Start online docs of the development version

author: Johannes Ranke <jranke@uni-bremen.de> 2022-11-24 09:02:26 +0100
committer: Johannes Ranke <jranke@uni-bremen.de> 2022-11-24 09:02:26 +0100
commit: af7c6de4db9981ac814362c441fbac22c8faa2d7 (patch)
tree: 33c2963936ce6c38abe6533afcce3994a08d4ba9 /docs/dev/articles
parent: 8e953c409e0020ea7e7c2a5121019c42cb66dde4 (diff)
45 files changed, 1468 insertions, 1315 deletions
diff --git a/docs/dev/articles/FOCUS_D.html b/docs/dev/articles/FOCUS_D.html
index a35a255a..a7617d55 100644
--- a/docs/dev/articles/FOCUS_D.html
+++ b/docs/dev/articles/FOCUS_D.html
@@ -20,6 +20,8 @@
 <![endif]-->
 </head>
 <body data-spy="scroll" data-target="#toc">
+    
+
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@@ -32,7 +34,7 @@
       </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">1.0.3.9000</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
       </span>
     </div>
 
@@ -42,7 +44,7 @@
   <a href="../reference/index.html">Functions and data</a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
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@@ -58,19 +60,28 @@
       <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
     </li>
     <li>
-      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+      <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
     </li>
     <li>
       <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
     </li>
     <li>
+      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+    </li>
+    <li>
       <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
     </li>
     <li>
       <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
     <li>
-      <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+      <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
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@@ -80,7 +91,7 @@
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+  <a href="https://github.com/jranke/mkin/" class="external-link">
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@@ -95,15 +106,15 @@
 
       
 
-      </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">
+      </header><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 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 class="date">Last change 31 January 2019 (rebuilt 2021-02-15)</h4>
+            <h4 data-toc-skip class="date">Last change 31 January 2019 (rebuilt 2022-11-24)</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>
+      <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/FOCUS_D.rmd" class="external-link"><code>vignettes/FOCUS_D.rmd</code></a></small>
       <div class="hidden name"><code>FOCUS_D.rmd</code></div>
 
