mkin <a href="https://pkgdown.jrwb.de/mkin/news/index.html#mkin-0-9-22-2013-10-26">version 0.9-22</a>. With <a href="https://pkgdown.jrwb.de/mkin/news/index.html#mkin-0-9-49-5-2019-07-04">release 0.9.49.5</a>, the IRLS algorithm has been replaced by direct or step-wise maximisation of the likelihood function, which makes it possible not only to fit the variance by variable error model but also a <a href="https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html">two-component error model</a> inspired by error models developed in analytical chemistry.</p>
 </div>
+<div id="unique-features" class="section level1">
+<h1 class="hasAnchor">
+<a href="#unique-features" class="anchor"></a>Unique features</h1>
+<p>Currently, the main unique features available in <code>mkin</code> are</p>
+<ul>
+<li>the <a href="https://pkgdown.jrwb.de/mkin/articles/web_only/compiled_models.html">speed increase</a> by using compiled code when a compiler is present,</li>
+<li>parallel model fitting on multicore machines using the <a href="https://pkgdown.jrwb.de/mkin/reference/mmkin.html"><code>mmkin</code> function</a>,</li>
+<li>the estimation of parameter confidence intervals based on transformed parameters (see below) and</li>
+<li>the possibility to use the <a href="https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html">two-component error model</a>
+</li>
+</ul>
+<p>The iteratively reweighted least squares fitting of different variances for each variable as introduced by <span class="citation">Gao et al. (2011)</span> has been available in mkin since <a href="https://pkgdown.jrwb.de/mkin/news/index.html#mkin-0-9-22-2013-10-26">version 0.9-22</a>. With <a href="https://pkgdown.jrwb.de/mkin/news/index.html#mkin-0-9-49-5-2019-07-04">release 0.9.49.5</a>, the IRLS algorithm has been complemented by direct or step-wise maximisation of the likelihood function, which makes it possible not only to fit the variance by variable error model but also a <a href="https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html">two-component error model</a> inspired by error models developed in analytical chemistry <span class="citation">(Ranke and Meinecke 2019)</span>.</p>
 </div>
 <div id="internal-parameter-transformations" class="section level1">
 <h1 class="hasAnchor">
@@ -179,13 +184,13 @@
 <p>For rate constants, the log transformation is used, as proposed by Bates and Watts <span class="citation">(1988, 77, 149)</span>. Approximate intervals are constructed for the transformed rate constants <span class="citation">(compare Bates and Watts 1988, 135)</span>, <em>i.e.</em> for their logarithms. Confidence intervals for the rate constants are then obtained using the appropriate backtransformation using the exponential function.</p>
 <p>In the first version of <code>mkin</code> allowing for specifying models using formation fractions, a home-made reparameterisation was used in order to ensure that the sum of formation fractions would not exceed unity.</p>
 <p>This method is still used in the current version of KinGUII (v2.1 from April 2014), with a modification that allows for fixing the pathway to sink to zero. CAKE uses penalties in the objective function in order to enforce this constraint.</p>
-<p>In 2012, an alternative reparameterisation of the formation fractions was proposed together with René Lehmann <span class="citation">(Ranke and Lehmann 2012)</span>, based on isometric logratio transformation (ILR). The aim was to improve the validity of the linear approximation of the objective function during the parameter estimation procedure as well as in the subsequent calculation of parameter confidence intervals.</p>
+<p>In 2012, an alternative reparameterisation of the formation fractions was proposed together with René Lehmann <span class="citation">(Ranke and Lehmann 2012)</span>, based on isometric logratio transformation (ILR). The aim was to improve the validity of the linear approximation of the objective function during the parameter estimation procedure as well as in the subsequent calculation of parameter confidence intervals. In the current version of mkin, a logit transformation is used for parameters that are bound between 0 and 1, such as the g parameter of the DFOP model.</p>
 <div id="confidence-intervals-based-on-transformed-parameters" class="section level2">
 <h2 class="hasAnchor">
 <a href="#confidence-intervals-based-on-transformed-parameters" class="anchor"></a>Confidence intervals based on transformed parameters</h2>
 <p>In the first attempt at providing improved parameter confidence intervals introduced to <code>mkin</code> in 2013, confidence intervals obtained from FME on the transformed parameters were simply all backtransformed one by one to yield asymmetric confidence intervals for the backtransformed parameters.</p>
 <p>However, while there is a 1:1 relation between the rate constants in the model and the transformed parameters fitted in the model, the parameters obtained by the isometric logratio transformation are calculated from the set of formation fractions that quantify the paths to each of the compounds formed from a specific parent compound, and no such 1:1 relation exists.</p>
-<p>Therefore, parameter confidence intervals for formation fractions obtained with this method only appear valid for the case of a single transformation product, where only one formation fraction is to be estimated, directly corresponding to one component of the ilr transformed parameter.</p>
+<p>Therefore, parameter confidence intervals for formation fractions obtained with this method only appear valid for the case of a single transformation product, where currently the logit transformation is used for the formation fraction.</p>
 <p>The confidence intervals obtained by backtransformation for the cases where a 1:1 relation between transformed and original parameter exist are considered by the author of this vignette to be more accurate than those obtained using a re-estimation of the Hessian matrix after backtransformation, as implemented in the FME package.</p>
 </div>
 <div id="parameter-t-test-based-on-untransformed-parameters" class="section level2">
@@ -200,36 +205,39 @@
 <h1 class="hasAnchor">
 <a href="#references" class="anchor"></a>References</h1>
 <!-- vim: set foldmethod=syntax: -->
-<div id="refs" class="references">
+<div id="refs" class="references hanging-indent">
 <div id="ref-bates1988">
 <p>Bates, D., and D. Watts. 1988. <em>Nonlinear Regression and Its Applications</em>. Wiley-Interscience.</p>
 </div>
 <div id="ref-FOCUS2006">
-<p>FOCUS Work Group on Degradation Kinetics. 2006. <em>Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration. Report of the Focus Work Group on Degradation Kinetics</em>. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="uri">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p>
+<p>FOCUS Work Group on Degradation Kinetics. 2006. <em>Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration. Report of the Focus Work Group on Degradation Kinetics</em>. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p>
 </div>
 <div id="ref-FOCUSkinetics2014">
-<p>———. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="uri">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p>
+<p>———. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p>
 </div>
 <div id="ref-gao11">
-<p>Gao, Z., J.W. Green, J. Vanderborght, and W. Schmitt. 2011. “Improving Uncertainty Analysis in Kinetic Evaluations Using Iteratively Reweighted Least Squares.” Journal. <em>Environmental Science and Technology</em> 45: 4429–37.</p>
+<p>Gao, Z., J. W. Green, J. Vanderborght, and W. Schmitt. 2011. “Improving Uncertainty Analysis in Kinetic Evaluations Using Iteratively Reweighted Least Squares.” Journal. <em>Environmental Science and Technology</em> 45: 4429–37.</p>
 </div>
 <div id="ref-pkg:mkin">
-<p>Ranke, J. 2019. <em>‘mkin‘: Kinetic Evaluation of Chemical Degradation Data</em>. <a href="https://CRAN.R-project.org/package=mkin" class="uri">https://CRAN.R-project.org/package=mkin</a>.</p>
+<p>Ranke, J. 2021. <em>‘mkin‘: Kinetic Evaluation of Chemical Degradation Data</em>. <a href="https://CRAN.R-project.org/package=mkin">https://CRAN.R-project.org/package=mkin</a>.</p>
 </div>
 <div id="ref-ranke2012">
 <p>Ranke, J., and R. Lehmann. 2012. “Parameter Reliability in Kinetic Evaluation of Environmental Metabolism Data - Assessment and the Influence of Model Specification.” In <em>SETAC World 20-24 May</em>. Berlin.</p>
 </div>
 <div id="ref-ranke2015">
-<p>———. 2015. “To T-Test or Not to T-Test, That Is the Question.” In <em>XV Symposium on Pesticide Chemistry 2-4 September 2015</em>. Piacenza. <a href="http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf" class="uri">http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf</a>.</p>
+<p>———. 2015. “To T-Test or Not to T-Test, That Is the Question.” In <em>XV Symposium on Pesticide Chemistry 2-4 September 2015</em>. Piacenza. <a href="http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf">http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf</a>.</p>
+</div>
+<div id="ref-ranke2019">
+<p>Ranke, Johannes, and Stefan Meinecke. 2019. “Error Models for the Kinetic Evaluation of Chemical Degradation Data.” <em>Environments</em> 6 (12). <a href="https://doi.org/10.3390/environments6120124">https://doi.org/10.3390/environments6120124</a>.</p>
 </div>
 <div id="ref-ranke2018">
-<p>Ranke, Johannes, Janina Wöltjen, and Stefan Meinecke. 2018. “Comparison of Software Tools for Kinetic Evaluation of Chemical Degradation Data.” <em>Environmental Sciences Europe</em> 30 (1): 17. <a href="https://doi.org/10.1186/s12302-018-0145-1" class="uri">https://doi.org/10.1186/s12302-018-0145-1</a>.</p>
+<p>Ranke, Johannes, Janina Wöltjen, and Stefan Meinecke. 2018. “Comparison of Software Tools for Kinetic Evaluation of Chemical Degradation Data.” <em>Environmental Sciences Europe</em> 30 (1): 17. <a href="https://doi.org/10.1186/s12302-018-0145-1">https://doi.org/10.1186/s12302-018-0145-1</a>.</p>
 </div>
 <div id="ref-schaefer2007">
 <p>Schäfer, D., B. Mikolasch, P. Rainbird, and B. Harvey. 2007. “KinGUI: A New Kinetic Software Tool for Evaluations According to FOCUS Degradation Kinetics.” In <em>Proceedings of the Xiii Symposium Pesticide Chemistry</em>, edited by Del Re A. A. M., Capri E., Fragoulis G., and Trevisan M., 916–23. Piacenza.</p>
 </div>
 <div id="ref-soetaert2010">
-<p>Soetaert, Karline, and Thomas Petzoldt. 2010. “Inverse Modelling, Sensitivity and Monte Carlo Analysis in R Using Package FME.” <em>Journal of Statistical Software</em> 33 (3): 1–28. <a href="https://www.jstatsoft.org/v33/i03/" class="uri">https://www.jstatsoft.org/v33/i03/</a>.</p>
+<p>Soetaert, Karline, and Thomas Petzoldt. 2010. “Inverse Modelling, Sensitivity and Monte Carlo Analysis in R Using Package FME.” <em>Journal of Statistical Software</em> 33 (3): 1–28. <a href="https://www.jstatsoft.org/v33/i03/">https://www.jstatsoft.org/v33/i03/</a>.</p>
 </div>
 </div>
 </div>
diff --git a/docs/dev/articles/mkin_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/dev/articles/mkin_files/accessible-code-block-0.0.1/empty-anchor.js
new file mode 100644
index 00000000..ca349fd6
--- /dev/null
+++ b/docs/dev/articles/mkin_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});
diff --git a/docs/dev/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/dev/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
index 9b82cd62..bf38fdd7 100644
--- a/docs/dev/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
+++ b/docs/dev/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
diff --git a/docs/dev/articles/mkin_files/header-attrs-2.6/header-attrs.js b/docs/dev/articles/mkin_files/header-attrs-2.6/header-attrs.js
new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/dev/articles/mkin_files/header-attrs-2.6/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
diff --git a/docs/dev/articles/twa.html b/docs/dev/articles/twa.html
index 42ed6fa5..30eeb5a6 100644
--- a/docs/dev/articles/twa.html
+++ b/docs/dev/articles/twa.html
@@ -32,7 +32,7 @@
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -81,7 +81,7 @@
 <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -95,14 +95,13 @@
 
       
 
-      </header><link href="twa_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
-<script src="twa_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
+      </header><script src="twa_files/header-attrs-2.6/header-attrs.js"></script><script src="twa_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Calculation of time weighted average concentrations with mkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2020-11-30</h4>
+            <h4 class="date">Last change 18 September 2019 (rebuilt 2021-02-15)</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>
@@ -143,9 +142,9 @@
   \frac{1}{k_1} \left( 1 - e^{- k_1 t_b} \right) +
   \frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)} \right)  \right) \]</span></p>
 <p>Note that a method for calculating maximum moving window time weighted average concentrations for a model fitted by ‘mkinfit’ or from parent decline model parameters is included in the <code><a href="../reference/max_twa_parent.html">max_twa_parent()</a></code> function. If the same is needed for metabolites, the function <code><a href="https://pkgdown.jrwb.de/pfm/reference/max_twa.html">pfm::max_twa()</a></code> from the ‘pfm’ package can be used.</p>
-<div id="refs" class="references">
+<div id="refs" class="references hanging-indent">
 <div id="ref-FOCUSkinetics2014">
-<p>FOCUS Work Group on Degradation Kinetics. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="uri">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p>
+<p>FOCUS Work Group on Degradation Kinetics. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p>
 </div>
 </div>
   </div>
diff --git a/docs/dev/articles/twa_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/dev/articles/twa_files/accessible-code-block-0.0.1/empty-anchor.js
new file mode 100644
index 00000000..ca349fd6
--- /dev/null
+++ b/docs/dev/articles/twa_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});
diff --git a/docs/dev/articles/twa_files/header-attrs-2.6/header-attrs.js b/docs/dev/articles/twa_files/header-attrs-2.6/header-attrs.js
new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/dev/articles/twa_files/header-attrs-2.6/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
diff --git a/docs/dev/articles/web_only/FOCUS_Z.html b/docs/dev/articles/web_only/FOCUS_Z.html
index 15c41eb7..694b33ca 100644
--- a/docs/dev/articles/web_only/FOCUS_Z.html
+++ b/docs/dev/articles/web_only/FOCUS_Z.html
@@ -32,7 +32,7 @@
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -81,7 +81,7 @@
 <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -95,14 +95,13 @@
 
       
 
-      </header><link href="FOCUS_Z_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
-<script src="FOCUS_Z_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
+      </header><script src="FOCUS_Z_files/header-attrs-2.6/header-attrs.js"></script><script src="FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Example evaluation of FOCUS dataset Z</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2020-11-30</h4>
+            <h4 class="date">Last change 16 January 2018 (rebuilt 2021-02-15)</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>
@@ -239,12 +238,12 @@
 <div class="sourceCode" id="cb34"><pre class="downlit sourceCode r">
 <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.Z.FOCUS</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></code></pre></div>
 <pre><code>##             Estimate se_notrans t value     Pr(&gt;t)     Lower      Upper
-## Z0_0       96.839001   1.994273 48.5585 4.0276e-42 92.827060 100.850943
-## k_Z0        2.215367   0.118456 18.7021 1.0410e-23  1.989432   2.466960
-## k_Z1        0.478310   0.028258 16.9265 6.2430e-22  0.424712   0.538673
-## k_Z2        0.451628   0.042139 10.7176 1.6313e-14  0.374337   0.544877
-## k_Z3        0.058692   0.015245  3.8498 1.7806e-04  0.034806   0.098972
-## f_Z2_to_Z3  0.471498   0.058350  8.0805 9.6614e-11  0.357741   0.588294
+## Z0_0       96.838822   1.994274 48.5584 4.0280e-42 92.826981 100.850664
+## k_Z0        2.215393   0.118458 18.7019 1.0413e-23  1.989456   2.466989
+## k_Z1        0.478305   0.028258 16.9266 6.2418e-22  0.424708   0.538666
+## k_Z2        0.451627   0.042139 10.7176 1.6314e-14  0.374339   0.544872
+## k_Z3        0.058692   0.015245  3.8499 1.7803e-04  0.034808   0.098965
+## f_Z2_to_Z3  0.471502   0.058351  8.0805 9.6608e-11  0.357769   0.588274
 ## sigma       3.984431   0.383402 10.3923 4.5575e-14  3.213126   4.755736</code></pre>
 <div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></code></pre></div>
@@ -255,9 +254,9 @@
 ## $distimes
 ##        DT50    DT90
 ## Z0  0.31288  1.0394
-## Z1  1.44916  4.8140
+## Z1  1.44917  4.8141
 ## Z2  1.53478  5.0984
-## Z3 11.80983 39.2314</code></pre>
+## Z3 11.80986 39.2315</code></pre>
 <p>This fit corresponds to the final result chosen in Appendix 7 of the FOCUS report. Confidence intervals returned by mkin are based on internally transformed parameters, however.</p>
 </div>
 <div id="using-the-sforb-model" class="section level1">
@@ -353,13 +352,13 @@
 ## 
 ## $SFORB
 ##     Z0_b1     Z0_b2     Z3_b1     Z3_b2 
-## 2.4471371 0.0075126 0.0800070 0.0000000 
+## 2.4471322 0.0075125 0.0800069 0.0000000 
 ## 
 ## $distimes
 ##      DT50   DT90 DT50back DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2
-## Z0 0.3043 1.1848  0.35666    0.28325     92.265         NA         NA
+## Z0 0.3043 1.1848  0.35666    0.28325     92.266         NA         NA
 ## Z1 1.5148 5.0320       NA         NA         NA         NA         NA
-## Z2 1.6414 5.4525       NA         NA         NA         NA         NA
+## Z2 1.6414 5.4526       NA         NA         NA         NA         NA
 ## Z3     NA     NA       NA         NA         NA     8.6636        Inf</code></pre>
 <p>It is clear the degradation rate of Z3 towards the end of the experiment is very low as DT50_Z3_b2 (the second Eigenvalue of the system of two differential equations representing the SFORB system for Z3, corresponding to the slower rate constant of the DFOP model) is reported to be infinity. However, this appears to be a feature of the data.</p>
 </div>
@@ -367,9 +366,9 @@
 <h1 class="hasAnchor">
 <a href="#references" class="anchor"></a>References</h1>
 <!-- vim: set foldmethod=syntax: -->
-<div id="refs" class="references">
+<div id="refs" class="references hanging-indent">
 <div id="ref-FOCUSkinetics2014">
-<p>FOCUS Work Group on Degradation Kinetics. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="uri">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p>
+<p>FOCUS Work Group on Degradation Kinetics. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p>
 </div>
 </div>
 </div>
diff --git a/docs/dev/articles/web_only/FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/dev/articles/web_only/FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js
new file mode 100644
index 00000000..ca349fd6
--- /dev/null
+++ b/docs/dev/articles/web_only/FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});
diff --git a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png
index 575def46..2213c446 100644
--- a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png
+++ b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png
diff --git a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png
index 22305ab1..61b04d3a 100644
--- a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png
+++ b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png
diff --git a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png
index 2213f493..409f1203 100644
--- a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png
+++ b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png
