From b9be19af5e3085216d0cd5af439332f631fa8b92 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 15 Feb 2021 17:36:12 +0100
Subject: Fully rebuild docs, rerun tests and check

---
 docs/dev/articles/FOCUS_D.html                     |  23 ++-
 .../accessible-code-block-0.0.1/empty-anchor.js    |  15 ++
 .../articles/FOCUS_D_files/figure-html/plot-1.png  | Bin 81432 -> 79176 bytes
 .../FOCUS_D_files/header-attrs-2.6/header-attrs.js |  12 ++
 docs/dev/articles/FOCUS_L.html                     | 129 ++++++++-------
 .../accessible-code-block-0.0.1/empty-anchor.js    |  15 ++
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 .../figure-html/unnamed-chunk-9-1.png              | Bin 41739 -> 40983 bytes
 .../FOCUS_L_files/header-attrs-2.6/header-attrs.js |  12 ++
 docs/dev/articles/index.html                       |   2 +-
 docs/dev/articles/mkin.html                        |  62 ++++---
 .../accessible-code-block-0.0.1/empty-anchor.js    |  15 ++
 .../mkin_files/figure-html/unnamed-chunk-2-1.png   | Bin 92716 -> 89958 bytes
 .../mkin_files/header-attrs-2.6/header-attrs.js    |  12 ++
 docs/dev/articles/twa.html                         |  13 +-
 .../accessible-code-block-0.0.1/empty-anchor.js    |  15 ++
 .../twa_files/header-attrs-2.6/header-attrs.js     |  12 ++
 docs/dev/articles/web_only/FOCUS_Z.html            |  35 ++--
 .../accessible-code-block-0.0.1/empty-anchor.js    |  15 ++
 .../figure-html/FOCUS_2006_Z_fits_1-1.png          | Bin 69227 -> 66640 bytes
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 .../figure-html/FOCUS_2006_Z_fits_9-1.png          | Bin 91586 -> 88890 bytes
 .../FOCUS_Z_files/header-attrs-2.6/header-attrs.js |  12 ++
 docs/dev/articles/web_only/NAFTA_examples.html     | 181 ++++++++++-----------
 .../accessible-code-block-0.0.1/empty-anchor.js    |  15 ++
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 .../header-attrs-2.6/header-attrs.js               |  12 ++
 docs/dev/articles/web_only/benchmarks.html         |  65 ++++++--
 .../accessible-code-block-0.0.1/empty-anchor.js    |  15 ++
 .../header-attrs-2.6/header-attrs.js               |  12 ++
 docs/dev/articles/web_only/compiled_models.html    |  27 ++-
 .../accessible-code-block-0.0.1/empty-anchor.js    |  15 ++
 .../header-attrs-2.6/header-attrs.js               |  12 ++
 62 files changed, 502 insertions(+), 251 deletions(-)
 create mode 100644 docs/dev/articles/FOCUS_D_files/accessible-code-block-0.0.1/empty-anchor.js
 create mode 100644 docs/dev/articles/FOCUS_D_files/header-attrs-2.6/header-attrs.js
 create mode 100644 docs/dev/articles/FOCUS_L_files/accessible-code-block-0.0.1/empty-anchor.js
 create mode 100644 docs/dev/articles/FOCUS_L_files/header-attrs-2.6/header-attrs.js
 create mode 100644 docs/dev/articles/mkin_files/accessible-code-block-0.0.1/empty-anchor.js
 create mode 100644 docs/dev/articles/mkin_files/header-attrs-2.6/header-attrs.js
 create mode 100644 docs/dev/articles/twa_files/accessible-code-block-0.0.1/empty-anchor.js
 create mode 100644 docs/dev/articles/twa_files/header-attrs-2.6/header-attrs.js
 create mode 100644 docs/dev/articles/web_only/FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js
 create mode 100644 docs/dev/articles/web_only/FOCUS_Z_files/header-attrs-2.6/header-attrs.js
 create mode 100644 docs/dev/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js
 create mode 100644 docs/dev/articles/web_only/NAFTA_examples_files/header-attrs-2.6/header-attrs.js
 create mode 100644 docs/dev/articles/web_only/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js
 create mode 100644 docs/dev/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js
 create mode 100644 docs/dev/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js
 create mode 100644 docs/dev/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js

(limited to 'docs/dev/articles')

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
Binary files a/docs/dev/articles/FOCUS_D_files/figure-html/plot-1.png and b/docs/dev/articles/FOCUS_D_files/figure-html/plot-1.png differ
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
index 00000000..ca349fd6
--- /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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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
Binary files a/docs/dev/articles/mkin_files/figure-html/unnamed-chunk-2-1.png and b/docs/dev/articles/mkin_files/figure-html/unnamed-chunk-2-1.png differ
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');
+      }
+    }
+  }
+});
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index ca191b00..e7501cbb 100644
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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');
+      }
+    }
+  }
+});
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
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index a6f4e763..3ce13a97 100644
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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
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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);
+  }
+});
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