     </div>
@@ -112,207 +123,207 @@
     
 <p>This is just a very simple vignette showing how to fit a degradation model for a parent compound with one transformation product using <code>mkin</code>. After loading the library we look at the data. We have observed concentrations in the column named <code>value</code> at the times specified in column <code>time</code> for the two observed variables named <code>parent</code> and <code>m1</code>.</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
-<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span><span class="op">)</span></code></pre></div>
-<pre><code>##      name time  value
-## 1  parent    0  99.46
-## 2  parent    0 102.04
-## 3  parent    1  93.50
-## 4  parent    1  92.50
-## 5  parent    3  63.23
-## 6  parent    3  68.99
-## 7  parent    7  52.32
-## 8  parent    7  55.13
-## 9  parent   14  27.27
-## 10 parent   14  26.64
-## 11 parent   21  11.50
-## 12 parent   21  11.64
-## 13 parent   35   2.85
-## 14 parent   35   2.91
-## 15 parent   50   0.69
-## 16 parent   50   0.63
-## 17 parent   75   0.05
-## 18 parent   75   0.06
-## 19 parent  100     NA
-## 20 parent  100     NA
-## 21 parent  120     NA
-## 22 parent  120     NA
-## 23     m1    0   0.00
-## 24     m1    0   0.00
-## 25     m1    1   4.84
-## 26     m1    1   5.64
-## 27     m1    3  12.91
-## 28     m1    3  12.96
-## 29     m1    7  22.97
-## 30     m1    7  24.47
-## 31     m1   14  41.69
-## 32     m1   14  33.21
-## 33     m1   21  44.37
-## 34     m1   21  46.44
-## 35     m1   35  41.22
-## 36     m1   35  37.95
-## 37     m1   50  41.19
-## 38     m1   50  40.01
-## 39     m1   75  40.09
-## 40     m1   75  33.85
-## 41     m1  100  31.04
-## 42     m1  100  33.13
-## 43     m1  120  25.15
-## 44     m1  120  33.31</code></pre>
+<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">##      name time  value</span></span>
+<span><span class="co">## 1  parent    0  99.46</span></span>
+<span><span class="co">## 2  parent    0 102.04</span></span>
+<span><span class="co">## 3  parent    1  93.50</span></span>
+<span><span class="co">## 4  parent    1  92.50</span></span>
+<span><span class="co">## 5  parent    3  63.23</span></span>
+<span><span class="co">## 6  parent    3  68.99</span></span>
+<span><span class="co">## 7  parent    7  52.32</span></span>
+<span><span class="co">## 8  parent    7  55.13</span></span>
+<span><span class="co">## 9  parent   14  27.27</span></span>
+<span><span class="co">## 10 parent   14  26.64</span></span>
+<span><span class="co">## 11 parent   21  11.50</span></span>
+<span><span class="co">## 12 parent   21  11.64</span></span>
+<span><span class="co">## 13 parent   35   2.85</span></span>
+<span><span class="co">## 14 parent   35   2.91</span></span>
+<span><span class="co">## 15 parent   50   0.69</span></span>
+<span><span class="co">## 16 parent   50   0.63</span></span>
+<span><span class="co">## 17 parent   75   0.05</span></span>
+<span><span class="co">## 18 parent   75   0.06</span></span>
+<span><span class="co">## 19 parent  100     NA</span></span>
+<span><span class="co">## 20 parent  100     NA</span></span>
+<span><span class="co">## 21 parent  120     NA</span></span>
+<span><span class="co">## 22 parent  120     NA</span></span>
+<span><span class="co">## 23     m1    0   0.00</span></span>
+<span><span class="co">## 24     m1    0   0.00</span></span>
+<span><span class="co">## 25     m1    1   4.84</span></span>
+<span><span class="co">## 26     m1    1   5.64</span></span>
+<span><span class="co">## 27     m1    3  12.91</span></span>
+<span><span class="co">## 28     m1    3  12.96</span></span>
+<span><span class="co">## 29     m1    7  22.97</span></span>
+<span><span class="co">## 30     m1    7  24.47</span></span>
+<span><span class="co">## 31     m1   14  41.69</span></span>
+<span><span class="co">## 32     m1   14  33.21</span></span>
+<span><span class="co">## 33     m1   21  44.37</span></span>
+<span><span class="co">## 34     m1   21  46.44</span></span>
+<span><span class="co">## 35     m1   35  41.22</span></span>
+<span><span class="co">## 36     m1   35  37.95</span></span>
+<span><span class="co">## 37     m1   50  41.19</span></span>
+<span><span class="co">## 38     m1   50  40.01</span></span>
+<span><span class="co">## 39     m1   75  40.09</span></span>
+<span><span class="co">## 40     m1   75  33.85</span></span>
+<span><span class="co">## 41     m1  100  31.04</span></span>
+<span><span class="co">## 42     m1  100  33.13</span></span>
+<span><span class="co">## 43     m1  120  25.15</span></span>
+<span><span class="co">## 44     m1  120  33.31</span></span></code></pre>
 <p>Next we specify the degradation model: The parent compound degrades with simple first-order kinetics (SFO) to one metabolite named m1, which also degrades with SFO kinetics.</p>
 <p>The call to mkinmod returns a degradation model. The differential equations represented in R code can be found in the character vector <code>$diffs</code> of the <code>mkinmod</code> object. If a C compiler (gcc) is installed and functional, the differential equation model will be compiled from auto-generated C code.</p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
-<pre><code>## Temporary DLL for differentials generated and loaded</code></pre>
+<code class="sourceCode R"><span><span class="va">SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">SFO_SFO</span><span class="op">$</span><span class="va">diffs</span><span class="op">)</span></code></pre></div>
-<pre><code>##                                                    parent 
-##                          "d_parent = - k_parent * parent" 
-##                                                        m1 
-## "d_m1 = + f_parent_to_m1 * k_parent * parent - k_m1 * m1"</code></pre>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">SFO_SFO</span><span class="op">$</span><span class="va">diffs</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">##                                                    parent </span></span>
+<span><span class="co">##                          "d_parent = - k_parent * parent" </span></span>
+<span><span class="co">##                                                        m1 </span></span>
+<span><span class="co">## "d_m1 = + f_parent_to_m1 * k_parent * parent - k_m1 * m1"</span></span></code></pre>
 <p>We do the fitting without progress report (<code>quiet = TRUE</code>).</p>
 <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">fit</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
-<pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with value
-## of zero were removed from the data</code></pre>
+<code class="sourceCode R"><span><span class="va">fit</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with value</span></span>
+<span><span class="co">## of zero were removed from the data</span></span></code></pre>
 <p>A plot of the fit including a residual plot for both observed variables is obtained using the <code>plot_sep</code> method for <code>mkinfit</code> objects, which shows separate graphs for all compounds and their residuals.</p>
 <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
 <p><img src="FOCUS_D_files/figure-html/plot-1.png" width="768"></p>