diff --git a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png
index fc5e5556..4d6820cd 100644
--- a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png
+++ b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png
diff --git a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png
index 5c29341c..2e504961 100644
--- a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png
+++ b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png
diff --git a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png
index 575def46..2213c446 100644
--- a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png
+++ b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png
diff --git a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png
index 98ce34a7..7ab743af 100644
--- a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png
+++ b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png
diff --git a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png
index d04a411e..2e0dce77 100644
--- a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png
+++ b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png
diff --git a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png
index 29a74490..458299c1 100644
--- a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png
+++ b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png
diff --git a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png
index 0acfa2a4..eb833066 100644
--- a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png
+++ b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png
diff --git a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png
index ca191b00..e7501cbb 100644
--- a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png
+++ b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png
diff --git a/docs/dev/articles/web_only/FOCUS_Z_files/header-attrs-2.6/header-attrs.js b/docs/dev/articles/web_only/FOCUS_Z_files/header-attrs-2.6/header-attrs.js
new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/dev/articles/web_only/FOCUS_Z_files/header-attrs-2.6/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
diff --git a/docs/dev/articles/web_only/NAFTA_examples.html b/docs/dev/articles/web_only/NAFTA_examples.html
index fca15672..b9784415 100644
--- a/docs/dev/articles/web_only/NAFTA_examples.html
+++ b/docs/dev/articles/web_only/NAFTA_examples.html
@@ -32,7 +32,7 @@
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -81,7 +81,7 @@
 <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -95,14 +95,13 @@
 
       
 
-      </header><link href="NAFTA_examples_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
-<script src="NAFTA_examples_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
+      </header><script src="NAFTA_examples_files/header-attrs-2.6/header-attrs.js"></script><script src="NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <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">2020-11-30</h4>
+            <h4 class="date">26 February 2019 (rebuilt 2021-02-15)</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>
@@ -158,7 +157,7 @@
 ##          Estimate   Pr(&gt;t)   Lower    Upper
 ## parent_0 9.99e+01 1.41e-26 98.8116 101.0810
 ## k1       2.67e-02 5.05e-06  0.0243   0.0295
-## k2       2.42e-12 5.00e-01  0.0000      Inf
+## k2       2.26e-12 5.00e-01  0.0000      Inf
 ## g        6.47e-01 3.67e-06  0.6248   0.6677
 ## sigma    1.27e+00 8.91e-06  0.8395   1.6929
 ## 
@@ -167,7 +166,7 @@
 ##      DT50     DT90 DT50_rep
 ## SFO  67.7 2.25e+02 6.77e+01
 ## IORE 58.2 1.07e+03 3.22e+02
-## DFOP 55.5 5.22e+11 2.86e+11
+## DFOP 55.5 5.59e+11 3.07e+11
 ## 
 ## Representative half-life:
 ## [1] 321.51</code></pre>
@@ -209,7 +208,7 @@
 ##          Estimate   Pr(&gt;t)   Lower   Upper
 ## parent_0 9.84e+01 1.24e-27 97.8078 98.9187
 ## k1       1.55e-02 4.10e-04  0.0143  0.0167
-## k2       1.10e-11 5.00e-01  0.0000     Inf
+## k2       8.63e-12 5.00e-01  0.0000     Inf
 ## g        6.89e-01 2.92e-03  0.6626  0.7142
 ## sigma    6.48e-01 2.38e-05  0.4147  0.8813
 ## 
@@ -218,7 +217,7 @@
 ##      DT50     DT90 DT50_rep
 ## SFO  86.6 2.88e+02 8.66e+01
 ## IORE 85.5 7.17e+02 2.16e+02
-## DFOP 83.6 1.03e+11 6.29e+10
+## DFOP 83.6 1.32e+11 8.04e+10
 ## 
 ## Representative half-life:
 ## [1] 215.87</code></pre>
@@ -260,7 +259,7 @@
 ##          Estimate   Pr(&gt;t)   Lower   Upper
 ## parent_0 9.66e+01 1.57e-25 95.3476 97.8979
 ## k1       2.55e-02 7.33e-06  0.0233  0.0278
-## k2       3.60e-11 5.00e-01  0.0000     Inf
+## k2       3.22e-11 5.00e-01  0.0000     Inf
 ## g        8.61e-01 7.55e-06  0.8314  0.8867
 ## sigma    1.46e+00 6.93e-06  0.9661  1.9483
 ## 
@@ -269,7 +268,7 @@
 ##      DT50     DT90 DT50_rep
 ## SFO  38.6 1.28e+02 3.86e+01
 ## IORE 34.0 1.77e+02 5.32e+01
-## DFOP 34.1 9.07e+09 1.93e+10
+## DFOP 34.1 1.01e+10 2.15e+10
 ## 
 ## Representative half-life:
 ## [1] 53.17</code></pre>
@@ -311,7 +310,7 @@
 ##          Estimate   Pr(&gt;t)   Lower    Upper
 ## parent_0 9.89e+01 9.44e-49 95.4640 102.2573
 ## k1       1.81e-02 1.75e-01  0.0116   0.0281
-## k2       2.89e-10 5.00e-01  0.0000      Inf
+## k2       3.63e-10 5.00e-01  0.0000      Inf
 ## g        6.06e-01 2.19e-01  0.4826   0.7178
 ## sigma    7.40e+00 2.97e-15  6.0201   8.7754
 ## 
@@ -320,7 +319,7 @@
 ##      DT50     DT90 DT50_rep
 ## SFO  94.3 3.13e+02 9.43e+01
 ## IORE 96.7 1.51e+03 4.55e+02
-## DFOP 96.4 4.75e+09 2.40e+09
+## DFOP 96.4 3.77e+09 1.91e+09
 ## 
 ## Representative half-life:
 ## [1] 454.55</code></pre>
@@ -422,7 +421,7 @@
 ##          Estimate   Pr(&gt;t)  Lower  Upper
 ## parent_0 9.85e+01 2.54e-20 97.390 99.672
 ## k1       1.38e-01 3.52e-05  0.131  0.146
-## k2       9.03e-13 5.00e-01  0.000    Inf
+## k2       9.02e-13 5.00e-01  0.000    Inf
 ## g        6.52e-01 8.13e-06  0.642  0.661
 ## sigma    7.88e-01 6.13e-02  0.481  1.095
 ## 
@@ -431,7 +430,7 @@
 ##      DT50     DT90 DT50_rep
 ## SFO  16.9 5.63e+01 1.69e+01
 ## IORE 11.6 3.37e+02 1.01e+02
-## DFOP 10.5 1.38e+12 7.67e+11
+## DFOP 10.5 1.38e+12 7.69e+11
 ## 
 ## Representative half-life:
 ## [1] 101.43</code></pre>
@@ -443,15 +442,16 @@
 <div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">p9b</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p9b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
 <pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre>
+<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre>
 <pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre>
 <pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
 ## doubtful</code></pre>
 <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
 <pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><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">p9b</span><span class="op">)</span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p>
-<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb45"><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">p9b</span><span class="op">)</span></code></pre></div>
 <pre><code>## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -475,12 +475,12 @@
 ## sigma             1.288 1.76e-04  0.7456  1.830
 ## 
 ## $DFOP
-##          Estimate Pr(&gt;t)   Lower   Upper
-## parent_0  94.7123     NA 93.1355 96.2891
-## k1         0.0389     NA  0.0266  0.0569
-## k2         0.0389     NA  0.0255  0.0592
-## g          0.5256     NA      NA      NA
-## sigma      1.5957     NA  0.9135  2.2779
+##          Estimate   Pr(&gt;t)   Lower   Upper
+## parent_0  94.7123 1.61e-16 93.1355 96.2891
+## k1         0.0389 1.08e-04  0.0266  0.0569
+## k2         0.0389 2.23e-04  0.0255  0.0592
+## g          0.5256      NaN      NA      NA
+## sigma      1.5957 2.50e-04  0.9135  2.2779
 ## 
 ## 
 ## DTx values:
@@ -496,15 +496,18 @@
 <div id="example-on-page-10" class="section level2">
 <h2 class="hasAnchor">
 <a href="#example-on-page-10" class="anchor"></a>Example on page 10</h2>
-<div class="sourceCode" id="cb46"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">p10</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p10"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
-<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre>
+<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre>
+<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre>
+<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
+## doubtful</code></pre>
 <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
 <pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb50"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb53"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><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">p10</span><span class="op">)</span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p>
-<div class="sourceCode" id="cb51"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb54"><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">p10</span><span class="op">)</span></code></pre></div>
 <pre><code>## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -530,9 +533,9 @@
 ## $DFOP
 ##          Estimate   Pr(&gt;t)   Lower    Upper
 ## parent_0 101.7315 1.41e-09 91.6534 111.8097
-## k1         0.0495 5.63e-03  0.0240   0.1020
-## k2         0.0495 1.93e-03  0.0272   0.0903
-## g          0.4487      NaN  0.0000   1.0000
+## k1         0.0495 6.58e-03  0.0303   0.0809
+## k2         0.0495 2.60e-03  0.0410   0.0598
+## g          0.4487 5.00e-01      NA       NA
 ## sigma      8.0152 2.50e-04  4.5886  11.4418
 ## 
 ## 
@@ -553,14 +556,14 @@
 <div id="example-on-page-11" class="section level2">
 <h2 class="hasAnchor">
 <a href="#example-on-page-11" class="anchor"></a>Example on page 11</h2>
-<div class="sourceCode" id="cb53"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb56"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">p11</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p11"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
 <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
 <pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb56"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb59"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><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">p11</span><span class="op">)</span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p>
-<div class="sourceCode" id="cb57"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb60"><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">p11</span><span class="op">)</span></code></pre></div>
 <pre><code>## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -596,10 +599,10 @@
 ##          DT50     DT90 DT50_rep
 ## SFO  2.16e+02 7.18e+02 2.16e+02
 ## IORE 9.73e+02 1.37e+08 4.11e+07
-## DFOP 3.07e+11 1.93e+12 6.97e+11
+## DFOP 3.07e+11 1.93e+12 6.98e+11
 ## 
 ## Representative half-life:
-## [1] 41148171</code></pre>
+## [1] 41148170</code></pre>
 <p>In this case, the DFOP fit reported for PestDF resulted in a negative value for the slower rate constant, which is not possible in mkin. The other results are in agreement.</p>
 </div>
 </div>
@@ -610,19 +613,21 @@
 <div id="example-on-page-12-upper-panel" class="section level2">
 <h2 class="hasAnchor">
 <a href="#example-on-page-12-upper-panel" class="anchor"></a>Example on page 12, upper panel</h2>
-<div class="sourceCode" id="cb59"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb62"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">p12a</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
 <pre><code>## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance
-## matrix
-
-## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance
 ## matrix</code></pre>
+<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre>
+<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre>
+<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre>
+<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
+## doubtful</code></pre>
 <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
 <pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb63"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb70"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><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">p12a</span><span class="op">)</span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p>
-<div class="sourceCode" id="cb64"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb71"><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">p12a</span><span class="op">)</span></code></pre></div>
 <pre><code>## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -646,12 +651,12 @@
 ## sigma             3.965     NA    NA    NA
 ## 
 ## $DFOP
-##          Estimate   Pr(&gt;t) Lower Upper
-## parent_0  100.521 2.74e-10    NA    NA
-## k1          0.124 2.53e-05    NA    NA
-## k2          0.124 2.52e-02    NA    NA
-## g           0.793 5.00e-01    NA    NA
-## sigma       7.048 2.50e-04    NA    NA
+##          Estimate   Pr(&gt;t)   Lower   Upper
+## parent_0  100.521 2.74e-10 92.2366 108.805
+## k1          0.124 2.53e-05  0.0908   0.170
+## k2          0.124 2.52e-02  0.0456   0.339
+## g           0.793      NaN      NA      NA
+## sigma       7.048 2.50e-04  4.0349  10.061
 ## 
 ## 
 ## DTx values:
@@ -666,20 +671,18 @@
 <div id="example-on-page-12-lower-panel" class="section level2">
 <h2 class="hasAnchor">
 <a href="#example-on-page-12-lower-panel" class="anchor"></a>Example on page 12, lower panel</h2>
-<div class="sourceCode" id="cb66"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb73"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">p12b</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
-<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre>
 <pre><code>## Warning in qt(alpha/2, rdf): NaNs produced</code></pre>
 <pre><code>## Warning in qt(1 - alpha/2, rdf): NaNs produced</code></pre>
-<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre>
-<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
-## doubtful</code></pre>
+<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre>
+<pre><code>## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced</code></pre>
 <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
 <pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb74"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb80"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><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">p12b</span><span class="op">)</span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p>
-<div class="sourceCode" id="cb75"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb81"><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">p12b</span><span class="op">)</span></code></pre></div>
 <pre><code>## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -704,11 +707,11 @@
 ## 
 ## $DFOP
 ##          Estimate Pr(&gt;t) Lower Upper
-## parent_0  97.6840     NA   NaN   NaN
-## k1         0.0589     NA    NA    NA
-## k2         0.0589     NA    NA    NA
-## g          0.6473     NA    NA    NA
-## sigma      3.4323     NA   NaN   NaN
+## parent_0  97.6840    NaN   NaN   NaN
+## k1         0.0589    NaN    NA    NA
+## k2         0.0589    NaN    NA    NA
+## g          0.6473    NaN    NA    NA
+## sigma      3.4323    NaN   NaN   NaN
 ## 
 ## 
 ## DTx values:
@@ -723,18 +726,14 @@
 <div id="example-on-page-13" class="section level2">
 <h2 class="hasAnchor">
 <a href="#example-on-page-13" class="anchor"></a>Example on page 13</h2>
-<div class="sourceCode" id="cb77"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb83"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">p13</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p13"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
-<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre>
-<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre>
-<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
-## doubtful</code></pre>
 <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
 <pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb83"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb86"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><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">p13</span><span class="op">)</span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p>
-<div class="sourceCode" id="cb84"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb87"><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">p13</span><span class="op">)</span></code></pre></div>
 <pre><code>## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -760,9 +759,9 @@
 ## $DFOP
 ##          Estimate Pr(&gt;t)    Lower    Upper
 ## parent_0 92.73500     NA 8.95e+01 95.92118
-## k1        0.00258     NA 4.25e-04  0.01569
-## k2        0.00258     NA 1.76e-03  0.00379
-## g         0.16452     NA       NA       NA
+## k1        0.00258     NA 4.14e-04  0.01611
+## k2        0.00258     NA 1.74e-03  0.00383
+## g         0.16452     NA 0.00e+00  1.00000
 ## sigma     3.41172     NA 2.02e+00  4.79960
 ## 
 ## 
@@ -779,7 +778,7 @@
 <div id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="section level1">
 <h1 class="hasAnchor">
 <a href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="anchor"></a>DT50 not observed in the study and DFOP problems in PestDF</h1>
-<div class="sourceCode" id="cb86"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb89"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">p14</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p14"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
 <pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre>
 <pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre>
@@ -787,10 +786,10 @@
 ## doubtful</code></pre>
 <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
 <pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb92"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb95"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><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">p14</span><span class="op">)</span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p>
-<div class="sourceCode" id="cb93"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb96"><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">p14</span><span class="op">)</span></code></pre></div>
 <pre><code>## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -817,7 +816,7 @@
 ##          Estimate   Pr(&gt;t)    Lower    Upper
 ## parent_0 1.00e+02 2.96e-28 99.40280 101.2768
 ## k1       9.53e-03 1.20e-01  0.00638   0.0143
-## k2       5.33e-12 5.00e-01  0.00000      Inf
+## k2       6.08e-12 5.00e-01  0.00000      Inf
 ## g        3.98e-01 2.19e-01  0.30481   0.4998
 ## sigma    1.17e+00 7.68e-06  0.77406   1.5610
 ## 
@@ -826,7 +825,7 @@
 ##          DT50     DT90 DT50_rep
 ## SFO  2.48e+02 8.25e+02 2.48e+02
 ## IORE 4.34e+02 2.22e+04 6.70e+03
-## DFOP 3.48e+10 3.37e+11 1.30e+11
+## DFOP 3.05e+10 2.95e+11 1.14e+11
 ## 
 ## Representative half-life:
 ## [1] 6697.44</code></pre>
@@ -835,14 +834,14 @@
 <div id="n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="section level1">
 <h1 class="hasAnchor">
 <a href="#n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="anchor"></a>N is less than 1 and DFOP fraction parameter is below zero</h1>
-<div class="sourceCode" id="cb95"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb98"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">p15a</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
 <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
 <pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb98"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb101"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><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">p15a</span><span class="op">)</span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p>
-<div class="sourceCode" id="cb99"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb102"><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">p15a</span><span class="op">)</span></code></pre></div>