 <p>Confidence intervals for the parameter estimates are obtained using the <code>mkinparplot</code> function.</p>
 <div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="../reference/mkinparplot.html">mkinparplot</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="../reference/mkinparplot.html">mkinparplot</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></code></pre></div>
 <p><img src="FOCUS_D_files/figure-html/plot_2-1.png" width="768"></p>
 <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:    1.0.3.9000 
-## R version used for fitting:       4.0.3 
-## 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
-## d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
-## 
-## Model predictions using solution type analytical 
-## 
-## Fitted using 401 model solutions performed in 0.161 s
-## 
-## Error model: Constant variance 
-## 
-## Error model algorithm: OLS 
-## 
-## Starting values for parameters to be optimised:
-##                   value   type
-## parent_0       100.7500  state
-## k_parent         0.1000 deparm
-## k_m1             0.1001 deparm
-## f_parent_to_m1   0.5000 deparm
-## 
-## Starting values for the transformed parameters actually optimised:
-##                      value lower upper
-## parent_0        100.750000  -Inf   Inf
-## log_k_parent     -2.302585  -Inf   Inf
-## log_k_m1         -2.301586  -Inf   Inf
-## f_parent_qlogis   0.000000  -Inf   Inf
-## 
-## Fixed parameter values:
-##      value  type
-## m1_0     0 state
-## 
-## 
-## Warning(s): 
-## Observations with value of zero were removed from the data
-## 
-## Results:
-## 
-##        AIC      BIC    logLik
-##   204.4486 212.6365 -97.22429
-## 
-## Optimised, transformed parameters with symmetric confidence intervals:
-##                 Estimate Std. Error   Lower    Upper
-## parent_0        99.60000    1.57000 96.4000 102.8000
-## log_k_parent    -2.31600    0.04087 -2.3990  -2.2330
-## log_k_m1        -5.24700    0.13320 -5.5180  -4.9770
-## f_parent_qlogis  0.05792    0.08926 -0.1237   0.2395
-## sigma            3.12600    0.35850  2.3960   3.8550
-## 
-## 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 -1.172e-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           -1.172e-06   -8.483e-07  8.205e-07       1.305e-06  1.000e+00
-## 
-## Backtransformed parameters:
-## Confidence intervals for internally transformed parameters are asymmetric.
-## t-test (unrealistically) based on the assumption of normal distribution
-## for estimators of untransformed parameters.
-##                 Estimate t value    Pr(&gt;t)     Lower     Upper
-## parent_0       99.600000  63.430 2.298e-36 96.400000 1.028e+02
-## k_parent        0.098700  24.470 4.955e-23  0.090820 1.073e-01
-## k_m1            0.005261   7.510 6.165e-09  0.004012 6.898e-03
-## f_parent_to_m1  0.514500  23.070 3.104e-22  0.469100 5.596e-01
-## sigma           3.126000   8.718 2.235e-10  2.396000 3.855e+00
-## 
-## FOCUS Chi2 error levels in percent:
-##          err.min n.optim df
-## All data   6.398       4 15
-## parent     6.459       2  7
-## m1         4.690       2  8
-## 
-## Resulting formation fractions:
-##                 ff
-## parent_m1   0.5145
-## parent_sink 0.4855
-## 
-## Estimated disappearance times:
-##           DT50   DT90
-## parent   7.023  23.33
-## m1     131.761 437.70
-## 
-## Data:
-##  time variable observed predicted   residual
-##     0   parent    99.46  99.59848 -1.385e-01
-##     0   parent   102.04  99.59848  2.442e+00
-##     1   parent    93.50  90.23787  3.262e+00
-##     1   parent    92.50  90.23787  2.262e+00
-##     3   parent    63.23  74.07319 -1.084e+01
-##     3   parent    68.99  74.07319 -5.083e+00
-##     7   parent    52.32  49.91207  2.408e+00
-##     7   parent    55.13  49.91207  5.218e+00
-##    14   parent    27.27  25.01258  2.257e+00
-##    14   parent    26.64  25.01258  1.627e+00
-##    21   parent    11.50  12.53462 -1.035e+00
-##    21   parent    11.64  12.53462 -8.946e-01
-##    35   parent     2.85   3.14787 -2.979e-01
-##    35   parent     2.91   3.14787 -2.379e-01
-##    50   parent     0.69   0.71624 -2.624e-02
-##    50   parent     0.63   0.71624 -8.624e-02
-##    75   parent     0.05   0.06074 -1.074e-02
-##    75   parent     0.06   0.06074 -7.382e-04
-##     1       m1     4.84   4.80296  3.704e-02
-##     1       m1     5.64   4.80296  8.370e-01
-##     3       m1    12.91  13.02400 -1.140e-01
-##     3       m1    12.96  13.02400 -6.400e-02
-##     7       m1    22.97  25.04476 -2.075e+00
-##     7       m1    24.47  25.04476 -5.748e-01
-##    14       m1    41.69  36.69003  5.000e+00
-##    14       m1    33.21  36.69003 -3.480e+00
-##    21       m1    44.37  41.65310  2.717e+00
-##    21       m1    46.44  41.65310  4.787e+00
-##    35       m1    41.22  43.31313 -2.093e+00
-##    35       m1    37.95  43.31313 -5.363e+00
-##    50       m1    41.19  41.21832 -2.832e-02
-##    50       m1    40.01  41.21832 -1.208e+00
-##    75       m1    40.09  36.44704  3.643e+00
-##    75       m1    33.85  36.44704 -2.597e+00
-##   100       m1    31.04  31.98162 -9.416e-01
-##   100       m1    33.13  31.98162  1.148e+00
-##   120       m1    25.15  28.78984 -3.640e+00
-##   120       m1    33.31  28.78984  4.520e+00</code></pre>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## mkin version used for fitting:    1.2.2 </span></span>
+<span><span class="co">## R version used for fitting:       4.2.2 </span></span>
+<span><span class="co">## Date of fit:     Thu Nov 24 08:12:04 2022 </span></span>
+<span><span class="co">## Date of summary: Thu Nov 24 08:12:05 2022 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Equations:</span></span>
+<span><span class="co">## d_parent/dt = - k_parent * parent</span></span>
+<span><span class="co">## d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Model predictions using solution type analytical </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Fitted using 401 model solutions performed in 0.152 s</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Error model: Constant variance </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Error model algorithm: OLS </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Starting values for parameters to be optimised:</span></span>
+<span><span class="co">##                   value   type</span></span>
+<span><span class="co">## parent_0       100.7500  state</span></span>
+<span><span class="co">## k_parent         0.1000 deparm</span></span>
+<span><span class="co">## k_m1             0.1001 deparm</span></span>
+<span><span class="co">## f_parent_to_m1   0.5000 deparm</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Starting values for the transformed parameters actually optimised:</span></span>
+<span><span class="co">##                      value lower upper</span></span>
+<span><span class="co">## parent_0        100.750000  -Inf   Inf</span></span>
+<span><span class="co">## log_k_parent     -2.302585  -Inf   Inf</span></span>
+<span><span class="co">## log_k_m1         -2.301586  -Inf   Inf</span></span>
+<span><span class="co">## f_parent_qlogis   0.000000  -Inf   Inf</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Fixed parameter values:</span></span>
+<span><span class="co">##      value  type</span></span>
+<span><span class="co">## m1_0     0 state</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Warning(s): </span></span>
+<span><span class="co">## Observations with value of zero were removed from the data</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Results:</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">##        AIC      BIC    logLik</span></span>
+<span><span class="co">##   204.4486 212.6365 -97.22429</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Optimised, transformed parameters with symmetric confidence intervals:</span></span>
+<span><span class="co">##                 Estimate Std. Error   Lower    Upper</span></span>
+<span><span class="co">## parent_0        99.60000    1.57000 96.4000 102.8000</span></span>
+<span><span class="co">## log_k_parent    -2.31600    0.04087 -2.3990  -2.2330</span></span>
+<span><span class="co">## log_k_m1        -5.24700    0.13320 -5.5180  -4.9770</span></span>
+<span><span class="co">## f_parent_qlogis  0.05792    0.08926 -0.1237   0.2395</span></span>
+<span><span class="co">## sigma            3.12600    0.35850  2.3960   3.8550</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameter correlation:</span></span>
+<span><span class="co">##                   parent_0 log_k_parent   log_k_m1 f_parent_qlogis      sigma</span></span>
+<span><span class="co">## parent_0         1.000e+00    5.174e-01 -1.688e-01      -5.471e-01 -1.172e-06</span></span>
+<span><span class="co">## log_k_parent     5.174e-01    1.000e+00 -3.263e-01      -5.426e-01 -8.483e-07</span></span>
+<span><span class="co">## log_k_m1        -1.688e-01   -3.263e-01  1.000e+00       7.478e-01  8.205e-07</span></span>
+<span><span class="co">## f_parent_qlogis -5.471e-01   -5.426e-01  7.478e-01       1.000e+00  1.305e-06</span></span>
+<span><span class="co">## sigma           -1.172e-06   -8.483e-07  8.205e-07       1.305e-06  1.000e+00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Backtransformed parameters:</span></span>
+<span><span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span></span>
+<span><span class="co">## t-test (unrealistically) based on the assumption of normal distribution</span></span>
+<span><span class="co">## for estimators of untransformed parameters.</span></span>
+<span><span class="co">##                 Estimate t value    Pr(&gt;t)     Lower     Upper</span></span>
+<span><span class="co">## parent_0       99.600000  63.430 2.298e-36 96.400000 1.028e+02</span></span>
+<span><span class="co">## k_parent        0.098700  24.470 4.955e-23  0.090820 1.073e-01</span></span>
+<span><span class="co">## k_m1            0.005261   7.510 6.165e-09  0.004012 6.898e-03</span></span>
+<span><span class="co">## f_parent_to_m1  0.514500  23.070 3.104e-22  0.469100 5.596e-01</span></span>
+<span><span class="co">## sigma           3.126000   8.718 2.235e-10  2.396000 3.855e+00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## FOCUS Chi2 error levels in percent:</span></span>
+<span><span class="co">##          err.min n.optim df</span></span>
+<span><span class="co">## All data   6.398       4 15</span></span>
+<span><span class="co">## parent     6.459       2  7</span></span>
+<span><span class="co">## m1         4.690       2  8</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Resulting formation fractions:</span></span>
+<span><span class="co">##                 ff</span></span>
+<span><span class="co">## parent_m1   0.5145</span></span>
+<span><span class="co">## parent_sink 0.4855</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Estimated disappearance times:</span></span>
+<span><span class="co">##           DT50   DT90</span></span>
+<span><span class="co">## parent   7.023  23.33</span></span>
+<span><span class="co">## m1     131.761 437.70</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Data:</span></span>
+<span><span class="co">##  time variable observed predicted   residual</span></span>
+<span><span class="co">##     0   parent    99.46  99.59848 -1.385e-01</span></span>
+<span><span class="co">##     0   parent   102.04  99.59848  2.442e+00</span></span>
+<span><span class="co">##     1   parent    93.50  90.23787  3.262e+00</span></span>
+<span><span class="co">##     1   parent    92.50  90.23787  2.262e+00</span></span>
+<span><span class="co">##     3   parent    63.23  74.07319 -1.084e+01</span></span>
+<span><span class="co">##     3   parent    68.99  74.07319 -5.083e+00</span></span>
+<span><span class="co">##     7   parent    52.32  49.91207  2.408e+00</span></span>
+<span><span class="co">##     7   parent    55.13  49.91207  5.218e+00</span></span>
+<span><span class="co">##    14   parent    27.27  25.01258  2.257e+00</span></span>
+<span><span class="co">##    14   parent    26.64  25.01258  1.627e+00</span></span>
+<span><span class="co">##    21   parent    11.50  12.53462 -1.035e+00</span></span>
+<span><span class="co">##    21   parent    11.64  12.53462 -8.946e-01</span></span>
+<span><span class="co">##    35   parent     2.85   3.14787 -2.979e-01</span></span>
+<span><span class="co">##    35   parent     2.91   3.14787 -2.379e-01</span></span>
+<span><span class="co">##    50   parent     0.69   0.71624 -2.624e-02</span></span>
+<span><span class="co">##    50   parent     0.63   0.71624 -8.624e-02</span></span>
+<span><span class="co">##    75   parent     0.05   0.06074 -1.074e-02</span></span>
+<span><span class="co">##    75   parent     0.06   0.06074 -7.382e-04</span></span>
+<span><span class="co">##     1       m1     4.84   4.80296  3.704e-02</span></span>
+<span><span class="co">##     1       m1     5.64   4.80296  8.370e-01</span></span>
+<span><span class="co">##     3       m1    12.91  13.02400 -1.140e-01</span></span>
+<span><span class="co">##     3       m1    12.96  13.02400 -6.400e-02</span></span>
+<span><span class="co">##     7       m1    22.97  25.04476 -2.075e+00</span></span>
+<span><span class="co">##     7       m1    24.47  25.04476 -5.748e-01</span></span>
+<span><span class="co">##    14       m1    41.69  36.69003  5.000e+00</span></span>
+<span><span class="co">##    14       m1    33.21  36.69003 -3.480e+00</span></span>
+<span><span class="co">##    21       m1    44.37  41.65310  2.717e+00</span></span>
+<span><span class="co">##    21       m1    46.44  41.65310  4.787e+00</span></span>
+<span><span class="co">##    35       m1    41.22  43.31313 -2.093e+00</span></span>
+<span><span class="co">##    35       m1    37.95  43.31313 -5.363e+00</span></span>
+<span><span class="co">##    50       m1    41.19  41.21832 -2.832e-02</span></span>
+<span><span class="co">##    50       m1    40.01  41.21832 -1.208e+00</span></span>
+<span><span class="co">##    75       m1    40.09  36.44704  3.643e+00</span></span>
+<span><span class="co">##    75       m1    33.85  36.44704 -2.597e+00</span></span>
+<span><span class="co">##   100       m1    31.04  31.98162 -9.416e-01</span></span>
+<span><span class="co">##   100       m1    33.13  31.98162  1.148e+00</span></span>
+<span><span class="co">##   120       m1    25.15  28.78984 -3.640e+00</span></span>
+<span><span class="co">##   120       m1    33.31  28.78984  4.520e+00</span></span></code></pre>
   </div>
 