 <pre><code>## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -866,12 +865,12 @@
 ## sigma             3.105 1.78e-04  1.795  4.416
 ## 
 ## $DFOP
-##          Estimate Pr(&gt;t)    Lower    Upper
-## parent_0 97.96751     NA 94.21913 101.7159
-## k1        0.00952     NA  0.00221   0.0411
-## k2        0.00952     NA  0.00626   0.0145
-## g         0.21241     NA  0.00000   1.0000
-## sigma     4.18778     NA  2.39747   5.9781
+##          Estimate   Pr(&gt;t)    Lower    Upper
+## parent_0 97.96751 2.85e-13 94.21913 101.7159
+## k1        0.00952 6.28e-02  0.00250   0.0363
+## k2        0.00952 1.27e-04  0.00646   0.0140
+## g         0.21241 5.00e-01  0.00000   1.0000
+## sigma     4.18778 2.50e-04  2.39747   5.9781
 ## 
 ## 
 ## DTx values:
@@ -882,7 +881,7 @@
 ## 
 ## Representative half-life:
 ## [1] 41.33</code></pre>
-<div class="sourceCode" id="cb101"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb104"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">p15b</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
 <pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre>
 <pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre>
@@ -890,10 +889,10 @@
 ## doubtful</code></pre>
 <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
 <pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb107"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb110"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><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">p15b</span><span class="op">)</span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p>
-<div class="sourceCode" id="cb108"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb111"><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">p15b</span><span class="op">)</span></code></pre></div>
 <pre><code>## Sums of squares:
 ##       SFO      IORE      DFOP 
@@ -911,7 +910,7 @@
 ## 
 ## $IORE
 ##                Estimate   Pr(&gt;t)    Lower  Upper
-## parent_0          99.83 1.81e-16 97.51348 102.14
+## parent_0          99.83 1.81e-16 97.51349 102.14
 ## k__iore_parent     0.38 3.22e-01  0.00352  41.05
 ## N_parent           0.00 5.00e-01 -1.07696   1.08
 ## sigma              2.21 2.57e-04  1.23245   3.19
@@ -938,16 +937,16 @@
 <div id="the-dfop-fraction-parameter-is-greater-than-1" class="section level1">
 <h1 class="hasAnchor">
 <a href="#the-dfop-fraction-parameter-is-greater-than-1" class="anchor"></a>The DFOP fraction parameter is greater than 1</h1>
-<div class="sourceCode" id="cb110"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb113"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">p16</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p16"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
 <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
 <pre><code>## The representative half-life of the IORE model is longer than the one corresponding</code></pre>
 <pre><code>## to the terminal degradation rate found with the DFOP model.</code></pre>
 <pre><code>## The representative half-life obtained from the DFOP model may be used</code></pre>
-<div class="sourceCode" id="cb115"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb118"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><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">p16</span><span class="op">)</span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p>
-<div class="sourceCode" id="cb116"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb119"><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">p16</span><span class="op">)</span></code></pre></div>
 <pre><code>## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -998,7 +997,7 @@
 <div id="references" class="section level1 unnumbered">
 <h1 class="hasAnchor">
 <a href="#references" class="anchor"></a>References</h1>
-<div id="refs" class="references">
+<div id="refs" class="references hanging-indent">
 <div id="ref-usepa2015">
 <p>US EPA. 2015. “Standard Operating Procedure for Using the NAFTA Guidance to Calculate Representative Half-Life Values and Characterizing Pesticide Degradation.”</p>
 </div>
diff --git a/docs/dev/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/dev/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js
new file mode 100644
index 00000000..ca349fd6
--- /dev/null
+++ b/docs/dev/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
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+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
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+});
diff --git a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png
index 38b251ea..f5420ce8 100644
--- a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png
+++ b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png
diff --git a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p11-1.png b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p11-1.png
index 77463495..0ae4bd9f 100644
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diff --git a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p12a-1.png b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p12a-1.png
index ccf8f77a..57a48119 100644
--- a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p12a-1.png
+++ b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p12a-1.png
diff --git a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p12b-1.png b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p12b-1.png
index 6b0dcaf2..c42d45f0 100644
--- a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p12b-1.png
+++ b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p12b-1.png
diff --git a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png
index ce177190..52dea51e 100644
--- a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png
+++ b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png
diff --git a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p14-1.png b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p14-1.png
index f2f59ff7..ca1f29be 100644
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+++ b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p14-1.png
diff --git a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png
index c5759a5b..f69e6d3b 100644
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index 3640ea68..71fcd257 100644
--- a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png
+++ b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png
diff --git a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p16-1.png b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p16-1.png
index b61f28e2..820501a3 100644
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index 8d38b89c..e264d2ea 100644
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index 3f2da285..e5b656a4 100644
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index 37274769..c9664c77 100644
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index ebcc326c..75d72e7c 100644
--- a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p8-1.png
+++ b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p8-1.png
diff --git a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png
index a6f4e763..3ce13a97 100644
--- a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png
+++ b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png
diff --git a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png
index 2a8cf947..e2cf2f83 100644
--- a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png
+++ b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png
diff --git a/docs/dev/articles/web_only/NAFTA_examples_files/header-attrs-2.6/header-attrs.js b/docs/dev/articles/web_only/NAFTA_examples_files/header-attrs-2.6/header-attrs.js
new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/dev/articles/web_only/NAFTA_examples_files/header-attrs-2.6/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
diff --git a/docs/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html
index 8e157c0f..a6d52649 100644
--- a/docs/dev/articles/web_only/benchmarks.html
+++ b/docs/dev/articles/web_only/benchmarks.html
@@ -32,7 +32,7 @@
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -81,7 +81,7 @@
 <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -95,14 +95,13 @@
 
       
 
-      </header><link href="benchmarks_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
-<script src="benchmarks_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
+      </header><script src="benchmarks_files/header-attrs-2.6/header-attrs.js"></script><script src="benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Benchmark timings for mkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2020-11-30</h4>
+            <h4 class="date">Last change 13 May 2020 (rebuilt 2021-02-15)</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>
@@ -137,17 +136,11 @@
   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>
-<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge:
-## iteration limit reached without convergence (10)
-
-## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge:
-## iteration limit reached without convergence (10)</code></pre>
-<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">t5</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>
+<span class="va">t5</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">"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">
+<div class="sourceCode" id="cb3"><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/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>,
@@ -174,7 +167,7 @@
     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>
 <span class="va">t11</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">m_synth_DFOP_par</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">DFOP_par_c</span><span class="op">)</span>,
     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>
-<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">mkin_benchmarks</span><span class="op">[</span><span class="va">system_string</span>, <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span><span class="op">(</span><span class="st">"t"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">11</span><span class="op">)</span><span class="op">]</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><span class="va">t1</span>, <span class="va">t2</span>, <span class="va">t3</span>, <span class="va">t4</span>, <span class="va">t5</span>, <span class="va">t6</span>, <span class="va">t7</span>, <span class="va">t8</span>, <span class="va">t9</span>, <span class="va">t10</span>, <span class="va">t11</span><span class="op">)</span>
 <span class="fu"><a href="https://rdrr.io/r/base/save.html">save</a></span><span class="op">(</span><span class="va">mkin_benchmarks</span>, file <span class="op">=</span> <span class="st">"~/git/mkin/vignettes/web_only/mkin_benchmarks.rda"</span><span class="op">)</span></code></pre></div>
@@ -235,6 +228,16 @@
 <td align="right">1.786</td>
 <td align="right">3.729</td>
 </tr>
+<tr class="odd">
+<td align="left">1.0.3</td>
+<td align="right">1.722</td>
+<td align="right">3.419</td>
+</tr>
+<tr class="even">
+<td align="left">1.0.3.9000</td>
+<td align="right">2.770</td>
+<td align="right">3.458</td>
+</tr>
 </tbody>
 </table>
 </div>
@@ -298,13 +301,25 @@
 <td align="right">7.251</td>
 <td align="right">2.810</td>
 </tr>
+<tr class="odd">
+<td align="left">1.0.3</td>
+<td align="right">1.402</td>
+<td align="right">6.343</td>
+<td align="right">2.802</td>
+</tr>
+<tr class="even">
+<td align="left">1.0.3.9000</td>
+<td align="right">1.405</td>
+<td align="right">6.417</td>
+<td align="right">2.824</td>
+</tr>
 </tbody>
 </table>
 </div>
 <div id="two-metabolites" class="section level3">
 <h3 class="hasAnchor">
 <a href="#two-metabolites" class="anchor"></a>Two metabolites</h3>
-<p>Constant variance (t6 and t7), two-component error model (t8 and t9), and variance by variable (t10 and t11) for one model fitted to one dataset, i.e. one fit for each test.</p>
+<p>Constant variance (t6 and t7), two-component error model (t8 and t9), and variance by variable (t10 and t11) for one model fitted to one dataset, i.e. one fit for each test.</p>
 <table class="table">
 <thead><tr class="header">
 <th align="left">mkin version</th>
@@ -388,6 +403,24 @@
 <td align="right">1.958</td>
 <td align="right">3.105</td>
 </tr>
+<tr class="odd">
+<td align="left">1.0.3</td>
+<td align="right">0.771</td>
+<td align="right">1.251</td>
+<td align="right">1.464</td>
+<td align="right">3.074</td>
+<td align="right">1.940</td>
+<td align="right">2.831</td>
+</tr>
+<tr class="even">
+<td align="left">1.0.3.9000</td>
+<td align="right">0.772</td>
+<td align="right">1.263</td>
+<td align="right">1.483</td>
+<td align="right">3.101</td>
+<td align="right">1.958</td>
+<td align="right">2.843</td>
+</tr>
 </tbody>
 </table>
 </div>
diff --git a/docs/dev/articles/web_only/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/dev/articles/web_only/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js
new file mode 100644
index 00000000..ca349fd6
--- /dev/null
+++ b/docs/dev/articles/web_only/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});
diff --git a/docs/dev/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js b/docs/dev/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js
new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/dev/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
diff --git a/docs/dev/articles/web_only/compiled_models.html b/docs/dev/articles/web_only/compiled_models.html
index a444f4bc..49a579fc 100644
--- a/docs/dev/articles/web_only/compiled_models.html
+++ b/docs/dev/articles/web_only/compiled_models.html
@@ -32,7 +32,7 @@
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -81,7 +81,7 @@
 <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -95,14 +95,13 @@
 
       
 
-      </header><link href="compiled_models_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
-<script src="compiled_models_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
+      </header><script src="compiled_models_files/header-attrs-2.6/header-attrs.js"></script><script src="compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Performance benefit by using compiled model definitions in mkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2020-11-30</h4>
+            <h4 class="date">2021-02-15</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>
@@ -160,10 +159,10 @@
   <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   0.187
-## 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>
+## 4            analytical            1    1.000   0.182
+## 3     deSolve, compiled            1    1.824   0.332
+## 2      Eigenvalue based            1    2.082   0.379
+## 1 deSolve, not compiled            1   46.181   8.405</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">
@@ -190,13 +189,13 @@
 <span class="op">}</span></code></pre></div>
 <pre><code>## Temporary DLL for differentials generated and loaded</code></pre>
 <pre><code>##                    test replications relative elapsed
-## 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>
+## 2     deSolve, compiled            1    1.000   0.541
+## 1 deSolve, not compiled            1   29.091  15.738</code></pre>
+<p>Here we get a performance benefit of a factor of 29 using the version of the differential equation model compiled from C code!</p>
+<p>This vignette was built with mkin 1.0.3.9000 on</p>
 <pre><code>## R version 4.0.3 (2020-10-10)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
-## Running under: Debian GNU/Linux 10 (buster)</code></pre>
+## Running under: Debian GNU/Linux bullseye/sid</code></pre>
 <pre><code>## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</code></pre>
 </div>
   </div>
diff --git a/docs/dev/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/dev/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js
new file mode 100644
index 00000000..ca349fd6
--- /dev/null
+++ b/docs/dev/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});
diff --git a/docs/dev/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js b/docs/dev/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js
new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/dev/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
diff --git a/docs/dev/authors.html b/docs/dev/authors.html
index 8ffb9f97..63050c0d 100644
--- a/docs/dev/authors.html
+++ b/docs/dev/authors.html
@@ -71,7 +71,7 @@
       </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">1.0.2.9000</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
diff --git a/docs/dev/index.html b/docs/dev/index.html
index ff9b201f..57328658 100644
--- a/docs/dev/index.html
+++ b/docs/dev/index.html
@@ -38,7 +38,7 @@
       </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">1.0.2.9000</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -133,23 +133,40 @@
 <div id="features" class="section level2">
 <h2 class="hasAnchor">
 <a href="#features" class="anchor"></a>Features</h2>
+<div id="general" class="section level3">
+<h3 class="hasAnchor">
+<a href="#general" class="anchor"></a>General</h3>
 <ul>
 <li>Highly flexible model specification using <a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html"><code>mkinmod</code></a>, including equilibrium reactions and using the single first-order reversible binding (SFORB) model, which will automatically create two latent state variables for the observed variable.</li>
-<li>As of version 0.9-39, fitting of several models to several datasets, optionally in parallel, is supported, see for example <a href="https://pkgdown.jrwb.de/mkin/reference/plot.mmkin.html"><code>plot.mmkin</code></a>.</li>
 <li>Model solution (forward modelling) in the function <a href="https://pkgdown.jrwb.de/mkin/reference/mkinpredict.html"><code>mkinpredict</code></a> is performed either using the analytical solution for the case of parent only degradation, an eigenvalue based solution if only simple first-order (SFO) or SFORB kinetics are used in the model, or using a numeric solver from the <code>deSolve</code> package (default is <code>lsoda</code>).</li>
-<li>If a C compiler is installed, the kinetic models are compiled from automatically generated C code, see <a href="https://pkgdown.jrwb.de/mkin/articles/web_only/compiled_models.html">vignette <code>compiled_models</code></a>. The autogeneration of C code was inspired by the <a href="https://github.com/karlines/ccSolve"><code>ccSolve</code></a> package. Thanks to Karline Soetaert for her work on that.</li>
-<li>By default, kinetic rate constants and kinetic formation fractions are transformed internally using <a href="https://pkgdown.jrwb.de/mkin/reference/transform_odeparms.html"><code>transform_odeparms</code></a> so their estimators can more reasonably be expected to follow a normal distribution. This has the side effect that no constraints are needed in the optimisation. Thanks to René Lehmann for the nice cooperation on this, especially the isometric log-ratio transformation that is now used for the formation fractions.</li>
-<li>A side effect of this is that when parameter estimates are backtransformed to match the model definition, confidence intervals calculated from standard errors are also backtransformed to the correct scale, and will not include meaningless values like negative rate constants or formation fractions adding up to more than 1, which can not occur in a single experiment with a single defined radiolabel position.</li>
 <li>The usual one-sided t-test for significant difference from zero is nevertheless shown based on estimators for the untransformed parameters.</li>
 <li>Summary and plotting functions. The <code>summary</code> of an <code>mkinfit</code> object is in fact a full report that should give enough information to be able to approximately reproduce the fit with other tools.</li>