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -324,11 +335,13 @@
 
 
       <footer><div class="copyright">
-  <p>Developed by Johannes Ranke.</p>
+  <p></p>
+<p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <p></p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer>
@@ -337,5 +350,7 @@
   
 
 
+  
+
   </body>
 </html>
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 abf26715..f0b51c1f 100644
--- a/docs/dev/articles/FOCUS_D_files/figure-html/plot-1.png
+++ b/docs/dev/articles/FOCUS_D_files/figure-html/plot-1.png
diff --git a/docs/dev/articles/FOCUS_D_files/figure-html/plot_2-1.png b/docs/dev/articles/FOCUS_D_files/figure-html/plot_2-1.png
index f4937894..f6180470 100644
--- a/docs/dev/articles/FOCUS_D_files/figure-html/plot_2-1.png
+++ b/docs/dev/articles/FOCUS_D_files/figure-html/plot_2-1.png
diff --git a/docs/dev/articles/FOCUS_L.html b/docs/dev/articles/FOCUS_L.html
index 43ed0f69..586a6a00 100644
--- a/docs/dev/articles/FOCUS_L.html
+++ b/docs/dev/articles/FOCUS_L.html
@@ -34,7 +34,7 @@
       </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">1.1.2</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
       </span>
     </div>
 
@@ -63,19 +63,25 @@
       <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
     </li>
     <li>
-      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+      <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
     </li>
     <li>
       <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
     </li>
     <li>
+      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+    </li>
+    <li>
       <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
     </li>
     <li>
       <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
     <li>
-      <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+      <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
   </ul>
 </li>
@@ -106,7 +112,7 @@
       <h1 data-toc-skip>Example evaluation of FOCUS Laboratory Data L1 to L3</h1>
                         <h4 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 data-toc-skip class="date">Last change 18 May 2022 (rebuilt 2022-09-16)</h4>
+            <h4 data-toc-skip class="date">Last change 18 May 2022 (rebuilt 2022-11-24)</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/FOCUS_L.rmd" class="external-link"><code>vignettes/FOCUS_L.rmd</code></a></small>
       <div class="hidden name"><code>FOCUS_L.rmd</code></div>
@@ -132,17 +138,17 @@
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><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>
 <span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L1.SFO</span><span class="op">)</span></span></code></pre></div>
-<pre><code><span><span class="co">## mkin version used for fitting:    1.1.2 </span></span>
-<span><span class="co">## R version used for fitting:       4.2.1 </span></span>
-<span><span class="co">## Date of fit:     Fri Sep 16 10:31:35 2022 </span></span>
-<span><span class="co">## Date of summary: Fri Sep 16 10:31:35 2022 </span></span>
+<pre><code><span><span class="co">## mkin version used for fitting:    1.2.2 </span></span>
+<span><span class="co">## R version used for fitting:       4.2.2 </span></span>
+<span><span class="co">## Date of fit:     Thu Nov 24 08:12:09 2022 </span></span>
+<span><span class="co">## Date of summary: Thu Nov 24 08:12:09 2022 </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Equations:</span></span>
 <span><span class="co">## d_parent/dt = - k_parent * parent</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Model predictions using solution type analytical </span></span>
 <span><span class="co">## </span></span>
-<span><span class="co">## Fitted using 133 model solutions performed in 0.032 s</span></span>
+<span><span class="co">## Fitted using 133 model solutions performed in 0.033 s</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Error model: Constant variance </span></span>
 <span><span class="co">## </span></span>
@@ -238,17 +244,17 @@
 <pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre>
 <pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span>
 <span><span class="co">## doubtful</span></span></code></pre>
-<pre><code><span><span class="co">## mkin version used for fitting:    1.1.2 </span></span>
-<span><span class="co">## R version used for fitting:       4.2.1 </span></span>
-<span><span class="co">## Date of fit:     Fri Sep 16 10:31:36 2022 </span></span>
-<span><span class="co">## Date of summary: Fri Sep 16 10:31:36 2022 </span></span>
+<pre><code><span><span class="co">## mkin version used for fitting:    1.2.2 </span></span>
+<span><span class="co">## R version used for fitting:       4.2.2 </span></span>
+<span><span class="co">## Date of fit:     Thu Nov 24 08:12:09 2022 </span></span>
+<span><span class="co">## Date of summary: Thu Nov 24 08:12:09 2022 </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Equations:</span></span>
 <span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Model predictions using solution type analytical </span></span>
 <span><span class="co">## </span></span>
-<span><span class="co">## Fitted using 369 model solutions performed in 0.081 s</span></span>
+<span><span class="co">## Fitted using 369 model solutions performed in 0.091 s</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Error model: Constant variance </span></span>
 <span><span class="co">## </span></span>
@@ -350,17 +356,17 @@
 <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><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L2.FOMC</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
-<pre><code><span><span class="co">## mkin version used for fitting:    1.1.2 </span></span>
-<span><span class="co">## R version used for fitting:       4.2.1 </span></span>
-<span><span class="co">## Date of fit:     Fri Sep 16 10:31:36 2022 </span></span>
-<span><span class="co">## Date of summary: Fri Sep 16 10:31:36 2022 </span></span>
+<pre><code><span><span class="co">## mkin version used for fitting:    1.2.2 </span></span>
+<span><span class="co">## R version used for fitting:       4.2.2 </span></span>
+<span><span class="co">## Date of fit:     Thu Nov 24 08:12:10 2022 </span></span>
+<span><span class="co">## Date of summary: Thu Nov 24 08:12:10 2022 </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Equations:</span></span>
 <span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Model predictions using solution type analytical </span></span>
 <span><span class="co">## </span></span>
-<span><span class="co">## Fitted using 239 model solutions performed in 0.049 s</span></span>
+<span><span class="co">## Fitted using 239 model solutions performed in 0.048 s</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Error model: Constant variance </span></span>
 <span><span class="co">## </span></span>
@@ -431,10 +437,10 @@
 <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><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L2.DFOP</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
-<pre><code><span><span class="co">## mkin version used for fitting:    1.1.2 </span></span>
-<span><span class="co">## R version used for fitting:       4.2.1 </span></span>
-<span><span class="co">## Date of fit:     Fri Sep 16 10:31:37 2022 </span></span>
-<span><span class="co">## Date of summary: Fri Sep 16 10:31:37 2022 </span></span>
+<pre><code><span><span class="co">## mkin version used for fitting:    1.2.2 </span></span>
+<span><span class="co">## R version used for fitting:       4.2.2 </span></span>
+<span><span class="co">## Date of fit:     Thu Nov 24 08:12:10 2022 </span></span>
+<span><span class="co">## Date of summary: Thu Nov 24 08:12:10 2022 </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Equations:</span></span>
 <span><span class="co">## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span></span>
@@ -443,7 +449,7 @@
 <span><span class="co">## </span></span>
 <span><span class="co">## Model predictions using solution type analytical </span></span>
 <span><span class="co">## </span></span>
-<span><span class="co">## Fitted using 581 model solutions performed in 0.132 s</span></span>
+<span><span class="co">## Fitted using 581 model solutions performed in 0.13 s</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Error model: Constant variance </span></span>
 <span><span class="co">## </span></span>
@@ -537,10 +543,10 @@
 <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><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">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></span></code></pre></div>
-<pre><code><span><span class="co">## mkin version used for fitting:    1.1.2 </span></span>
-<span><span class="co">## R version used for fitting:       4.2.1 </span></span>
-<span><span class="co">## Date of fit:     Fri Sep 16 10:31:37 2022 </span></span>
-<span><span class="co">## Date of summary: Fri Sep 16 10:31:38 2022 </span></span>
+<pre><code><span><span class="co">## mkin version used for fitting:    1.2.2 </span></span>
+<span><span class="co">## R version used for fitting:       4.2.2 </span></span>
+<span><span class="co">## Date of fit:     Thu Nov 24 08:12:11 2022 </span></span>
+<span><span class="co">## Date of summary: Thu Nov 24 08:12:11 2022 </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Equations:</span></span>
 <span><span class="co">## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span></span>
@@ -549,7 +555,7 @@
 <span><span class="co">## </span></span>
 <span><span class="co">## Model predictions using solution type analytical </span></span>
 <span><span class="co">## </span></span>
-<span><span class="co">## Fitted using 376 model solutions performed in 0.079 s</span></span>
+<span><span class="co">## Fitted using 376 model solutions performed in 0.078 s</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Error model: Constant variance </span></span>
 <span><span class="co">## </span></span>
@@ -650,17 +656,17 @@
 <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><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">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></span></code></pre></div>
-<pre><code><span><span class="co">## mkin version used for fitting:    1.1.2 </span></span>
-<span><span class="co">## R version used for fitting:       4.2.1 </span></span>
-<span><span class="co">## Date of fit:     Fri Sep 16 10:31:38 2022 </span></span>
-<span><span class="co">## Date of summary: Fri Sep 16 10:31:38 2022 </span></span>
+<pre><code><span><span class="co">## mkin version used for fitting:    1.2.2 </span></span>
+<span><span class="co">## R version used for fitting:       4.2.2 </span></span>
+<span><span class="co">## Date of fit:     Thu Nov 24 08:12:12 2022 </span></span>
+<span><span class="co">## Date of summary: Thu Nov 24 08:12:12 2022 </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Equations:</span></span>
 <span><span class="co">## d_parent/dt = - k_parent * parent</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Model predictions using solution type analytical </span></span>
 <span><span class="co">## </span></span>
-<span><span class="co">## Fitted using 142 model solutions performed in 0.03 s</span></span>
+<span><span class="co">## Fitted using 142 model solutions performed in 0.029 s</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Error model: Constant variance </span></span>
 <span><span class="co">## </span></span>
@@ -715,17 +721,17 @@
 <span><span class="co">## parent  106  352</span></span></code></pre>
 <div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">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></span></code></pre></div>
-<pre><code><span><span class="co">## mkin version used for fitting:    1.1.2 </span></span>
-<span><span class="co">## R version used for fitting:       4.2.1 </span></span>
-<span><span class="co">## Date of fit:     Fri Sep 16 10:31:38 2022 </span></span>
-<span><span class="co">## Date of summary: Fri Sep 16 10:31:38 2022 </span></span>
+<pre><code><span><span class="co">## mkin version used for fitting:    1.2.2 </span></span>
+<span><span class="co">## R version used for fitting:       4.2.2 </span></span>
+<span><span class="co">## Date of fit:     Thu Nov 24 08:12:12 2022 </span></span>
+<span><span class="co">## Date of summary: Thu Nov 24 08:12:12 2022 </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Equations:</span></span>
 <span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Model predictions using solution type analytical </span></span>
 <span><span class="co">## </span></span>
-<span><span class="co">## Fitted using 224 model solutions performed in 0.045 s</span></span>
+<span><span class="co">## Fitted using 224 model solutions performed in 0.044 s</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Error model: Constant variance </span></span>
 <span><span class="co">## </span></span>
diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html
index 395b5f7c..e04302ef 100644
--- a/docs/dev/articles/index.html
+++ b/docs/dev/articles/index.html
@@ -17,7 +17,7 @@
       </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">1.2.0</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
       </span>
     </div>
 
diff --git a/docs/dev/articles/mkin.html b/docs/dev/articles/mkin.html
index 27e532af..df4df718 100644
--- a/docs/dev/articles/mkin.html
+++ b/docs/dev/articles/mkin.html
@@ -34,7 +34,7 @@
       </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">1.2.0</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
       </span>
     </div>
 
@@ -112,7 +112,7 @@
       <h1 data-toc-skip>Introduction to mkin</h1>
                         <h4 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 data-toc-skip class="date">Last change 15 February 2021 (rebuilt 2022-11-16)</h4>
+            <h4 data-toc-skip class="date">Last change 15 February 2021 (rebuilt 2022-11-24)</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/mkin.rmd" class="external-link"><code>vignettes/mkin.rmd</code></a></small>
       <div class="hidden name"><code>mkin.rmd</code></div>
diff --git a/docs/dev/articles/twa.html b/docs/dev/articles/twa.html
index 30eeb5a6..673d753a 100644
--- a/docs/dev/articles/twa.html
+++ b/docs/dev/articles/twa.html
@@ -20,6 +20,8 @@
 <![endif]-->
 </head>
 <body data-spy="scroll" data-target="#toc">
+    
+
     <div class="container template-article">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
@@ -32,7 +34,7 @@
       </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">1.0.3.9000</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
       </span>
     </div>
 
@@ -42,7 +44,7 @@
   <a href="../reference/index.html">Functions and data</a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
     Articles
      
     <span class="caret"></span>
@@ -58,19 +60,28 @@
       <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
     </li>
     <li>
-      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+      <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
     </li>
     <li>
       <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
     </li>
     <li>
+      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+    </li>
+    <li>
       <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
     </li>
     <li>
       <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
     <li>
-      <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+      <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
   </ul>
 </li>
@@ -80,7 +91,7 @@
       </ul>
 <ul class="nav navbar-nav navbar-right">
 <li>
-  <a href="https://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/" class="external-link">
     <span class="fab fa-github fa-lg"></span>
      
   </a>
@@ -95,15 +106,15 @@
 
       
 