 <li>The chi-squared error level as defined in the FOCUS kinetics guidance (see below) is calculated for each observed variable.</li>
-<li>When a metabolite decline phase is not described well by SFO kinetics, SFORB kinetics can be used for the metabolite.</li>
-<li>Three different error models can be selected using the argument <code>error_model</code> to the <a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html"><code>mkinfit</code></a> function.</li>
 <li>The ‘variance by variable’ error model which is often fitted using Iteratively Reweighted Least Squares (IRLS) should now be specified as <code>error_model = "obs"</code>.</li>
-<li>A two-component error model similar to the one proposed by <a href="https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html">Rocke and Lorenzato</a> can be selected using the argument <code>error_model = "tc"</code>.</li>
+</ul>
+</div>
+<div id="unique-in-mkin" class="section level3">
+<h3 class="hasAnchor">
+<a href="#unique-in-mkin" class="anchor"></a>Unique in mkin</h3>
+<ul>
+<li>Three different error models can be selected using the argument <code>error_model</code> to the <a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html"><code>mkinfit</code></a> function. A two-component error model similar to the one proposed by <a href="https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html">Rocke and Lorenzato</a> can be selected using the argument <code>error_model = "tc"</code>.</li>
+<li>Model comparisons using the Akaike Information Criterion (AIC) are supported which can also be used for non-constant variance. In such cases the FOCUS chi-squared error level is not meaningful.</li>
+<li>By default, kinetic rate constants and kinetic formation fractions are transformed internally using <a href="https://pkgdown.jrwb.de/mkin/reference/transform_odeparms.html"><code>transform_odeparms</code></a> so their estimators can more reasonably be expected to follow a normal distribution.</li>
+<li>When parameter estimates are backtransformed to match the model definition, confidence intervals calculated from standard errors are also backtransformed to the correct scale, and will not include meaningless values like negative rate constants or formation fractions adding up to more than 1, which cannot occur in a single experiment with a single defined radiolabel position.</li>
+<li>When a metabolite decline phase is not described well by SFO kinetics, SFORB kinetics can be used for the metabolite. Mathematically, the SFORB model is equivalent to the DFOP model used by other tools for biphasic metabolite curves. However, the SFORB model has the advantage that there is a mechanistic interpretation of the model parameters.</li>
 <li>Nonlinear mixed-effects models can be created from fits of the same degradation model to different datasets for the same compound by using the <a href="https://pkgdown.jrwb.de/mkin/reference/nlme.mmkin.html">nlme.mmkin</a> method. Note that the convergence of the nlme fits depends on the quality of the data. Convergence is better for simple models and data for many groups (e.g. soils).</li>
 </ul>
 </div>
+<div id="performance" class="section level3">
+<h3 class="hasAnchor">
+<a href="#performance" class="anchor"></a>Performance</h3>
+<ul>
+<li>Parallel fitting of several models to several datasets is supported, see for example <a href="https://pkgdown.jrwb.de/mkin/reference/plot.mmkin.html"><code>plot.mmkin</code></a>.</li>
+<li>If a C compiler is installed, the kinetic models are compiled from automatically generated C code, see <a href="https://pkgdown.jrwb.de/mkin/articles/web_only/compiled_models.html">vignette <code>compiled_models</code></a>. The autogeneration of C code was inspired by the <a href="https://github.com/karlines/ccSolve"><code>ccSolve</code></a> package. Thanks to Karline Soetaert for her work on that.</li>
+<li>Even if no compiler is installed, many degradation models still give <a href="https://pkgdown.jrwb.de/mkin/articles/web_only/benchmarks.html">very good performance</a>, as current versions of mkin also have <a href="https://jrwb.de/performance-improvements-mkin/">analytical solutions for some models with one metabolite</a>, and if SFO or SFORB are used for the parent compound, Eigenvalue based solutions of the degradation model are available.</li>
+</ul>
+</div>
+</div>
 <div id="gui" class="section level2">
 <h2 class="hasAnchor">
 <a href="#gui" class="anchor"></a>GUI</h2>
@@ -158,7 +175,7 @@
 <div id="news" class="section level2">
 <h2 class="hasAnchor">
 <a href="#news" class="anchor"></a>News</h2>
-<p>There is a ChangeLog, for the latest <a href="https://cran.r-project.org/package=mkin/news/news.html">CRAN release</a> and one for the <a href="https://github.com/jranke/mkin/blob/master/NEWS.md">github master branch</a>.</p>
+<p>There is a list of changes for the latest <a href="https://cran.r-project.org/package=mkin/news/news.html">CRAN release</a> and one for each github branch, e.g. <a href="https://github.com/jranke/mkin/blob/master/NEWS.md">the main branch</a>.</p>
 </div>
 <div id="credits-and-historical-remarks" class="section level2">
 <h2 class="hasAnchor">
@@ -171,6 +188,16 @@
 <p>In 2011, Bayer Crop Science started to distribute an R based successor to KinGUI named KinGUII whose R code is based on <code>mkin</code>, but which added, among other refinements, a closed source graphical user interface (GUI), iteratively reweighted least squares (IRLS) optimisation of the variance for each of the observed variables, and Markov Chain Monte Carlo (MCMC) simulation functionality, similar to what is available e.g. in the <code>FME</code> package.</p>
 <p>Somewhat in parallel, Syngenta has sponsored the development of an <code>mkin</code> and KinGUII based GUI application called CAKE, which also adds IRLS and MCMC, is more limited in the model formulation, but puts more weight on usability. CAKE is available for download from the <a href="https://www.tessella.com/showcase/computer-assisted-kinetic-evaluation">CAKE website</a>, where you can also find a zip archive of the R scripts derived from <code>mkin</code>, published under the GPL license.</p>
 <p>Finally, there is <a href="https://github.com/zhenglei-gao/KineticEval">KineticEval</a>, which contains a further development of the scripts used for KinGUII, so the different tools will hopefully be able to learn from each other in the future as well.</p>
+<p>Thanks to René Lehmann, formerly working at the Umweltbundesamt, for the nice cooperation cooperation on parameter transformations, especially the isometric log-ratio transformation that is now used for formation fractions in case there are more than two transformation targets.</p>
+<p>Many inspirations for improvements of mkin resulted from doing kinetic evaluations of degradation data for my clients while working at Harlan Laboratories and at Eurofins Regulatory AG, and now as an independent consultant.</p>
+<p>Funding was received from the Umweltbundesamt in the course of the projects</p>
+<ul>
+<li>Grant Number 112407 (Testing and validation of modelling software as an alternative to ModelMaker 4.0, 2014-2015)</li>
+<li>Project Number 56703 (Optimization of gmkin for routine use in the Umweltbundesamt, 2015)</li>
+<li>Project Number 112407 (Testing the feasibility of using an error model according to Rocke and Lorenzato for more realistic parameter estimates in the kinetic evaluation of degradation data, 2018-2019)</li>
+<li>Project Number 120667 (Development of objective criteria for the evaluation of the visual fit in the kinetic evaluation of degradation data, 2019-2020)</li>
+<li>Project 146839 (Checking the feasibility of using mixed-effects models for the derivation of kinetic modelling parameters from degradation studies, 2020-2021)</li>
+</ul>
 </div>
 <div id="references" class="section level2">
 <h2 class="hasAnchor">
diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html
index 1421edf4..31c392f7 100644
--- a/docs/dev/news/index.html
+++ b/docs/dev/news/index.html
@@ -71,7 +71,7 @@
       </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">1.0.2.9000</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -141,9 +141,9 @@
       <small>Source: <a href='https://github.com/jranke/mkin/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="mkin-1029000" class="section level1">
-<h1 class="page-header" data-toc-text="1.0.2.9000">
-<a href="#mkin-1029000" class="anchor"></a>mkin 1.0.2.9000<small> Unreleased </small>
+    <div id="mkin-1039000" class="section level1">
+<h1 class="page-header" data-toc-text="1.0.3.9000">
+<a href="#mkin-1039000" class="anchor"></a>mkin 1.0.3.9000<small> Unreleased </small>
 </h1>
 <div id="general" class="section level2">
 <h2 class="hasAnchor">
@@ -162,6 +162,14 @@
 </ul>
 </div>
 </div>
+    <div id="mkin-103" class="section level1">
+<h1 class="page-header" data-toc-text="1.0.3">
+<a href="#mkin-103" class="anchor"></a>mkin 1.0.3<small> Unreleased </small>
+</h1>
+<ul>
+<li>Review and update README, the ‘Introduction to mkin’ vignette and some of the help pages</li>
+</ul>
+</div>
     <div id="mkin-102" class="section level1">
 <h1 class="page-header" data-toc-text="1.0.2">
 <a href="#mkin-102" class="anchor"></a>mkin 1.0.2<small> Unreleased </small>
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index c74efaf7..4df60994 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: 2021-02-13T12:27Z
+last_built: 2021-02-15T16:08Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/AIC.mmkin.html b/docs/dev/reference/AIC.mmkin.html
index b332257e..8c791755 100644
--- a/docs/dev/reference/AIC.mmkin.html
+++ b/docs/dev/reference/AIC.mmkin.html
@@ -73,7 +73,7 @@ same dataset." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -122,7 +122,7 @@ same dataset." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -187,8 +187,7 @@ dataframe if there are several fits in the column).</p>
   <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 A"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_A</span>,
          <span class='st'>"FOCUS C"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_C</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>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation did not converge:</span>
-#&gt; <span class='warning'>false convergence (8)</span></div><div class='input'>  <span class='co'># We get a warning because the FOMC model does not converge for the</span>
+  <span class='co'># We get a warning because the FOMC model does not converge for the</span>
   <span class='co'># FOCUS A dataset, as it is well described by SFO</span>
 
   <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># We get a single number for a single fit</span>
@@ -199,15 +198,15 @@ dataframe if there are several fits in the column).</p>
   <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt;      df      AIC
 #&gt; SFO   3 55.28197
-#&gt; FOMC  4 57.28211
+#&gt; FOMC  4 57.28222
 #&gt; DFOP  5 59.28197</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span>, k <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span> <span class='co'># If we do not penalize additional parameters, we get nearly the same</span>
 </div><div class='output co'>#&gt;      df      AIC
 #&gt; SFO   3 49.28197
-#&gt; FOMC  4 49.28211
+#&gt; FOMC  4 49.28222
 #&gt; DFOP  5 49.28197</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>BIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>)</span>        <span class='co'># Comparing the BIC gives a very similar picture</span>
 </div><div class='output co'>#&gt;      df      BIC
 #&gt; SFO   3 55.52030
-#&gt; FOMC  4 57.59987
+#&gt; FOMC  4 57.59999
 #&gt; DFOP  5 59.67918</div><div class='input'>
   <span class='co'># For FOCUS C, the more complex models fit better</span>
   <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS C"</span><span class='op'>]</span><span class='op'>)</span>
diff --git a/docs/dev/reference/CAKE_export.html b/docs/dev/reference/CAKE_export.html
index d3f45bf0..e187772f 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -122,7 +122,7 @@ specified as well." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/D24_2014.html b/docs/dev/reference/D24_2014.html
index 2498c58e..9ecb6330 100644
--- a/docs/dev/reference/D24_2014.html
+++ b/docs/dev/reference/D24_2014.html
@@ -77,7 +77,7 @@ constrained by data protection regulations." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
diff --git a/docs/dev/reference/DFOP.solution.html b/docs/dev/reference/DFOP.solution.html
index 22b28732..3ee660f2 100644
--- a/docs/dev/reference/DFOP.solution.html
+++ b/docs/dev/reference/DFOP.solution.html
@@ -73,7 +73,7 @@ two exponential decline functions." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -122,7 +122,7 @@ two exponential decline functions." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/Extract.mmkin.html b/docs/dev/reference/Extract.mmkin.html
index 0c02355f..8381337a 100644
--- a/docs/dev/reference/Extract.mmkin.html
+++ b/docs/dev/reference/Extract.mmkin.html
@@ -72,7 +72,7 @@
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -121,7 +121,7 @@
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -220,7 +220,7 @@ either a list of mkinfit objects or a single mkinfit object.</p></td>
   <span class='op'>)</span>
 </div><div class='output co'>#&gt; $par
 #&gt;  parent_0 log_alpha  log_beta     sigma 
-#&gt; 99.666193  2.549849  5.050586  1.890202 
+#&gt; 99.666192  2.549850  5.050586  1.890202 
 #&gt; 
 #&gt; $objective
 #&gt; [1] 28.58291
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 16d12378..a188430d 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -125,7 +125,7 @@ in this fit." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
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 6b8a6119..0bee1c16 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -125,7 +125,7 @@ in this fit." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
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 076a66c6..460fdf0d 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -125,7 +125,7 @@ in this fit." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
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 08f1d416..c1a5fdff 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -125,7 +125,7 @@ in this fit." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/FOCUS_2006_datasets.html b/docs/dev/reference/FOCUS_2006_datasets.html
index df4651f8..fb3a8f17 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -121,7 +121,7 @@
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/FOMC.solution.html b/docs/dev/reference/FOMC.solution.html
index ed5c4d21..1a5124e0 100644
--- a/docs/dev/reference/FOMC.solution.html
+++ b/docs/dev/reference/FOMC.solution.html
@@ -73,7 +73,7 @@ a decreasing rate constant." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -122,7 +122,7 @@ a decreasing rate constant." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/HS.solution.html b/docs/dev/reference/HS.solution.html
index 8cf5c7f9..1b79e8b6 100644
--- a/docs/dev/reference/HS.solution.html
+++ b/docs/dev/reference/HS.solution.html
@@ -73,7 +73,7 @@ between them." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -122,7 +122,7 @@ between them." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/IORE.solution.html b/docs/dev/reference/IORE.solution.html
index 29d615dc..bc17319e 100644
--- a/docs/dev/reference/IORE.solution.html
+++ b/docs/dev/reference/IORE.solution.html
@@ -73,7 +73,7 @@ a concentration dependent rate constant." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -122,7 +122,7 @@ a concentration dependent rate constant." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/NAFTA_SOP_2015-1.png b/docs/dev/reference/NAFTA_SOP_2015-1.png
index 4d823d77..4f0d7833 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 4243faba..fb65fec8 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -121,7 +121,7 @@
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/NAFTA_SOP_Attachment-1.png b/docs/dev/reference/NAFTA_SOP_Attachment-1.png
index 6eb10cde..9417685e 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 de984984..311a7c61 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -121,7 +121,7 @@
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -193,7 +193,7 @@
 #&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       2.42e-12 5.00e-01  0.0000      Inf
+#&gt; k2       2.26e-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; 
@@ -202,7 +202,7 @@
 #&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 5.22e+11 2.86e+11
+#&gt; DFOP 55.5 5.59e+11 3.07e+11
 #&gt; 
 #&gt; Representative half-life:
 #&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>
diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png
index 17a35806..7f498242 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 9b97a634..54c31a3f 100644
--- a/docs/dev/reference/Rplot002.png
+++ b/docs/dev/reference/Rplot002.png
diff --git a/docs/dev/reference/Rplot006.png b/docs/dev/reference/Rplot006.png
index 730a7481..81525882 100644
--- a/docs/dev/reference/Rplot006.png
+++ b/docs/dev/reference/Rplot006.png
diff --git a/docs/dev/reference/Rplot007.png b/docs/dev/reference/Rplot007.png
index fce3b6ee..10b7455a 100644
--- a/docs/dev/reference/Rplot007.png
+++ b/docs/dev/reference/Rplot007.png
diff --git a/docs/dev/reference/SFO.solution.html b/docs/dev/reference/SFO.solution.html
index b3e7ef9a..43c434c6 100644
--- a/docs/dev/reference/SFO.solution.html
+++ b/docs/dev/reference/SFO.solution.html
@@ -72,7 +72,7 @@
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -121,7 +121,7 @@
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/SFORB.solution.html b/docs/dev/reference/SFORB.solution.html
index 9310212f..807fbe5c 100644
--- a/docs/dev/reference/SFORB.solution.html
+++ b/docs/dev/reference/SFORB.solution.html
@@ -76,7 +76,7 @@ and no substance in the bound fraction." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -125,7 +125,7 @@ and no substance in the bound fraction." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/add_err-1.png b/docs/dev/reference/add_err-1.png
index d2ce797f..9ba106db 100644
--- a/docs/dev/reference/add_err-1.png
+++ b/docs/dev/reference/add_err-1.png
diff --git a/docs/dev/reference/add_err-2.png b/docs/dev/reference/add_err-2.png
index ac220c9e..3088c40e 100644
--- a/docs/dev/reference/add_err-2.png
+++ b/docs/dev/reference/add_err-2.png
diff --git a/docs/dev/reference/add_err-3.png b/docs/dev/reference/add_err-3.png
index 40465b71..493a761a 100644
--- a/docs/dev/reference/add_err-3.png
+++ b/docs/dev/reference/add_err-3.png
diff --git a/docs/dev/reference/add_err.html b/docs/dev/reference/add_err.html
index 6ea30515..b94cef29 100644
--- a/docs/dev/reference/add_err.html
+++ b/docs/dev/reference/add_err.html
@@ -74,7 +74,7 @@ may depend on the predicted value and is specified as a standard deviation." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -123,7 +123,7 @@ may depend on the predicted value and is specified as a standard deviation." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/aw.html b/docs/dev/reference/aw.html
index ef808dd8..3b06f2a6 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -123,7 +123,7 @@ by Burnham and Anderson (2004)." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/confint.mkinfit.html b/docs/dev/reference/confint.mkinfit.html
index 89bb3d89..2237a539 100644
--- a/docs/dev/reference/confint.mkinfit.html
+++ b/docs/dev/reference/confint.mkinfit.html
@@ -79,7 +79,7 @@ method of Venzon and Moolgavkar (1988)." />
       </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">1.0.1.9000</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -285,13 +285,13 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