-      </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">
+      </header><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 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 class="date">Last change 18 September 2019 (rebuilt 2021-02-15)</h4>
+            <h4 data-toc-skip class="date">Last change 18 September 2019 (rebuilt 2022-11-24)</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>
+      <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/twa.rmd" class="external-link"><code>vignettes/twa.rmd</code></a></small>
       <div class="hidden name"><code>twa.rmd</code></div>
 
     </div>
@@ -141,10 +152,10 @@
 <p><span class="math display">\[f_\textrm{twa} = \frac{1}{t} \left(
   \frac{1}{k_1} \left( 1 - e^{- k_1 t_b} \right) +
   \frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)} \right)  \right) \]</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>
+<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" class="external-link">pfm::max_twa()</a></code> from the ‘pfm’ package can be used.</p>
 <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">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" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p>
 </div>
 </div>
   </div>
@@ -158,11 +169,13 @@
 
 
       <footer><div class="copyright">
-  <p>Developed by Johannes Ranke.</p>
+  <p></p>
+<p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <p></p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer>
@@ -171,5 +184,7 @@
   
 
 
+  
+
   </body>
 </html>
diff --git a/docs/dev/articles/web_only/FOCUS_Z.html b/docs/dev/articles/web_only/FOCUS_Z.html
index 694b33ca..eec1ba66 100644
--- a/docs/dev/articles/web_only/FOCUS_Z.html
+++ b/docs/dev/articles/web_only/FOCUS_Z.html
@@ -20,6 +20,8 @@
 <![endif]-->
 </head>
 <body data-spy="scroll" data-target="#toc">
+    
+
     <div class="container template-article">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
@@ -32,7 +34,7 @@
       </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">1.0.3.9000</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
       </span>
     </div>
 
@@ -42,7 +44,7 @@
   <a href="../../reference/index.html">Functions and data</a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
     Articles
      
     <span class="caret"></span>
@@ -58,19 +60,28 @@
       <a href="../../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
     </li>
     <li>
-      <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+      <a href="../../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+    </li>
+    <li>
+      <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a>
     </li>
     <li>
       <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
     </li>
     <li>
+      <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+    </li>
+    <li>
       <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
     </li>
     <li>
       <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
     <li>
-      <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a>
+      <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+    </li>
+    <li>
+      <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
   </ul>
 </li>
@@ -80,7 +91,7 @@
       </ul>
 <ul class="nav navbar-nav navbar-right">
 <li>
-  <a href="https://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/" class="external-link">
     <span class="fab fa-github fa-lg"></span>
      
   </a>
@@ -95,280 +106,283 @@
 
       
 
-      </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">
+      </header><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 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 class="date">Last change 16 January 2018 (rebuilt 2021-02-15)</h4>
+            <h4 data-toc-skip class="date">Last change 16 January 2018 (rebuilt 2022-11-24)</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>
+      <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/FOCUS_Z.rmd" class="external-link"><code>vignettes/web_only/FOCUS_Z.rmd</code></a></small>
       <div class="hidden name"><code>FOCUS_Z.rmd</code></div>
 
     </div>
 
     
     