 <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;   4.258   0.916   3.889 </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;   4.295   1.008   3.959 </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 if we use at least 4 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;    user  system elapsed 
-#&gt;   1.459   0.088   0.907 </div><div class='input'><span class='va'>ci_profile</span>
+#&gt;   1.451   0.126   0.923 </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_sink  0.040762501 5.549764e-02
diff --git a/docs/dev/reference/create_deg_func.html b/docs/dev/reference/create_deg_func.html
index 4945d157..65a682bb 100644
--- a/docs/dev/reference/create_deg_func.html
+++ b/docs/dev/reference/create_deg_func.html
@@ -72,7 +72,7 @@
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -121,7 +121,7 @@
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -181,8 +181,8 @@
     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   0.396    1.000     0.395        0          0
-#&gt; 2    deSolve            2   0.694    1.753     0.693        0          0
+#&gt; 1 analytical            2   0.396     1.00     0.396        0          0
+#&gt; 2    deSolve            2   0.709     1.79     0.707        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>
@@ -193,8 +193,8 @@
     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   0.838    1.000     0.838    0.001          0
-#&gt; 2    deSolve            2   1.573    1.877     1.572    0.000          0
+#&gt; 1 analytical            2   0.844    1.000     0.844        0          0
+#&gt; 2    deSolve            2   1.624    1.924     1.624        0          0
 #&gt;   sys.child
 #&gt; 1         0
 #&gt; 2         0</div><div class='input'><span class='co'># }</span>
diff --git a/docs/dev/reference/dimethenamid_2018.html b/docs/dev/reference/dimethenamid_2018.html
index 21dea623..a06599df 100644
--- a/docs/dev/reference/dimethenamid_2018.html
+++ b/docs/dev/reference/dimethenamid_2018.html
@@ -77,7 +77,7 @@ constrained by data protection regulations." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
diff --git a/docs/dev/reference/endpoints.html b/docs/dev/reference/endpoints.html
index 301b454f..c9912f9c 100644
--- a/docs/dev/reference/endpoints.html
+++ b/docs/dev/reference/endpoints.html
@@ -78,7 +78,7 @@ advantage that the SFORB model can also be used for metabolites." />
       </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">1.0.2.9000</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
diff --git a/docs/dev/reference/experimental_data_for_UBA-1.png b/docs/dev/reference/experimental_data_for_UBA-1.png
index 24cb54c5..33946ded 100644
--- a/docs/dev/reference/experimental_data_for_UBA-1.png
+++ b/docs/dev/reference/experimental_data_for_UBA-1.png
diff --git a/docs/dev/reference/experimental_data_for_UBA.html b/docs/dev/reference/experimental_data_for_UBA.html
index 78e57fb0..9904370f 100644
--- a/docs/dev/reference/experimental_data_for_UBA.html
+++ b/docs/dev/reference/experimental_data_for_UBA.html
@@ -100,7 +100,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -149,7 +149,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/f_time_norm_focus.html b/docs/dev/reference/f_time_norm_focus.html
index 3421043d..852e00a0 100644
--- a/docs/dev/reference/f_time_norm_focus.html
+++ b/docs/dev/reference/f_time_norm_focus.html
@@ -73,7 +73,7 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
diff --git a/docs/dev/reference/focus_soil_moisture.html b/docs/dev/reference/focus_soil_moisture.html
index c46fd69a..0e6fea28 100644
--- a/docs/dev/reference/focus_soil_moisture.html
+++ b/docs/dev/reference/focus_soil_moisture.html
@@ -73,7 +73,7 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -122,7 +122,7 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/get_deg_func.html b/docs/dev/reference/get_deg_func.html
index a266bf5f..fb661085 100644
--- a/docs/dev/reference/get_deg_func.html
+++ b/docs/dev/reference/get_deg_func.html
@@ -72,7 +72,7 @@
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -121,7 +121,7 @@
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/ilr.html b/docs/dev/reference/ilr.html
index 98e51211..452647d6 100644
--- a/docs/dev/reference/ilr.html
+++ b/docs/dev/reference/ilr.html
@@ -73,7 +73,7 @@ transformations." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -122,7 +122,7 @@ transformations." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html
index b52ecb22..03a21517 100644
--- a/docs/dev/reference/index.html
+++ b/docs/dev/reference/index.html
@@ -71,7 +71,7 @@
       </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">1.0.2.9000</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
diff --git a/docs/dev/reference/loftest-1.png b/docs/dev/reference/loftest-1.png
index 6b918fec..d6006ecc 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 60874bd3..4d0dc551 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 4837e7f2..6afd084b 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 9c18ac30..f94eede1 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 11f2bda7..43460a65 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 abbbd3b9..9dbd547d 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -124,7 +124,7 @@ lrtest.default from the lmtest package." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/logLik.mkinfit.html b/docs/dev/reference/logLik.mkinfit.html
index 82c0654f..3e9452c6 100644
--- a/docs/dev/reference/logLik.mkinfit.html
+++ b/docs/dev/reference/logLik.mkinfit.html
@@ -76,7 +76,7 @@ the error model." />
       </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">1.0.1.9000</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
diff --git a/docs/dev/reference/logistic.solution-2.png b/docs/dev/reference/logistic.solution-2.png
index 764996df..73e6436d 100644
--- a/docs/dev/reference/logistic.solution-2.png
+++ b/docs/dev/reference/logistic.solution-2.png
diff --git a/docs/dev/reference/logistic.solution.html b/docs/dev/reference/logistic.solution.html
index 950e8a8e..ab68c99e 100644
--- a/docs/dev/reference/logistic.solution.html
+++ b/docs/dev/reference/logistic.solution.html
@@ -73,7 +73,7 @@ an increasing rate constant, supposedly caused by microbial growth" />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -122,7 +122,7 @@ an increasing rate constant, supposedly caused by microbial growth" />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -240,10 +240,10 @@ Version 1.1, 18 December 2014
   <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>m</span><span class='op'>)</span>
 </div><div class='img'><img src='logistic.solution-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='op'>(</span><span class='va'>m</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 1.057896e+02 1.9023449703 55.610119 3.768361e-16 1.016451e+02
-#&gt; kmax     6.398190e-02 0.0143201031  4.467978 3.841829e-04 3.929235e-02
+#&gt; parent_0 1.057896e+02 1.9023449590 55.610120 3.768360e-16 1.016451e+02
+#&gt; kmax     6.398190e-02 0.0143201029  4.467978 3.841828e-04 3.929235e-02
 #&gt; k0       1.612775e-04 0.0005866813  0.274898 3.940351e-01 5.846688e-08
-#&gt; r        2.263946e-01 0.1718110715  1.317695 1.061044e-01 4.335843e-02
+#&gt; r        2.263946e-01 0.1718110662  1.317695 1.061043e-01 4.335843e-02
 #&gt; sigma    5.332935e+00 0.9145907310  5.830952 4.036926e-05 3.340213e+00
 #&gt;                Upper
 #&gt; parent_0 109.9341588
diff --git a/docs/dev/reference/lrtest.mkinfit.html b/docs/dev/reference/lrtest.mkinfit.html
index b76ebc87..f2d8472e 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -125,7 +125,7 @@ and can be expressed by fixing the parameters of the other." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/max_twa_parent.html b/docs/dev/reference/max_twa_parent.html
index 25f745e9..a358568a 100644
--- a/docs/dev/reference/max_twa_parent.html
+++ b/docs/dev/reference/max_twa_parent.html
@@ -78,7 +78,7 @@ soil section of the FOCUS guidance." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -127,7 +127,7 @@ soil section of the FOCUS guidance." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/mccall81_245T-1.png b/docs/dev/reference/mccall81_245T-1.png
index 5daa5f18..91fe060e 100644
--- a/docs/dev/reference/mccall81_245T-1.png
+++ b/docs/dev/reference/mccall81_245T-1.png
diff --git a/docs/dev/reference/mccall81_245T.html b/docs/dev/reference/mccall81_245T.html
index 7179533d..f79137be 100644
--- a/docs/dev/reference/mccall81_245T.html
+++ b/docs/dev/reference/mccall81_245T.html
@@ -74,7 +74,7 @@
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -181,30 +181,30 @@
     <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)
-#&gt; T245_0              1.038550e+02 2.1847074888 47.537272 4.472189e-18
+#&gt; T245_0              1.038550e+02 2.1847074945 47.537272 4.472189e-18
 #&gt; k_T245              4.337042e-02 0.0018983965 22.845818 2.276911e-13
-#&gt; k_phenol            4.050581e-01 0.2986993400  1.356073 9.756988e-02
-#&gt; k_anisole           6.678742e-03 0.0008021439  8.326114 2.623176e-07
-#&gt; f_T245_to_phenol    6.227599e-01 0.3985340295  1.562627 6.949412e-02
-#&gt; f_phenol_to_anisole 1.000000e+00 0.6718439378  1.488441 7.867787e-02
-#&gt; sigma               2.514628e+00 0.4907558750  5.123989 6.233156e-05
+#&gt; k_phenol            4.050581e-01 0.2986993563  1.356073 9.756989e-02
+#&gt; k_anisole           6.678742e-03 0.0008021439  8.326114 2.623177e-07
+#&gt; f_T245_to_phenol    6.227599e-01 0.3985340558  1.562627 6.949413e-02
+#&gt; f_phenol_to_anisole 1.000000e+00 0.6718439825  1.488441 7.867789e-02
+#&gt; sigma               2.514628e+00 0.4907558883  5.123989 6.233157e-05
 #&gt;                            Lower        Upper
-#&gt; T245_0              99.246061370 1.084640e+02
+#&gt; T245_0              99.246061385 1.084640e+02
 #&gt; k_T245               0.039631621 4.746194e-02
-#&gt; k_phenol             0.218013878 7.525762e-01
+#&gt; k_phenol             0.218013879 7.525762e-01
 #&gt; k_anisole            0.005370739 8.305299e-03
-#&gt; f_T245_to_phenol     0.547559083 6.924813e-01
+#&gt; f_T245_to_phenol     0.547559081 6.924813e-01
 #&gt; f_phenol_to_anisole  0.000000000 1.000000e+00
 #&gt; sigma                1.706607296 3.322649e+00</div><div class='input'>    <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; $ff
 #&gt;    T245_phenol      T245_sink phenol_anisole    phenol_sink 
-#&gt;   6.227599e-01   3.772401e-01   1.000000e+00   6.894640e-11 
+#&gt;   6.227599e-01   3.772401e-01   1.000000e+00   3.773626e-10 
 #&gt; 
 #&gt; $distimes
 #&gt;               DT50      DT90
 #&gt; T245     15.982025  53.09114
 #&gt; phenol    1.711229   5.68458
-#&gt; anisole 103.784092 344.76329
+#&gt; anisole 103.784093 344.76329
 #&gt; </div><div class='input'>    <span class='co'># formation fraction from phenol to anisol is practically 1. As we cannot</span>
     <span class='co'># fix formation fractions when using the ilr transformation, we can turn of</span>
     <span class='co'># the sink in the model generation</span>
@@ -215,28 +215,28 @@
       quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>    <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span>
 </div><div class='output co'>#&gt;                      Estimate   se_notrans   t value       Pr(&gt;t)        Lower
-#&gt; T245_0           1.038550e+02 2.1623653027 48.028439 4.993108e-19 99.271020526
-#&gt; k_T245           4.337042e-02 0.0018343666 23.643268 3.573555e-14  0.039650977
-#&gt; k_phenol         4.050582e-01 0.1177237248  3.440752 1.679252e-03  0.218746585
-#&gt; k_anisole        6.678741e-03 0.0006829745  9.778903 1.872894e-08  0.005377083
-#&gt; f_T245_to_phenol 6.227599e-01 0.0342197865 18.198825 2.039410e-12  0.547975628
+#&gt; T245_0           1.038550e+02 2.1623653066 48.028439 4.993108e-19 99.271020284
+#&gt; k_T245           4.337042e-02 0.0018343666 23.643268 3.573556e-14  0.039650976
+#&gt; k_phenol         4.050582e-01 0.1177237473  3.440752 1.679254e-03  0.218746587
+#&gt; k_anisole        6.678742e-03 0.0006829745  9.778903 1.872894e-08  0.005377083
+#&gt; f_T245_to_phenol 6.227599e-01 0.0342197875 18.198824 2.039411e-12  0.547975637
 #&gt; sigma            2.514628e+00 0.3790944250  6.633250 2.875782e-06  1.710983655
 #&gt;                         Upper
-#&gt; T245_0           108.43904097
+#&gt; T245_0           108.43904074
 #&gt; k_T245             0.04743877
-#&gt; k_phenol           0.75005577
+#&gt; k_phenol           0.75005585
 #&gt; k_anisole          0.00829550
-#&gt; f_T245_to_phenol   0.69212306
+#&gt; f_T245_to_phenol   0.69212308
 #&gt; sigma              3.31827222</div><div class='input'>    <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; $ff
 #&gt;    T245_phenol      T245_sink phenol_anisole    phenol_sink 
-#&gt;   6.227599e-01   3.772401e-01   1.000000e+00   6.894640e-11 
+#&gt;   6.227599e-01   3.772401e-01   1.000000e+00   3.773626e-10 
 #&gt; 
 #&gt; $distimes
 #&gt;               DT50      DT90
 #&gt; T245     15.982025  53.09114
 #&gt; phenol    1.711229   5.68458
-#&gt; anisole 103.784092 344.76329
+#&gt; anisole 103.784093 344.76329
 #&gt; </div><div class='input'>    <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span>
 </div><div class='img'><img src='mccall81_245T-1.png' alt='' width='700' height='433' /></div><div class='input'>  <span class='co'># }</span>
 </div></pre>
diff --git a/docs/dev/reference/mixed-1.png b/docs/dev/reference/mixed-1.png
index 3400c4aa..28a376f4 100644
--- a/docs/dev/reference/mixed-1.png
+++ b/docs/dev/reference/mixed-1.png
diff --git a/docs/dev/reference/mixed.html b/docs/dev/reference/mixed.html
index 18a67af8..7bf8dd56 100644
--- a/docs/dev/reference/mixed.html
+++ b/docs/dev/reference/mixed.html
@@ -72,7 +72,7 @@
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -121,7 +121,7 @@
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -235,18 +235,16 @@
 #&gt; Status of individual fits:
 #&gt; 
 #&gt;           dataset
-#&gt; model      1  2  3  4  5  6 7  8 
-#&gt;   DFOP-SFO OK OK OK OK OK C OK OK
+#&gt; model      1  2  3  4  5  6  7  8 
+#&gt;   DFOP-SFO OK OK OK OK OK OK OK OK
 #&gt; 
 #&gt; OK: No warnings
-#&gt; C: Optimisation did not converge:
-#&gt; iteration limit reached without convergence (10)
 #&gt; 
 #&gt; Mean fitted parameters:
 #&gt;        parent_0        log_k_m1 f_parent_qlogis          log_k1          log_k2 
-#&gt;      100.606304       -8.759216       -0.002001       -3.350539       -3.989549 
+#&gt;      100.674757       -8.761916       -0.004347       -3.348812       -3.986853 
 #&gt;        g_qlogis 
-#&gt;       -0.090353 </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_mixed</span><span class='op'>)</span>
+#&gt;       -0.087392 </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_mixed</span><span class='op'>)</span>
 </div><div class='img'><img src='mixed-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
 </div></pre>
   </div>
diff --git a/docs/dev/reference/mkin_long_to_wide.html b/docs/dev/reference/mkin_long_to_wide.html
index 28a37800..6246fbe2 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -123,7 +123,7 @@ variable and several dependent variables as columns." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/mkin_wide_to_long.html b/docs/dev/reference/mkin_wide_to_long.html
index f085d162..f2bf00c1 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -123,7 +123,7 @@ mkinfit." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/mkinds.html b/docs/dev/reference/mkinds.html
index 907f8ad3..0d1de46d 100644
--- a/docs/dev/reference/mkinds.html
+++ b/docs/dev/reference/mkinds.html
@@ -75,7 +75,7 @@ provided by this package come as mkinds objects nevertheless." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -124,7 +124,7 @@ provided by this package come as mkinds objects nevertheless." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/mkindsg.html b/docs/dev/reference/mkindsg.html
index 3e4dfb39..67c6e5df 100644
--- a/docs/dev/reference/mkindsg.html
+++ b/docs/dev/reference/mkindsg.html
@@ -75,7 +75,7 @@ dataset if no data are supplied." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -124,7 +124,7 @@ dataset if no data are supplied." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -239,12 +239,12 @@ or covariates like soil pH).</p></dd>
 <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>mdsg</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; &lt;mkindsg&gt; holding 5 mkinds objects
 #&gt; Title $title:  Experimental X 
-#&gt; Occurrene of observed compounds $observed_n:
+#&gt; Occurrence of observed compounds $observed_n:
 #&gt; parent     A1 
 #&gt;      5      5 </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'>mdsg</span>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; &lt;mkindsg&gt; holding 5 mkinds objects
 #&gt; Title $title:  Experimental X 
-#&gt; Occurrene of observed compounds $observed_n:
+#&gt; Occurrence of observed compounds $observed_n:
 #&gt; parent     A1 
 #&gt;      5      5 
 #&gt; 
@@ -290,7 +290,7 @@ or covariates like soil pH).</p></dd>
 #&gt; Observation unit:  \%AR </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'>mdsg</span>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; &lt;mkindsg&gt; holding 5 mkinds objects
 #&gt; Title $title:  Experimental X 
-#&gt; Occurrene of observed compounds $observed_n:
+#&gt; Occurrence of observed compounds $observed_n:
 #&gt; parent     A1 
 #&gt;      5      5 
 #&gt; 
diff --git a/docs/dev/reference/mkinerrmin.html b/docs/dev/reference/mkinerrmin.html
index 1cff040d..94c575cb 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -122,7 +122,7 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/mkinerrplot.html b/docs/dev/reference/mkinerrplot.html
index 2324b968..7f1fd048 100644
--- a/docs/dev/reference/mkinerrplot.html
+++ b/docs/dev/reference/mkinerrplot.html
@@ -76,7 +76,7 @@ using the argument show_errplot = TRUE." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -125,7 +125,7 @@ using the argument show_errplot = TRUE." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/mkinfit-1.png b/docs/dev/reference/mkinfit-1.png
index eed9064f..de2a90a9 100644
--- a/docs/dev/reference/mkinfit-1.png
+++ b/docs/dev/reference/mkinfit-1.png
diff --git a/docs/dev/reference/mkinfit.html b/docs/dev/reference/mkinfit.html
index 6ae7b343..5910038f 100644
--- a/docs/dev/reference/mkinfit.html
+++ b/docs/dev/reference/mkinfit.html
@@ -80,7 +80,7 @@ likelihood function." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -431,17 +431,17 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6
 <span class='co'># Use shorthand notation for parent only degradation</span>
 <span class='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 <span 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 
+</div><div class='output co'>#&gt; mkin version used for fitting:    1.0.3.9000 
 #&gt; R version used for fitting:       4.0.3 
-#&gt; Date of fit:     Mon Jan 11 12:41:45 2021 
-#&gt; Date of summary: Mon Jan 11 12:41:45 2021 
+#&gt; Date of fit:     Mon Feb 15 17:09:39 2021 
+#&gt; Date of summary: Mon Feb 15 17:09:39 2021 
 #&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 0.046 s
+#&gt; Fitted using 222 model solutions performed in 0.045 s
 #&gt; 
 #&gt; Error model: Constant variance 
 #&gt; 
@@ -476,10 +476,10 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6
 #&gt; 
 #&gt; Parameter correlation:
 #&gt;             parent_0  log_alpha   log_beta     sigma
-#&gt; parent_0   1.000e+00 -1.565e-01 -3.142e-01 4.758e-08
-#&gt; log_alpha -1.565e-01  1.000e+00  9.564e-01 1.007e-07
-#&gt; log_beta  -3.142e-01  9.564e-01  1.000e+00 8.568e-08
-#&gt; sigma      4.758e-08  1.007e-07  8.568e-08 1.000e+00
+#&gt; parent_0   1.000e+00 -1.565e-01 -3.142e-01 4.772e-08
+#&gt; log_alpha -1.565e-01  1.000e+00  9.564e-01 1.005e-07
+#&gt; log_beta  -3.142e-01  9.564e-01  1.000e+00 8.541e-08
+#&gt; sigma      4.772e-08  1.005e-07  8.541e-08 1.000e+00
 #&gt; 
 #&gt; Backtransformed parameters:
 #&gt; Confidence intervals for internally transformed parameters are asymmetric.