-<p><a href="http://www.jrwb.de">Wissenschaftlicher Berater, Kronacher Str. 12, 79639 Grenzach-Wyhlen, Germany</a><br><a href="http://chem.uft.uni-bremen.de/ranke">Privatdozent at the University of Bremen</a></p>
-<div id="the-data" class="section level1">
-<h1 class="hasAnchor">
-<a href="#the-data" class="anchor"></a>The data</h1>
+<p><a href="http://www.jrwb.de" class="external-link">Wissenschaftlicher Berater, Kronacher Str. 12, 79639 Grenzach-Wyhlen, Germany</a><br><a href="http://chem.uft.uni-bremen.de/ranke" class="external-link">Privatdozent at the University of Bremen</a></p>
+<div class="section level2">
+<h2 id="the-data">The data<a class="anchor" aria-label="anchor" href="#the-data"></a>
+</h2>
 <p>The following code defines the example dataset from Appendix 7 to the FOCUS kinetics report <span class="citation">(FOCUS Work Group on Degradation Kinetics 2014, 354)</span>.</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
-<span class="va">LOD</span> <span class="op">=</span> <span class="fl">0.5</span>
-<span class="va">FOCUS_2006_Z</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>
-  t <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">0.04</span>, <span class="fl">0.125</span>, <span class="fl">0.29</span>, <span class="fl">0.54</span>, <span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span>, <span class="fl">4</span>, <span class="fl">7</span>, <span class="fl">10</span>, <span class="fl">14</span>, <span class="fl">21</span>,
-        <span class="fl">42</span>, <span class="fl">61</span>, <span class="fl">96</span>, <span class="fl">124</span><span class="op">)</span>,
-  Z0 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fl">100</span>, <span class="fl">81.7</span>, <span class="fl">70.4</span>, <span class="fl">51.1</span>, <span class="fl">41.2</span>, <span class="fl">6.6</span>, <span class="fl">4.6</span>, <span class="fl">3.9</span>, <span class="fl">4.6</span>, <span class="fl">4.3</span>, <span class="fl">6.8</span>,
-         <span class="fl">2.9</span>, <span class="fl">3.5</span>, <span class="fl">5.3</span>, <span class="fl">4.4</span>, <span class="fl">1.2</span>, <span class="fl">0.7</span><span class="op">)</span>,
-  Z1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">18.3</span>, <span class="fl">29.6</span>, <span class="fl">46.3</span>, <span class="fl">55.1</span>, <span class="fl">65.7</span>, <span class="fl">39.1</span>, <span class="fl">36</span>, <span class="fl">15.3</span>, <span class="fl">5.6</span>, <span class="fl">1.1</span>,
-         <span class="fl">1.6</span>, <span class="fl">0.6</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span><span class="op">)</span>,
-  Z2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="cn">NA</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="fl">2.6</span>, <span class="fl">3.8</span>, <span class="fl">15.3</span>, <span class="fl">37.2</span>, <span class="fl">31.7</span>, <span class="fl">35.6</span>, <span class="fl">14.5</span>,
-         <span class="fl">0.8</span>, <span class="fl">2.1</span>, <span class="fl">1.9</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span><span class="op">)</span>,
-  Z3 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="fl">9.2</span>, <span class="fl">13.1</span>, <span class="fl">22.3</span>, <span class="fl">28.4</span>, <span class="fl">32.5</span>,
-         <span class="fl">25.2</span>, <span class="fl">17.2</span>, <span class="fl">4.8</span>, <span class="fl">4.5</span>, <span class="fl">2.8</span>, <span class="fl">4.4</span><span class="op">)</span><span class="op">)</span>
-
-<span class="va">FOCUS_2006_Z_mkin</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">FOCUS_2006_Z</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span><span class="va">LOD</span> <span class="op">=</span> <span class="fl">0.5</span></span>
+<span><span class="va">FOCUS_2006_Z</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span>
+<span>  t <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">0.04</span>, <span class="fl">0.125</span>, <span class="fl">0.29</span>, <span class="fl">0.54</span>, <span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span>, <span class="fl">4</span>, <span class="fl">7</span>, <span class="fl">10</span>, <span class="fl">14</span>, <span class="fl">21</span>,</span>
+<span>        <span class="fl">42</span>, <span class="fl">61</span>, <span class="fl">96</span>, <span class="fl">124</span><span class="op">)</span>,</span>
+<span>  Z0 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">100</span>, <span class="fl">81.7</span>, <span class="fl">70.4</span>, <span class="fl">51.1</span>, <span class="fl">41.2</span>, <span class="fl">6.6</span>, <span class="fl">4.6</span>, <span class="fl">3.9</span>, <span class="fl">4.6</span>, <span class="fl">4.3</span>, <span class="fl">6.8</span>,</span>
+<span>         <span class="fl">2.9</span>, <span class="fl">3.5</span>, <span class="fl">5.3</span>, <span class="fl">4.4</span>, <span class="fl">1.2</span>, <span class="fl">0.7</span><span class="op">)</span>,</span>
+<span>  Z1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">18.3</span>, <span class="fl">29.6</span>, <span class="fl">46.3</span>, <span class="fl">55.1</span>, <span class="fl">65.7</span>, <span class="fl">39.1</span>, <span class="fl">36</span>, <span class="fl">15.3</span>, <span class="fl">5.6</span>, <span class="fl">1.1</span>,</span>
+<span>         <span class="fl">1.6</span>, <span class="fl">0.6</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span><span class="op">)</span>,</span>
+<span>  Z2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="cn">NA</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="fl">2.6</span>, <span class="fl">3.8</span>, <span class="fl">15.3</span>, <span class="fl">37.2</span>, <span class="fl">31.7</span>, <span class="fl">35.6</span>, <span class="fl">14.5</span>,</span>
+<span>         <span class="fl">0.8</span>, <span class="fl">2.1</span>, <span class="fl">1.9</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span><span class="op">)</span>,</span>
+<span>  Z3 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="fl">9.2</span>, <span class="fl">13.1</span>, <span class="fl">22.3</span>, <span class="fl">28.4</span>, <span class="fl">32.5</span>,</span>
+<span>         <span class="fl">25.2</span>, <span class="fl">17.2</span>, <span class="fl">4.8</span>, <span class="fl">4.5</span>, <span class="fl">2.8</span>, <span class="fl">4.4</span><span class="op">)</span><span class="op">)</span></span>
+<span></span>
+<span><span class="va">FOCUS_2006_Z_mkin</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">FOCUS_2006_Z</span><span class="op">)</span></span></code></pre></div>
 </div>
-<div id="parent-and-one-metabolite" class="section level1">
-<h1 class="hasAnchor">
-<a href="#parent-and-one-metabolite" class="anchor"></a>Parent and one metabolite</h1>
+<div class="section level2">
+<h2 id="parent-and-one-metabolite">Parent and one metabolite<a class="anchor" aria-label="anchor" href="#parent-and-one-metabolite"></a>
+</h2>
 <p>The next step is to set up the models used for the kinetic analysis. As the simultaneous fit of parent and the first metabolite is usually straightforward, Step 1 (SFO for parent only) is skipped here. We start with the model 2a, with formation and decline of metabolite Z1 and the pathway from parent directly to sink included (default in mkin).</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">Z.2a</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span><span class="op">)</span>,
-                Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
-<pre><code>## Temporary DLL for differentials generated and loaded</code></pre>
+<code class="sourceCode R"><span><span class="va">Z.2a</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span><span class="op">)</span>,</span>
+<span>                Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">m.Z.2a</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.2a</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
-<pre><code>## Warning in mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
-## value of zero were removed from the data</code></pre>
+<code class="sourceCode R"><span><span class="va">m.Z.2a</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.2a</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Warning in mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span>
+<span><span class="co">## value of zero were removed from the data</span></span></code></pre>
 <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.2a</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.2a</span><span class="op">)</span></span></code></pre></div>
 <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png" width="700"></p>
 <div class="sourceCode" id="cb7"><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.2a</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></code></pre></div>
-<pre><code>##            Estimate se_notrans t value     Pr(&gt;t)    Lower    Upper
-## Z0_0       97.01488   3.301084 29.3888 3.2971e-21 91.66556 102.3642
-## k_Z0        2.23601   0.207078 10.7979 3.3309e-11  1.95303   2.5600
-## k_Z1        0.48212   0.063265  7.6207 2.8154e-08  0.40341   0.5762
-## f_Z0_to_Z1  1.00000   0.094764 10.5525 5.3560e-11  0.00000   1.0000
-## sigma       4.80411   0.635638  7.5579 3.2592e-08  3.52677   6.0815</code></pre>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.2a</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div>
+<pre><code><span><span class="co">##            Estimate se_notrans t value     Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## Z0_0       97.01488   3.301084 29.3888 3.2971e-21 91.66556 102.3642</span></span>
+<span><span class="co">## k_Z0        2.23601   0.207078 10.7979 3.3309e-11  1.95303   2.5600</span></span>
+<span><span class="co">## k_Z1        0.48212   0.063265  7.6207 2.8154e-08  0.40341   0.5762</span></span>
+<span><span class="co">## f_Z0_to_Z1  1.00000   0.094764 10.5525 5.3560e-11  0.00000   1.0000</span></span>
+<span><span class="co">## sigma       4.80411   0.635638  7.5579 3.2592e-08  3.52677   6.0815</span></span></code></pre>
 <p>As obvious from the parameter summary (the  component of the summary), the kinetic rate constant from parent compound Z to sink is very small and the t-test for this parameter suggests that it is not significantly different from zero. This suggests, in agreement with the analysis in the FOCUS kinetics report, to simplify the model by removing the pathway to sink.</p>
 <p>A similar result can be obtained when formation fractions are used in the model formulation:</p>
 <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">Z.2a.ff</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span><span class="op">)</span>,
-                   Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,
-                   use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></code></pre></div>
-<pre><code>## Temporary DLL for differentials generated and loaded</code></pre>
+<code class="sourceCode R"><span><span class="va">Z.2a.ff</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span><span class="op">)</span>,</span>
+<span>                   Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span>
+<span>                   use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre>
 <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">m.Z.2a.ff</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.2a.ff</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