@@ -548,7 +548,7 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6
 #&gt; ---
 #&gt; Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span><span class='op'>(</span><span class='va'>fit.tc</span><span class='op'>)</span>
 </div><div class='output co'>#&gt;       parent_0       k_parent           k_m1 f_parent_to_m1      sigma_low 
-#&gt;   1.007343e+02   1.005562e-01   5.166712e-03   5.083933e-01   3.049884e-03 
+#&gt;   1.007343e+02   1.005562e-01   5.166712e-03   5.083933e-01   3.049883e-03 
 #&gt;       rsd_high 
 #&gt;   7.928118e-02 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.tc</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; $ff
@@ -574,10 +574,10 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6
     analytical <span class='op'>=</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>,
       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; <span class='message'>Loading required package: rbenchmark</span></div><div class='output co'>#&gt;               test relative elapsed
-#&gt; 3       analytical    1.000   0.526
-#&gt; 1 deSolve_compiled    1.903   1.001
-#&gt; 2            eigen    2.308   1.214</div><div class='input'><span class='co'># }</span>
+</div><div class='output co'>#&gt;               test relative elapsed
+#&gt; 3       analytical    1.000   0.563
+#&gt; 1 deSolve_compiled    1.702   0.958
+#&gt; 2            eigen    2.597   1.462</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>
@@ -587,22 +587,21 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6
 </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>
-#&gt; <span class='warning'>iteration limit reached without convergence (10)</span></div><div class='input'><span class='co'># This model has a higher likelihood, but not significantly so</span>
+<span class='co'># This model has a higher likelihood, but not significantly so</span>
 <span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>fit.tc</span>, <span class='va'>fit.FOMC_SFO.tc</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Likelihood ratio test
 #&gt; 
 #&gt; Model 1: FOMC_SFO with error model tc and fixed parameter(s) m1_0
 #&gt; Model 2: SFO_SFO with error model tc and fixed parameter(s) m1_0
 #&gt;   #Df  LogLik Df  Chisq Pr(&gt;Chisq)
-#&gt; 1   7 -64.870                     
-#&gt; 2   6 -64.983 -1 0.2259     0.6346</div><div class='input'><span class='co'># Also, the missing standard error for log_beta and the t-tests for alpha</span>
+#&gt; 1   7 -64.829                     
+#&gt; 2   6 -64.983 -1 0.3075     0.5792</div><div class='input'><span class='co'># Also, the missing standard error for log_beta and the t-tests for alpha</span>
 <span class='co'># and beta indicate overparameterisation</span>
 <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 
+</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:    1.0.3.9000 
 #&gt; R version used for fitting:       4.0.3 
-#&gt; Date of fit:     Mon Jan 11 12:41:56 2021 
-#&gt; Date of summary: Mon Jan 11 12:41:56 2021 
+#&gt; Date of fit:     Mon Feb 15 17:09:50 2021 
+#&gt; Date of summary: Mon Feb 15 17:09:50 2021 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -611,12 +610,12 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6
 #&gt; 
 #&gt; Model predictions using solution type deSolve 
 #&gt; 
-#&gt; Fitted using 4273 model solutions performed in 3.456 s
+#&gt; Fitted using 3729 model solutions performed in 2.815 s
 #&gt; 
 #&gt; Error model: Two-component variance function 
 #&gt; 
 #&gt; Error model algorithm: d_3 
-#&gt; Three-step fitting yielded a higher likelihood than direct fitting 
+#&gt; Direct fitting and three-step fitting yield approximately the same likelihood 
 #&gt; 
 #&gt; Starting values for parameters to be optimised:
 #&gt;                 value   type
@@ -642,72 +641,67 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6
 #&gt;      value  type
 #&gt; m1_0     0 state
 #&gt; 
-#&gt; 
-#&gt; Warning(s): 
-#&gt; Optimisation did not converge:
-#&gt; iteration limit reached without convergence (10)
-#&gt; 
 #&gt; Results:
 #&gt; 
-#&gt;        AIC      BIC    logLik
-#&gt;   143.7396 155.2027 -64.86982
+#&gt;       AIC      BIC    logLik
+#&gt;   143.658 155.1211 -64.82902
 #&gt; 
 #&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt;                   Estimate Std. Error   Lower    Upper
-#&gt; parent_0         1.016e+02    1.90600 97.7400 105.5000
-#&gt; log_k_m1        -5.285e+00    0.09286 -5.4740  -5.0950
-#&gt; f_parent_qlogis  6.482e-04    0.06164 -0.1251   0.1264
-#&gt; log_alpha        5.467e+00        NaN     NaN      NaN
-#&gt; log_beta         7.750e+00        NaN     NaN      NaN
-#&gt; sigma_low        0.000e+00        NaN     NaN      NaN
-#&gt; rsd_high         7.989e-02        NaN     NaN      NaN
+#&gt;                   Estimate Std. Error     Lower      Upper
+#&gt; parent_0        101.600000  2.6400000 96.240000 107.000000
+#&gt; log_k_m1         -5.284000  0.0929100 -5.474000  -5.095000
+#&gt; f_parent_qlogis   0.001426  0.0767000 -0.155000   0.157800
+#&gt; log_alpha         5.522000  0.0077320  5.506000   5.538000
+#&gt; log_beta          7.806000        NaN       NaN        NaN
+#&gt; sigma_low         0.002488  0.0002431  0.001992   0.002984
+#&gt; rsd_high          0.079210  0.0093280  0.060180   0.098230
 #&gt; 
 #&gt; Parameter correlation:
-#&gt;                   parent_0   log_k_m1 f_parent_qlogis log_alpha log_beta
-#&gt; parent_0         1.0000000 -0.0002167         -0.6060       NaN      NaN
-#&gt; log_k_m1        -0.0002167  1.0000000          0.5474       NaN      NaN
-#&gt; f_parent_qlogis -0.6060320  0.5474423          1.0000       NaN      NaN
-#&gt; log_alpha              NaN        NaN             NaN         1      NaN
-#&gt; log_beta               NaN        NaN             NaN       NaN        1
-#&gt; sigma_low              NaN        NaN             NaN       NaN      NaN
-#&gt; rsd_high               NaN        NaN             NaN       NaN      NaN
-#&gt;                 sigma_low rsd_high
-#&gt; parent_0              NaN      NaN
-#&gt; log_k_m1              NaN      NaN
-#&gt; f_parent_qlogis       NaN      NaN
-#&gt; log_alpha             NaN      NaN
-#&gt; log_beta              NaN      NaN
-#&gt; sigma_low               1      NaN
-#&gt; rsd_high              NaN        1
+#&gt;                  parent_0  log_k_m1 f_parent_qlogis log_alpha log_beta
+#&gt; parent_0         1.000000 -0.095226        -0.76678   0.70544      NaN
+#&gt; log_k_m1        -0.095226  1.000000         0.51432  -0.14387      NaN
+#&gt; f_parent_qlogis -0.766780  0.514321         1.00000  -0.61396      NaN
+#&gt; log_alpha        0.705444 -0.143872        -0.61396   1.00000      NaN
+#&gt; log_beta              NaN       NaN             NaN       NaN        1
+#&gt; sigma_low        0.016073  0.001586         0.01548   5.87007      NaN
+#&gt; rsd_high         0.006626 -0.011700        -0.05357   0.04849      NaN
+#&gt;                 sigma_low  rsd_high
+#&gt; parent_0         0.016073  0.006626
+#&gt; log_k_m1         0.001586 -0.011700
+#&gt; f_parent_qlogis  0.015476 -0.053566
+#&gt; log_alpha        5.870075  0.048487
+#&gt; log_beta              NaN       NaN
+#&gt; sigma_low        1.000000 -0.652558
+#&gt; rsd_high        -0.652558  1.000000
 #&gt; 
 #&gt; Backtransformed parameters:
 #&gt; Confidence intervals for internally transformed parameters are asymmetric.
 #&gt; t-test (unrealistically) based on the assumption of normal distribution
 #&gt; for estimators of untransformed parameters.
 #&gt;                 Estimate t value    Pr(&gt;t)     Lower     Upper
-#&gt; parent_0       1.016e+02 32.5400 7.812e-26 97.740000 1.055e+02
-#&gt; k_m1           5.069e-03 10.0400 1.448e-11  0.004194 6.126e-03
-#&gt; f_parent_to_m1 5.002e-01 20.7300 5.001e-20  0.468800 5.315e-01
-#&gt; alpha          2.367e+02  0.6205 2.697e-01        NA        NA
-#&gt; beta           2.322e+03  0.6114 2.727e-01        NA        NA
-#&gt; sigma_low      0.000e+00     NaN       NaN       NaN       NaN
-#&gt; rsd_high       7.989e-02  8.6630 4.393e-10       NaN       NaN
+#&gt; parent_0       1.016e+02 32.7800 6.311e-26 9.624e+01 1.070e+02
+#&gt; k_m1           5.072e-03 10.1200 1.216e-11 4.196e-03 6.130e-03
+#&gt; f_parent_to_m1 5.004e-01 20.8300 4.317e-20 4.613e-01 5.394e-01
+#&gt; alpha          2.502e+02  0.5624 2.889e-01 2.463e+02 2.542e+02
+#&gt; beta           2.455e+03  0.5549 2.915e-01        NA        NA
+#&gt; sigma_low      2.488e-03  0.4843 3.158e-01 1.992e-03 2.984e-03
+#&gt; rsd_high       7.921e-02  8.4300 8.001e-10 6.018e-02 9.823e-02
 #&gt; 
 #&gt; FOCUS Chi2 error levels in percent:
 #&gt;          err.min n.optim df
-#&gt; All data   6.782       5 14
-#&gt; parent     7.142       3  6
-#&gt; m1         4.639       2  8
+#&gt; All data   6.781       5 14
+#&gt; parent     7.141       3  6
+#&gt; m1         4.640       2  8
 #&gt; 
 #&gt; Resulting formation fractions:
 #&gt;                 ff
-#&gt; parent_m1   0.5002
-#&gt; parent_sink 0.4998
+#&gt; parent_m1   0.5004
+#&gt; parent_sink 0.4996
 #&gt; 
 #&gt; Estimated disappearance times:
-#&gt;          DT50  DT90 DT50back
-#&gt; parent   6.81  22.7    6.833
-#&gt; m1     136.74 454.2       NA</div><div class='input'>
+#&gt;           DT50  DT90 DT50back
+#&gt; parent   6.812  22.7    6.834
+#&gt; m1     136.661 454.0       NA</div><div class='input'>
 <span class='co'># We can easily use starting parameters from the parent only fit (only for illustration)</span>
 <span class='va'>fit.FOMC</span> <span class='op'>=</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
 <span 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>,
diff --git a/docs/dev/reference/mkinmod.html b/docs/dev/reference/mkinmod.html
index 9a7dac6f..413f0ae1 100644
--- a/docs/dev/reference/mkinmod.html
+++ b/docs/dev/reference/mkinmod.html
@@ -78,7 +78,7 @@ mkinmod." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -127,7 +127,7 @@ mkinmod." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -348,7 +348,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
    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>,
    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/Rtmpy4eiQb/file554e573761a7.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>
+</div><div class='output co'>#&gt; <span class='message'>Copied DLL from /tmp/Rtmp92fCb2/file133ad522561845.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>
@@ -397,7 +397,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
 #&gt;     })
 #&gt;     return(predicted)
 #&gt; }
-#&gt; &lt;environment: 0x55555cac8d00&gt;</div><div class='input'>
+#&gt; &lt;environment: 0x5555572517f8&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>
diff --git a/docs/dev/reference/mkinparplot-1.png b/docs/dev/reference/mkinparplot-1.png
index dcf3e4b5..c9ed49eb 100644
--- a/docs/dev/reference/mkinparplot-1.png
+++ b/docs/dev/reference/mkinparplot-1.png
diff --git a/docs/dev/reference/mkinparplot.html b/docs/dev/reference/mkinparplot.html
index 0a989ef9..bac6e71c 100644
--- a/docs/dev/reference/mkinparplot.html
+++ b/docs/dev/reference/mkinparplot.html
@@ -73,7 +73,7 @@ mkinfit." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -122,7 +122,7 @@ mkinfit." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -176,7 +176,8 @@ effect, namely to produce a plot.</p>
   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='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='warning'>Warning: Optimisation did not converge:</span>
+#&gt; <span class='warning'>false convergence (8)</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>
   </div>
diff --git a/docs/dev/reference/mkinplot.html b/docs/dev/reference/mkinplot.html
index 417c8c73..120bddb3 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -122,7 +122,7 @@ plot.mkinfit." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/mkinpredict.html b/docs/dev/reference/mkinpredict.html
index 3221fc23..1ebaecb5 100644
--- a/docs/dev/reference/mkinpredict.html
+++ b/docs/dev/reference/mkinpredict.html
@@ -74,7 +74,7 @@ kinetic parameters and initial values for the state variables." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -123,7 +123,7 @@ kinetic parameters and initial values for the state variables." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -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     44.2   0.221</div><div class='input'>
+#&gt; 1            eigen      4.4   0.022
+#&gt; 3          deSolve     46.8   0.234</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 2e10d5f6..30377f2c 100644
--- a/docs/dev/reference/mkinresplot.html
+++ b/docs/dev/reference/mkinresplot.html
@@ -75,7 +75,7 @@ argument show_residuals = TRUE." />
       </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">1.0.1.9000</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
diff --git a/docs/dev/reference/mmkin.html b/docs/dev/reference/mmkin.html
index 65c91adf..5da1b1de 100644
--- a/docs/dev/reference/mmkin.html
+++ b/docs/dev/reference/mmkin.html
@@ -75,7 +75,7 @@ datasets specified in its first two arguments." />
       </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">1.0.1.9000</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -234,9 +234,9 @@ plotting.</p></div>
 
 <span class='va'>time_default</span>
 </div><div class='output co'>#&gt;    user  system elapsed 
-#&gt;   4.438   0.334   1.640 </div><div class='input'><span class='va'>time_1</span>
+#&gt;   4.921   0.475   1.707 </div><div class='input'><span class='va'>time_1</span>
 </div><div class='output co'>#&gt;    user  system elapsed 
-#&gt;   5.535   0.004   5.539 </div><div class='input'>
+#&gt;   5.680   0.003   5.684 </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/nafta-1.png b/docs/dev/reference/nafta-1.png
index 4d823d77..4f0d7833 100644
--- a/docs/dev/reference/nafta-1.png
+++ b/docs/dev/reference/nafta-1.png
diff --git a/docs/dev/reference/nafta.html b/docs/dev/reference/nafta.html
index bbc8797d..6fb797a5 100644
--- a/docs/dev/reference/nafta.html
+++ b/docs/dev/reference/nafta.html
@@ -76,7 +76,7 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -125,7 +125,7 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/nlme-1.png b/docs/dev/reference/nlme-1.png
index 193722c7..728cc557 100644
--- a/docs/dev/reference/nlme-1.png
+++ b/docs/dev/reference/nlme-1.png
diff --git a/docs/dev/reference/nlme-2.png b/docs/dev/reference/nlme-2.png
index c0fb6dcf..e8167455 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 b3e88428..b850eb3d 100644
--- a/docs/dev/reference/nlme.html
+++ b/docs/dev/reference/nlme.html
@@ -75,7 +75,7 @@ datasets. They are used internally by the nlme.mmkin() method." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -124,7 +124,7 @@ datasets. They are used internally by the nlme.mmkin() method." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -224,37 +224,37 @@ nlme for the case of a single grouping variable ds.</p>
 <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>m_nlme</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by maximum likelihood
 #&gt;   Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink) 
-#&gt;  Data: grouped_data 
+#&gt;   Data: grouped_data 
 #&gt;        AIC      BIC    logLik
-#&gt;   252.7798 262.1358 -121.3899
+#&gt;   300.6824 310.2426 -145.3412
 #&gt; 
 #&gt; Random effects:
 #&gt;  Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1)
 #&gt;  Level: ds
 #&gt;  Structure: Diagonal
-#&gt;             parent_0 log_k_parent_sink Residual
-#&gt; StdDev: 0.0006768135         0.6800777 2.489397
+#&gt;         parent_0 log_k_parent_sink Residual
+#&gt; StdDev: 1.697361         0.6801209 3.666073
 #&gt; 
-#&gt; Fixed effects: parent_0 + log_k_parent_sink ~ 1 
-#&gt;                       Value Std.Error DF   t-value p-value
-#&gt; parent_0          101.74884 0.6456014 44 157.60321       0
-#&gt; log_k_parent_sink  -3.05575 0.4015811 44  -7.60929       0
+#&gt; Fixed effects:  parent_0 + log_k_parent_sink ~ 1 
+#&gt;                       Value Std.Error DF  t-value p-value
+#&gt; parent_0          100.99378 1.3890416 46 72.70753       0
+#&gt; log_k_parent_sink  -3.07521 0.4018589 46 -7.65246       0
 #&gt;  Correlation: 
 #&gt;                   prnt_0
-#&gt; log_k_parent_sink 0.026 
+#&gt; log_k_parent_sink 0.027 
 #&gt; 
 #&gt; Standardized Within-Group Residuals:
 #&gt;        Min         Q1        Med         Q3        Max 
-#&gt; -2.1317488 -0.6878121  0.0828385  0.8592270  2.9529864 
+#&gt; -1.9942823 -0.5622565  0.1791579  0.7165038  2.0704781 
 #&gt; 
-#&gt; Number of Observations: 48
+#&gt; Number of Observations: 50
 #&gt; Number of Groups: 3 </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='fu'><a href='https://rdrr.io/pkg/nlme/man/augPred.html'>augPred</a></span><span class='op'>(</span><span class='va'>m_nlme</span>, level <span class='op'>=</span> <span class='fl'>0</span><span class='op'>:</span><span class='fl'>1</span><span class='op'>)</span>, layout <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'>1</span><span class='op'>)</span><span class='op'>)</span>
 </div><div class='img'><img src='nlme-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># augPred does not work on fits with more than one state</span>
 <span class='co'># variable</span>
 <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>
-</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>
+<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">
diff --git a/docs/dev/reference/nlme.mmkin.html b/docs/dev/reference/nlme.mmkin.html
index 2649c111..925cf7cf 100644
--- a/docs/dev/reference/nlme.mmkin.html
+++ b/docs/dev/reference/nlme.mmkin.html
@@ -74,7 +74,7 @@ have been obtained by fitting the same model to a list of datasets." />
       </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">1.0.1.9000</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -157,7 +157,7 @@ have been obtained by fitting the same model to a list of datasets.</p>
   data <span class='op'>=</span> <span class='st'>"auto"</span>,
   fixed <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>as.list</a></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='fu'><a href='nlme_function.html'>mean_degparms</a></span><span class='op'>(</span><span class='va'>model</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>el</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/eval.html'>eval</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/parse.html'>parse</a></span><span class='op'>(</span>text <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='va'>el</span>, <span class='fl'>1</span>, sep <span class='op'>=</span> <span class='st'>"~"</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
-  random <span class='op'>=</span> <span class='fu'>pdDiag</span><span class='op'>(</span><span class='va'>fixed</span><span class='op'>)</span>,
+  random <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/pdDiag.html'>pdDiag</a></span><span class='op'>(</span><span class='va'>fixed</span><span class='op'>)</span>,
   <span class='va'>groups</span>,
   start <span class='op'>=</span> <span class='fu'><a href='nlme_function.html'>mean_degparms</a></span><span class='op'>(</span><span class='va'>model</span>, random <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
   correlation <span class='op'>=</span> <span class='cn'>NULL</span>,
diff --git a/docs/dev/reference/nobs.mkinfit.html b/docs/dev/reference/nobs.mkinfit.html
index 621eb622..0b6c963c 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -121,7 +121,7 @@
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/parms.html b/docs/dev/reference/parms.html
index ba0e89bb..9f6f4225 100644
--- a/docs/dev/reference/parms.html
+++ b/docs/dev/reference/parms.html
@@ -74,7 +74,7 @@ considering the error structure that was assumed for the fit." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -123,7 +123,7 @@ considering the error structure that was assumed for the fit." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -219,10 +219,10 @@ such matrices is returned.</p>
 #&gt; 
 #&gt; $DFOP
 #&gt;             Dataset 7
-#&gt; parent_0 91.058971597
+#&gt; parent_0 91.058971589
 #&gt; k1        0.044946770
 #&gt; k2        0.002868336
-#&gt; g         0.526942414
+#&gt; g         0.526942415
 #&gt; sigma     2.221302196
 #&gt; </div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; $SFO
@@ -233,17 +233,17 @@ such matrices is returned.</p>
 #&gt; 
 #&gt; $FOMC
 #&gt;          Dataset 6  Dataset 7 Dataset 8 Dataset 9 Dataset 10
-#&gt; parent_0 95.558575 92.6837649 90.719787 98.383939 94.8481458
+#&gt; parent_0 95.558575 92.6837649 90.719787 98.383939 94.8481459
 #&gt; alpha     1.338667  0.4967832  1.639099  1.074460  0.2805272
 #&gt; beta     13.033315 14.1451255  5.007077  4.397126  6.9052224
 #&gt; sigma     1.847671  1.9167519  1.066063  3.146056  1.6222778
 #&gt; 
 #&gt; $DFOP
 #&gt;            Dataset 6    Dataset 7   Dataset 8   Dataset 9   Dataset 10
-#&gt; parent_0 96.55213663 91.058971597 90.34509493 98.14858820 94.311323733
+#&gt; parent_0 96.55213663 91.058971589 90.34509493 98.14858820 94.311323734
 #&gt; k1        0.21954588  0.044946770  0.41232288  0.31697588  0.080663857
 #&gt; k2        0.02957934  0.002868336  0.07581766  0.03260384  0.003425417
-#&gt; g         0.44845068  0.526942414  0.66091967  0.65322767  0.342652880
+#&gt; g         0.44845068  0.526942415  0.66091967  0.65322767  0.342652880
 #&gt; sigma     1.35690468  2.221302196  1.34169076  2.87159846  1.942067831
 #&gt; </div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span>, transformed <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; $SFO
diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html
index ef169074..630e95a3 100644
--- a/docs/dev/reference/plot.mixed.mmkin.html
+++ b/docs/dev/reference/plot.mixed.mmkin.html
@@ -72,7 +72,7 @@
       </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">1.0.2.9000</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -283,10 +283,10 @@ corresponding model prediction lines for the different datasets.</p></td>
 </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>, transformations <span class='op'>=</span> <span class='st'>"saemix"</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Feb 13 12:33:07 2021"
+#&gt; [1] "Mon Feb 15 17:12:17 2021"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Sat Feb 13 12:33:13 2021"</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 Feb 15 17:12:24 2021"</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'># We can overlay the two variants if we generate predictions</span>
 <span class='va'>pred_nlme</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>dfop_sfo</span>,
diff --git a/docs/dev/reference/plot.mkinfit-2.png b/docs/dev/reference/plot.mkinfit-2.png
index 376c812f..a11d1680 100644
--- a/docs/dev/reference/plot.mkinfit-2.png
+++ b/docs/dev/reference/plot.mkinfit-2.png
diff --git a/docs/dev/reference/plot.mkinfit-5.png b/docs/dev/reference/plot.mkinfit-5.png
index bc44de88..6631aa68 100644
--- a/docs/dev/reference/plot.mkinfit-5.png
+++ b/docs/dev/reference/plot.mkinfit-5.png
diff --git a/docs/dev/reference/plot.mkinfit-6.png b/docs/dev/reference/plot.mkinfit-6.png
index eb8cbd92..946b20c5 100644
--- a/docs/dev/reference/plot.mkinfit-6.png
+++ b/docs/dev/reference/plot.mkinfit-6.png
diff --git a/docs/dev/reference/plot.mkinfit-7.png b/docs/dev/reference/plot.mkinfit-7.png
index 92a664f4..10807ea8 100644
--- a/docs/dev/reference/plot.mkinfit-7.png
+++ b/docs/dev/reference/plot.mkinfit-7.png
diff --git a/docs/dev/reference/plot.mkinfit.html b/docs/dev/reference/plot.mkinfit.html
index c5bfb528..c5249ecd 100644
--- a/docs/dev/reference/plot.mkinfit.html
+++ b/docs/dev/reference/plot.mkinfit.html
@@ -74,7 +74,7 @@ observed data together with the solution of the fitted model." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
diff --git a/docs/dev/reference/plot.mmkin-1.png b/docs/dev/reference/plot.mmkin-1.png
index f12b7907..647dfb8a 100644
--- a/docs/dev/reference/plot.mmkin-1.png
+++ b/docs/dev/reference/plot.mmkin-1.png
diff --git a/docs/dev/reference/plot.mmkin-2.png b/docs/dev/reference/plot.mmkin-2.png
index e3127554..1bc1c9db 100644
--- a/docs/dev/reference/plot.mmkin-2.png
+++ b/docs/dev/reference/plot.mmkin-2.png
diff --git a/docs/dev/reference/plot.mmkin-3.png b/docs/dev/reference/plot.mmkin-3.png
index 5448976e..50d6ffac 100644
--- a/docs/dev/reference/plot.mmkin-3.png
+++ b/docs/dev/reference/plot.mmkin-3.png
diff --git a/docs/dev/reference/plot.mmkin-4.png b/docs/dev/reference/plot.mmkin-4.png
index 9a25fc50..e049fa16 100644
--- a/docs/dev/reference/plot.mmkin-4.png
+++ b/docs/dev/reference/plot.mmkin-4.png
diff --git a/docs/dev/reference/plot.mmkin-5.png b/docs/dev/reference/plot.mmkin-5.png
index 82b422b5..2421995b 100644
--- a/docs/dev/reference/plot.mmkin-5.png
+++ b/docs/dev/reference/plot.mmkin-5.png
diff --git a/docs/dev/reference/plot.mmkin.html b/docs/dev/reference/plot.mmkin.html
index ee80c6e4..9ca0df94 100644
--- a/docs/dev/reference/plot.mmkin.html
+++ b/docs/dev/reference/plot.mmkin.html
@@ -76,7 +76,7 @@ the fit of at least one model to the same dataset is shown." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
diff --git a/docs/dev/reference/plot.nafta.html b/docs/dev/reference/plot.nafta.html
index 9fc59f94..c24fba99 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -122,7 +122,7 @@ function (SFO, then IORE, then DFOP)." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/reexports.html b/docs/dev/reference/reexports.html
index f12a2690..371567d8 100644
--- a/docs/dev/reference/reexports.html
+++ b/docs/dev/reference/reexports.html
@@ -79,7 +79,7 @@ below to see their documentation.
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -128,7 +128,7 @@ below to see their documentation.
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/residuals.mkinfit.html b/docs/dev/reference/residuals.mkinfit.html
index 95114dae..3f518ab7 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -121,7 +121,7 @@
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -175,7 +175,7 @@ standard deviation obtained from the fitted error model?</p></td>
 </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>
+#&gt; [7] -0.04695355  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">
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html
index 02483bec..bdb1226e 100644
--- a/docs/dev/reference/saem.html
+++ b/docs/dev/reference/saem.html
@@ -74,7 +74,7 @@ Expectation Maximisation algorithm (SAEM)." />
       </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">1.0.2.9000</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -261,27 +261,27 @@ using <a href='mmkin.html'>mmkin</a>.</p>
   state.ini <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, fixed_initials <span class='op'>=</span> <span class='st'>"parent"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 <span class='va'>f_saem_p0_fixed</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_p0_fixed</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Feb 13 12:33:16 2021"
+#&gt; [1] "Mon Feb 15 17:12:32 2021"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Sat Feb 13 12:33:18 2021"</div><div class='input'>
+#&gt; [1] "Mon Feb 15 17:12:34 2021"</div><div class='input'>
 <span class='va'>f_mmkin_parent</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 <span class='va'>f_saem_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Feb 13 12:33:19 2021"
+#&gt; [1] "Mon Feb 15 17:12:35 2021"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Sat Feb 13 12:33:20 2021"</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 Feb 15 17:12:36 2021"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Feb 13 12:33:20 2021"
+#&gt; [1] "Mon Feb 15 17:12:36 2021"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Sat Feb 13 12:33:22 2021"</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 Feb 15 17:12:38 2021"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Feb 13 12:33:23 2021"
+#&gt; [1] "Mon Feb 15 17:12:39 2021"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Sat Feb 13 12:33:25 2021"</div><div class='input'>
+#&gt; [1] "Mon Feb 15 17:12:42 2021"</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>
@@ -324,10 +324,10 @@ using <a href='mmkin.html'>mmkin</a>.</p>
 <span class='va'>f_mmkin_parent_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_mmkin_parent</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
 <span class='va'>f_saem_fomc_tc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_tc</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Feb 13 12:33:28 2021"
+#&gt; [1] "Mon Feb 15 17:12:44 2021"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Sat Feb 13 12:33:32 2021"</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 Feb 15 17:12:49 2021"</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; <span class='error'>Error in compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)): 'compare.saemix' requires at least two models.</span></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='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>
@@ -346,15 +346,15 @@ using <a href='mmkin.html'>mmkin</a>.</p>
 <span class='co'># 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] "Sat Feb 13 12:33:35 2021"
+#&gt; [1] "Mon Feb 15 17:12:51 2021"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Sat Feb 13 12:33:39 2021"</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 Feb 15 17:12:56 2021"</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] "Sat Feb 13 12:33:40 2021"
+#&gt; [1] "Mon Feb 15 17:12:56 2021"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Sat Feb 13 12:33:48 2021"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span>
+#&gt; [1] "Mon Feb 15 17:13:05 2021"</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:
@@ -395,10 +395,10 @@ using <a href='mmkin.html'>mmkin</a>.</p>
 #&gt; SD.g_qlogis          0.44771 -0.86417  1.7596</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_dfop_sfo</span><span class='op'>)</span>
 </div><div class='img'><img src='saem-5.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_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:  1.0.2.9000 
+#&gt; mkin version used for pre-fitting:  1.0.3.9000 
 #&gt; R version used for fitting:         4.0.3 
-#&gt; Date of fit:     Sat Feb 13 12:33:48 2021 
-#&gt; Date of summary: Sat Feb 13 12:33:48 2021 
+#&gt; Date of fit:     Mon Feb 15 17:13:05 2021 
+#&gt; Date of summary: Mon Feb 15 17:13:06 2021 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -413,7 +413,7 @@ using <a href='mmkin.html'>mmkin</a>.</p>
 #&gt; 
 #&gt; Model predictions using solution type analytical 
 #&gt; 
-#&gt; Fitted in 8.875 s using 300, 100 iterations
+#&gt; Fitted in 8.985 s using 300, 100 iterations
 #&gt; 
 #&gt; Variance model: Constant variance 
 #&gt; 
diff --git a/docs/dev/reference/schaefer07_complex_case-1.png b/docs/dev/reference/schaefer07_complex_case-1.png
index 16e657dd..96aab2dc 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 83555b99..4ccad5c4 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -123,7 +123,7 @@
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -186,15 +186,15 @@
 </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;   0.3809620   0.1954665   0.4235715   0.0000000   0.4479662   0.5520338 
+#&gt;   0.3809620   0.1954667   0.4235713   0.0000000   0.4479619   0.5520381 
 #&gt; 
 #&gt; $distimes
 #&gt;            DT50      DT90
 #&gt; parent 13.95078  46.34350
-#&gt; A1     49.75343 165.27731
-#&gt; B1     37.26912 123.80533
-#&gt; C1     11.23131  37.30959
-#&gt; A2     28.50569  94.69386
+#&gt; A1     49.75342 165.27728
+#&gt; B1     37.26908 123.80520
+#&gt; C1     11.23131  37.30961
+#&gt; A2     28.50624  94.69567
 #&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='op'>(</span><span class='va'>schaefer07_complex_results</span><span class='op'>)</span>
diff --git a/docs/dev/reference/sigma_twocomp-1.png b/docs/dev/reference/sigma_twocomp-1.png
index 21db3145..6e61684e 100644
--- a/docs/dev/reference/sigma_twocomp-1.png
+++ b/docs/dev/reference/sigma_twocomp-1.png
diff --git a/docs/dev/reference/sigma_twocomp.html b/docs/dev/reference/sigma_twocomp.html
index 8212e480..b7d295b2 100644
--- a/docs/dev/reference/sigma_twocomp.html
+++ b/docs/dev/reference/sigma_twocomp.html
@@ -73,7 +73,7 @@ dependence of the measured value \(y\):" />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -122,7 +122,7 @@ dependence of the measured value \(y\):" />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -188,6 +188,10 @@ Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry
 24(11), 1895-1898.</p>
 <p>Rocke, David M. and Lorenzato, Stefan (1995) A two-component model for
 measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p>
+<p>Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical
+Degradation Data. <em>Environments</em> 6(12) 124
+doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6120124</a>
+.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='va'>times</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><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/summary.mkinfit.html b/docs/dev/reference/summary.mkinfit.html
index f314dfa8..494731e9 100644
--- a/docs/dev/reference/summary.mkinfit.html
+++ b/docs/dev/reference/summary.mkinfit.html
@@ -76,7 +76,7 @@ values." />
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -125,7 +125,7 @@ values." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -236,17 +236,17 @@ 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='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 
+</div><div class='output co'>#&gt; mkin version used for fitting:    1.0.3.9000 
 #&gt; R version used for fitting:       4.0.3 
-#&gt; Date of fit:     Mon Nov 30 16:01:20 2020 
-#&gt; Date of summary: Mon Nov 30 16:01:20 2020 
+#&gt; Date of fit:     Mon Feb 15 17:13:09 2021 
+#&gt; Date of summary: Mon Feb 15 17:13:09 2021 
 #&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 0.028 s
+#&gt; Fitted using 131 model solutions performed in 0.027 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 2aeadc46..b2f6624a 100644
--- a/docs/dev/reference/summary.nlme.mmkin.html
+++ b/docs/dev/reference/summary.nlme.mmkin.html
@@ -76,7 +76,7 @@ endpoints such as formation fractions and DT50 values. Optionally
       </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 class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -125,7 +125,7 @@ endpoints such as formation fractions and DT50 values. Optionally
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -263,12 +263,12 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p>
 <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>
 </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 
+</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='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:      3.1.152 
+#&gt; mkin version used for pre-fitting:  1.0.3.9000 
 #&gt; R version used for fitting:         4.0.3 
-#&gt; Date of fit:     Mon Nov 30 16:01:23 2020 
-#&gt; Date of summary: Mon Nov 30 16:01:23 2020 
+#&gt; Date of fit:     Mon Feb 15 17:13:12 2021 
+#&gt; Date of summary: Mon Feb 15 17:13:12 2021 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - k_parent * parent
@@ -278,148 +278,146 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p>
 #&gt; 
 #&gt; Model predictions using solution type analytical 
 #&gt; 
-#&gt; Fitted in 0.996 s using 6 iterations
+#&gt; Fitted in 0.544 s using 4 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;   101.568773    -4.454103 
+#&gt;      101.569       -4.454 
 #&gt; 
 #&gt; Fixed degradation parameter values:
 #&gt; None
 #&gt; 
 #&gt; Results:
 #&gt; 
-#&gt;        AIC      BIC    logLik
-#&gt;   586.4159 603.9145 -286.2079
+#&gt;     AIC   BIC logLik
+#&gt;   584.5 599.5 -286.2
 #&gt; 
 #&gt; Optimised, transformed parameters with symmetric confidence intervals:
 #&gt;               lower    est.   upper
-#&gt; parent_0     99.360 101.593 103.825
-#&gt; log_k_parent -4.979  -4.451  -3.924
+#&gt; parent_0     99.371 101.592 103.814
+#&gt; log_k_parent -4.973  -4.449  -3.926
 #&gt; 
 #&gt; Correlation: 
 #&gt;              prnt_0
-#&gt; log_k_parent 0.155 
+#&gt; log_k_parent 0.051 
 #&gt; 
 #&gt; Random effects:
 #&gt;  Formula: list(parent_0 ~ 1, log_k_parent ~ 1)
 #&gt;  Level: ds
-#&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;  Structure: Diagonal
+#&gt;          parent_0 log_k_parent Residual
+#&gt; StdDev: 6.924e-05       0.5863        1
 #&gt; 
 #&gt; Variance function:
 #&gt;  Structure: Constant plus proportion of variance covariate
 #&gt;  Formula: ~fitted(.) 
 #&gt;  Parameter estimates:
-#&gt;       const        prop 
-#&gt; 6.56706e-24 7.89583e-02 
+#&gt;        const         prop 
+#&gt; 0.0001208853 0.0789968036 
 #&gt; 
 #&gt; Backtransformed parameters with asymmetric confidence intervals:
 #&gt;              lower      est.     upper
-#&gt; parent_0 99.360213 101.59280 103.82539
-#&gt; k_parent  0.006883   0.01166   0.01976
+#&gt; parent_0 99.370882 101.59243 103.81398
+#&gt; k_parent  0.006923   0.01168   0.01972
 #&gt; 
 #&gt; Estimated disappearance times:
 #&gt;         DT50  DT90
-#&gt; parent 59.44 197.4
+#&gt; parent 59.32 197.1
 #&gt; 
 #&gt; Data:
 #&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'>
+#&gt;  ds 1 parent    0    104.1   101.592   2.50757 8.0255     0.312451
+#&gt;  ds 1 parent    0    105.0   101.592   3.40757 8.0255     0.424594
+#&gt;  ds 1 parent    1     98.5   100.796  -2.29571 7.9625    -0.288313
+#&gt;  ds 1 parent    1     96.1   100.796  -4.69571 7.9625    -0.589725
+#&gt;  ds 1 parent    3    101.9    99.221   2.67904 7.8381     0.341796
+#&gt;  ds 1 parent    3     85.2    99.221 -14.02096 7.8381    -1.788812
+#&gt;  ds 1 parent    7     99.1    96.145   2.95512 7.5951     0.389081
+#&gt;  ds 1 parent    7     93.0    96.145  -3.14488 7.5951    -0.414065
+#&gt;  ds 1 parent   14     88.1    90.989  -2.88944 7.1879    -0.401987
+#&gt;  ds 1 parent   14     84.1    90.989  -6.88944 7.1879    -0.958480
+#&gt;  ds 1 parent   28     80.2    81.493  -1.29305 6.4377    -0.200857
+#&gt;  ds 1 parent   28     91.3    81.493   9.80695 6.4377     1.523364
+#&gt;  ds 1 parent   60     65.1    63.344   1.75642 5.0039     0.351008
+#&gt;  ds 1 parent   60     65.8    63.344   2.45642 5.0039     0.490898
+#&gt;  ds 1 parent   90     47.8    50.018  -2.21764 3.9512    -0.561252
+#&gt;  ds 1 parent   90     53.5    50.018   3.48236 3.9512     0.881335
+#&gt;  ds 1 parent  120     37.6    39.495  -1.89515 3.1200    -0.607423
+#&gt;  ds 1 parent  120     39.3    39.495  -0.19515 3.1200    -0.062549
+#&gt;  ds 2 parent    0    107.9   101.592   6.30757 8.0255     0.785943
+#&gt;  ds 2 parent    0    102.1   101.592   0.50757 8.0255     0.063245
+#&gt;  ds 2 parent    1    103.8   100.058   3.74159 7.9043     0.473361
+#&gt;  ds 2 parent    1    108.6   100.058   8.54159 7.9043     1.080626
+#&gt;  ds 2 parent    3     91.0    97.060  -6.05952 7.6674    -0.790297
+#&gt;  ds 2 parent    3     84.9    97.060 -12.15952 7.6674    -1.585874
+#&gt;  ds 2 parent    7     79.3    91.329 -12.02867 7.2147    -1.667251
+#&gt;  ds 2 parent    7    100.9    91.329   9.57133 7.2147     1.326647
+#&gt;  ds 2 parent   14     77.3    82.102  -4.80185 6.4858    -0.740366
+#&gt;  ds 2 parent   14     83.5    82.102   1.39815 6.4858     0.215571
+#&gt;  ds 2 parent   28     66.8    66.351   0.44945 5.2415     0.085748
+#&gt;  ds 2 parent   28     63.3    66.351  -3.05055 5.2415    -0.582002
+#&gt;  ds 2 parent   60     40.8    40.775   0.02474 3.2211     0.007679
+#&gt;  ds 2 parent   60     44.8    40.775   4.02474 3.2211     1.249485
+#&gt;  ds 2 parent   90     27.8    25.832   1.96762 2.0407     0.964198
+#&gt;  ds 2 parent   90     27.0    25.832   1.16762 2.0407     0.572171
+#&gt;  ds 2 parent  120     15.2    16.366  -1.16561 1.2928    -0.901595
+#&gt;  ds 2 parent  120     15.5    16.366  -0.86561 1.2928    -0.669547
+#&gt;  ds 3 parent    0     97.7   101.592  -3.89243 8.0255    -0.485009
+#&gt;  ds 3 parent    0     88.2   101.592 -13.39243 8.0255    -1.668739
+#&gt;  ds 3 parent    1    109.9    99.218  10.68196 7.8379     1.362858
+#&gt;  ds 3 parent    1     97.8    99.218  -1.41804 7.8379    -0.180921
+#&gt;  ds 3 parent    3    100.5    94.634   5.86555 7.4758     0.784603
+#&gt;  ds 3 parent    3     77.4    94.634 -17.23445 7.4758    -2.305360
+#&gt;  ds 3 parent    7     78.3    86.093  -7.79273 6.8011    -1.145813
+#&gt;  ds 3 parent    7     90.3    86.093   4.20727 6.8011     0.618620
+#&gt;  ds 3 parent   14     76.0    72.958   3.04222 5.7634     0.527848
+#&gt;  ds 3 parent   14     79.1    72.958   6.14222 5.7634     1.065722
+#&gt;  ds 3 parent   28     46.0    52.394  -6.39404 4.1390    -1.544842
+#&gt;  ds 3 parent   28     53.4    52.394   1.00596 4.1390     0.243046
+#&gt;  ds 3 parent   60     25.1    24.582   0.51786 1.9419     0.266676
+#&gt;  ds 3 parent   60     21.4    24.582  -3.18214 1.9419    -1.638664
+#&gt;  ds 3 parent   90     11.0    12.092  -1.09202 0.9552    -1.143199
+#&gt;  ds 3 parent   90     14.2    12.092   2.10798 0.9552     2.206776
+#&gt;  ds 3 parent  120      5.8     5.948  -0.14810 0.4699    -0.315178
+#&gt;  ds 3 parent  120      6.1     5.948   0.15190 0.4699     0.323282
+#&gt;  ds 4 parent    0     95.3   101.592  -6.29243 8.0255    -0.784057
+#&gt;  ds 4 parent    0    102.0   101.592   0.40757 8.0255     0.050784
+#&gt;  ds 4 parent    1    104.4   101.125   3.27549 7.9885     0.410025
+#&gt;  ds 4 parent    1    105.4   101.125   4.27549 7.9885     0.535205
+#&gt;  ds 4 parent    3    113.7   100.195  13.50487 7.9151     1.706218
+#&gt;  ds 4 parent    3     82.3   100.195 -17.89513 7.9151    -2.260886
+#&gt;  ds 4 parent    7     98.1    98.362  -0.26190 7.7703    -0.033706
+#&gt;  ds 4 parent    7     87.8    98.362 -10.56190 7.7703    -1.359270
+#&gt;  ds 4 parent   14     97.9    95.234   2.66590 7.5232     0.354357
+#&gt;  ds 4 parent   14    104.8    95.234   9.56590 7.5232     1.271521
+#&gt;  ds 4 parent   28     85.0    89.274  -4.27372 7.0523    -0.606001
+#&gt;  ds 4 parent   28     77.2    89.274 -12.07372 7.0523    -1.712017
+#&gt;  ds 4 parent   60     82.2    77.013   5.18661 6.0838     0.852526
+#&gt;  ds 4 parent   60     86.1    77.013   9.08661 6.0838     1.493571
+#&gt;  ds 4 parent   90     70.5    67.053   3.44692 5.2970     0.650733
+#&gt;  ds 4 parent   90     61.7    67.053  -5.35308 5.2970    -1.010591
+#&gt;  ds 4 parent  120     60.0    58.381   1.61905 4.6119     0.351058
+#&gt;  ds 4 parent  120     56.4    58.381  -1.98095 4.6119    -0.429530
+#&gt;  ds 5 parent    0     92.6   101.592  -8.99243 8.0255    -1.120485
+#&gt;  ds 5 parent    0    116.5   101.592  14.90757 8.0255     1.857531
+#&gt;  ds 5 parent    1    108.0    99.914   8.08560 7.8929     1.024413
+#&gt;  ds 5 parent    1    104.9    99.914   4.98560 7.8929     0.631655
+#&gt;  ds 5 parent    3    100.5    96.641   3.85898 7.6343     0.505477
+#&gt;  ds 5 parent    3     89.5    96.641  -7.14102 7.6343    -0.935382
+#&gt;  ds 5 parent    7     91.7    90.412   1.28752 7.1423     0.180267
+#&gt;  ds 5 parent    7     95.1    90.412   4.68752 7.1423     0.656304
+#&gt;  ds 5 parent   14     82.2    80.463   1.73715 6.3563     0.273295
+#&gt;  ds 5 parent   14     84.5    80.463   4.03715 6.3563     0.635141
+#&gt;  ds 5 parent   28     60.5    63.728  -3.22788 5.0343    -0.641178
+#&gt;  ds 5 parent   28     72.8    63.728   9.07212 5.0343     1.802062
+#&gt;  ds 5 parent   60     38.3    37.399   0.90061 2.9544     0.304835
+#&gt;  ds 5 parent   60     40.7    37.399   3.30061 2.9544     1.117174
+#&gt;  ds 5 parent   90     22.5    22.692  -0.19165 1.7926    -0.106913
+#&gt;  ds 5 parent   90     20.8    22.692  -1.89165 1.7926    -1.055273
+#&gt;  ds 5 parent  120     13.4    13.768  -0.36790 1.0876    -0.338259
+#&gt;  ds 5 parent  120     13.8    13.768   0.03210 1.0876     0.029517</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.html b/docs/dev/reference/summary.saem.mmkin.html
index 81054813..0d661ee9 100644
--- a/docs/dev/reference/summary.saem.mmkin.html
+++ b/docs/dev/reference/summary.saem.mmkin.html
@@ -76,7 +76,7 @@ endpoints such as formation fractions and DT50 values. Optionally
       </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">1.0.2.9000</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -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] "Sat Feb 13 12:33:52 2021"
+#&gt; [1] "Mon Feb 15 17:13:15 2021"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Sat Feb 13 12:34:03 2021"</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 Feb 15 17:13:26 2021"</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:  1.0.2.9000 
+#&gt; mkin version used for pre-fitting:  1.0.3.9000 
 #&gt; R version used for fitting:         4.0.3 
-#&gt; Date of fit:     Sat Feb 13 12:34:04 2021 
-#&gt; Date of summary: Sat Feb 13 12:34:04 2021 
+#&gt; Date of fit:     Mon Feb 15 17:13:27 2021 
+#&gt; Date of summary: Mon Feb 15 17:13:27 2021 
 #&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 11.899 s using 300, 100 iterations
+#&gt; Fitted in 12.204 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 351b21aa..89975db5 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 1edc7c1e..33a0ace2 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -136,7 +136,7 @@ Compare also the code in the example section to see the degradation models." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -297,10 +297,10 @@ Compare also the code in the example section to see the degradation models." />
                  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 
+</div><div class='output co'>#&gt; mkin version used for fitting:    1.0.3.9000 
 #&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; Date of fit:     Mon Feb 15 17:13:29 2021 
+#&gt; Date of summary: Mon Feb 15 17:13:29 2021 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - k_parent * parent
@@ -309,7 +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 822 model solutions performed in 0.652 s
+#&gt; Fitted using 833 model solutions performed in 0.649 s
 #&gt; 
 #&gt; Error model: Constant variance 
 #&gt; 
@@ -361,15 +361,15 @@ Compare also the code in the example section to see the degradation models." />
 #&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; sigma           -2.900e-08   -8.030e-09 -2.741e-08  3.938e-08      -2.681e-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; parent_0          1.614e-01 -2.900e-08
+#&gt; log_k_parent      4.102e-01 -8.030e-09
+#&gt; log_k_M1         -8.109e-01 -2.741e-08
+#&gt; log_k_M2          5.419e-01  3.938e-08
+#&gt; f_parent_qlogis  -8.605e-01 -2.681e-08
+#&gt; f_M1_qlogis       1.000e+00  4.971e-08
+#&gt; sigma             4.971e-08  1.000e+00
 #&gt; 
 #&gt; Backtransformed parameters:
 #&gt; Confidence intervals for internally transformed parameters are asymmetric.
@@ -416,7 +416,7 @@ 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  9.532e-10  0.60000
+#&gt;    90   parent      0.6  9.530e-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
@@ -427,7 +427,7 @@ 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 -9.671e-10  3.20000
+#&gt;    90       M1      3.2 -9.670e-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
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 9e0afad2..7bf0bd0f 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 e889efde..fc1f77e0 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 89ec3480..539b8287 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -122,7 +122,7 @@
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -203,25 +203,25 @@
 </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; parent_0       76.55425650 0.859186399 89.1008710 1.113861e-26 74.755959418
 #&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; k_M1            0.84258615 0.806160102  1.0451846 1.545268e-01  0.113779609
+#&gt; k_M2            0.04210880 0.017083034  2.4649483 1.170188e-02  0.018013857
+#&gt; k_M3            0.01122918 0.007245856  1.5497385 6.885052e-02  0.002909431
+#&gt; f_parent_to_M1  0.32240200 0.240783943  1.3389680 9.819076e-02           NA
+#&gt; f_parent_to_M2  0.16099855 0.033691952  4.7785464 6.531136e-05           NA
+#&gt; f_M1_to_M3      0.27921507 0.269423780  1.0363416 1.565267e-01  0.022978205
+#&gt; f_M2_to_M3      0.55641252 0.595119966  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       78.35255357
+#&gt; parent_0       78.35255358
 #&gt; k_parent        0.13084582
-#&gt; k_M1            6.23970352
+#&gt; k_M1            6.23970702
 #&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      0.86450768
+#&gt; f_M1_to_M3      0.86450775
 #&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
diff --git a/docs/dev/reference/transform_odeparms.html b/docs/dev/reference/transform_odeparms.html
index 6e19505f..75d6a1f9 100644
--- a/docs/dev/reference/transform_odeparms.html
+++ b/docs/dev/reference/transform_odeparms.html
@@ -77,7 +77,7 @@ the ilr transformation is used." />
       </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">1.0.1.9000</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
diff --git a/docs/dev/reference/update.mkinfit-1.png b/docs/dev/reference/update.mkinfit-1.png
index 7d2f1bdb..df8473c1 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 8dcabcdc..13c99b44 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 10a93373..83f45028 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -124,7 +124,7 @@ override these starting values." />
       <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>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
author	Johannes Ranke <jranke@uni-bremen.de>	2021-02-15 17:36:12 +0100
committer	Johannes Ranke <jranke@uni-bremen.de>	2021-02-15 17:36:12 +0100
commit	b9be19af5e3085216d0cd5af439332f631fa8b92 (patch)
tree	e10511f60e7f1713b781d5ea2acf885f3d1e6767 /docs
parent	11c7f26dd6c532d977d9875f3c16952c7bba37ca (diff)