-<pre><code>## Warning in mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
-## value of zero were removed from the data</code></pre>
+<code class="sourceCode R"><span><span class="va">m.Z.2a.ff</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.2a.ff</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Warning in mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span>
+<span><span class="co">## value of zero were removed from the data</span></span></code></pre>
 <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.2a.ff</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.2a.ff</span><span class="op">)</span></span></code></pre></div>
 <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png" width="700"></p>
 <div class="sourceCode" id="cb14"><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.2a.ff</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></code></pre></div>
-<pre><code>##            Estimate se_notrans t value     Pr(&gt;t)    Lower    Upper
-## Z0_0       97.01488   3.301084 29.3888 3.2971e-21 91.66556 102.3642
-## k_Z0        2.23601   0.207078 10.7979 3.3309e-11  1.95303   2.5600
-## k_Z1        0.48212   0.063265  7.6207 2.8154e-08  0.40341   0.5762
-## f_Z0_to_Z1  1.00000   0.094764 10.5525 5.3560e-11  0.00000   1.0000
-## sigma       4.80411   0.635638  7.5579 3.2592e-08  3.52677   6.0815</code></pre>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.2a.ff</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div>
+<pre><code><span><span class="co">##            Estimate se_notrans t value     Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## Z0_0       97.01488   3.301084 29.3888 3.2971e-21 91.66556 102.3642</span></span>
+<span><span class="co">## k_Z0        2.23601   0.207078 10.7979 3.3309e-11  1.95303   2.5600</span></span>
+<span><span class="co">## k_Z1        0.48212   0.063265  7.6207 2.8154e-08  0.40341   0.5762</span></span>
+<span><span class="co">## f_Z0_to_Z1  1.00000   0.094764 10.5525 5.3560e-11  0.00000   1.0000</span></span>
+<span><span class="co">## sigma       4.80411   0.635638  7.5579 3.2592e-08  3.52677   6.0815</span></span></code></pre>
 <p>Here, the ilr transformed formation fraction fitted in the model takes a very large value, and the backtransformed formation fraction from parent Z to Z1 is practically unity. Here, the covariance matrix used for the calculation of confidence intervals is not returned as the model is overparameterised.</p>
 <p>A simplified model is obtained by removing the pathway to the sink. </p>
 <p>In the following, we use the parameterisation with formation fractions in order to be able to compare with the results in the FOCUS guidance, and as it makes it easier to use parameters obtained in a previous fit when adding a further metabolite.</p>
 <div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">Z.3</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-               Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></code></pre></div>
-<pre><code>## Temporary DLL for differentials generated and loaded</code></pre>
+<code class="sourceCode R"><span><span class="va">Z.3</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>               Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre>
 <div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">m.Z.3</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.3</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
-<pre><code>## Warning in mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
-## value of zero were removed from the data</code></pre>
+<code class="sourceCode R"><span><span class="va">m.Z.3</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.3</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Warning in mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span>
+<span><span class="co">## value of zero were removed from the data</span></span></code></pre>
 <div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.3</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.3</span><span class="op">)</span></span></code></pre></div>
 <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png" width="700"></p>
 <div class="sourceCode" id="cb21"><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.3</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></code></pre></div>
-<pre><code>##       Estimate se_notrans t value     Pr(&gt;t)    Lower    Upper
-## Z0_0  97.01488   2.597342  37.352 2.0106e-24 91.67597 102.3538
-## k_Z0   2.23601   0.146904  15.221 9.1477e-15  1.95354   2.5593
-## k_Z1   0.48212   0.041727  11.554 4.8268e-12  0.40355   0.5760
-## sigma  4.80411   0.620208   7.746 1.6110e-08  3.52925   6.0790</code></pre>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.3</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div>
+<pre><code><span><span class="co">##       Estimate se_notrans t value     Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## Z0_0  97.01488   2.597342  37.352 2.0106e-24 91.67597 102.3538</span></span>
+<span><span class="co">## k_Z0   2.23601   0.146904  15.221 9.1477e-15  1.95354   2.5593</span></span>
+<span><span class="co">## k_Z1   0.48212   0.041727  11.554 4.8268e-12  0.40355   0.5760</span></span>
+<span><span class="co">## sigma  4.80411   0.620208   7.746 1.6110e-08  3.52925   6.0790</span></span></code></pre>
 <p>As there is only one transformation product for Z0 and no pathway to sink, the formation fraction is internally fixed to unity.</p>
 </div>
-<div id="metabolites-z2-and-z3" class="section level1">
-<h1 class="hasAnchor">
-<a href="#metabolites-z2-and-z3" class="anchor"></a>Metabolites Z2 and Z3</h1>
+<div class="section level2">
+<h2 id="metabolites-z2-and-z3">Metabolites Z2 and Z3<a class="anchor" aria-label="anchor" href="#metabolites-z2-and-z3"></a>
+</h2>
 <p>As suggested in the FOCUS report, the pathway to sink was removed for metabolite Z1 as well in the next step. While this step appears questionable on the basis of the above results, it is followed here for the purpose of comparison. Also, in the FOCUS report, it is assumed that there is additional empirical evidence that Z1 quickly and exclusively hydrolyses to Z2.</p>
 <div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">Z.5</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-               Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-               Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></code></pre></div>
-<pre><code>## Temporary DLL for differentials generated and loaded</code></pre>
+<code class="sourceCode R"><span><span class="va">Z.5</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>               Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>               Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre>
 <div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">m.Z.5</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
-<pre><code>## Warning in mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
-## value of zero were removed from the data</code></pre>
+<code class="sourceCode R"><span><span class="va">m.Z.5</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Warning in mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span>
+<span><span class="co">## value of zero were removed from the data</span></span></code></pre>
 <div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.5</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.5</span><span class="op">)</span></span></code></pre></div>
 <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png" width="700"></p>
 <p>Finally, metabolite Z3 is added to the model. We use the optimised differential equation parameter values from the previous fit in order to accelerate the optimization.</p>
 <div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">Z.FOCUS</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-                   Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-                   Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,
-                   Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,
-                   use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></code></pre></div>
-<pre><code>## Temporary DLL for differentials generated and loaded</code></pre>
+<code class="sourceCode R"><span><span class="va">Z.FOCUS</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>                   Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>                   Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,</span>
+<span>                   Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span>
+<span>                   use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre>
 <div class="sourceCode" id="cb30"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">m.Z.FOCUS</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.FOCUS</span>, <span class="va">FOCUS_2006_Z_mkin</span>,
-                     parms.ini <span class="op">=</span> <span class="va">m.Z.5</span><span class="op">$</span><span class="va">bparms.ode</span>,
-                     quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
-<pre><code>## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, :
-## Observations with value of zero were removed from the data</code></pre>
-<pre><code>## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : Optimisation did not converge:
-## false convergence (8)</code></pre>
+<code class="sourceCode R"><span><span class="va">m.Z.FOCUS</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.FOCUS</span>, <span class="va">FOCUS_2006_Z_mkin</span>,</span>
+<span>                     parms.ini <span class="op">=</span> <span class="va">m.Z.5</span><span class="op">$</span><span class="va">bparms.ode</span>,</span>
+<span>                     quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, :</span></span>
+<span><span class="co">## Observations with value of zero were removed from the data</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : Optimisation did not converge:</span></span>
+<span><span class="co">## false convergence (8)</span></span></code></pre>
 <div class="sourceCode" id="cb33"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></span></code></pre></div>
 <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png" width="700"></p>
 <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">$</span><span class="va">bpar</span></code></pre></div>
-<pre><code>##             Estimate se_notrans t value     Pr(&gt;t)     Lower      Upper
-## Z0_0       96.838822   1.994274 48.5584 4.0280e-42 92.826981 100.850664
-## k_Z0        2.215393   0.118458 18.7019 1.0413e-23  1.989456   2.466989
-## k_Z1        0.478305   0.028258 16.9266 6.2418e-22  0.424708   0.538666
-## k_Z2        0.451627   0.042139 10.7176 1.6314e-14  0.374339   0.544872
-## k_Z3        0.058692   0.015245  3.8499 1.7803e-04  0.034808   0.098965
-## f_Z2_to_Z3  0.471502   0.058351  8.0805 9.6608e-11  0.357769   0.588274
-## sigma       3.984431   0.383402 10.3923 4.5575e-14  3.213126   4.755736</code></pre>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div>
+<pre><code><span><span class="co">##             Estimate se_notrans t value     Pr(&gt;t)     Lower      Upper</span></span>
+<span><span class="co">## Z0_0       96.838822   1.994274 48.5584 4.0280e-42 92.826981 100.850664</span></span>
+<span><span class="co">## k_Z0        2.215393   0.118458 18.7019 1.0413e-23  1.989456   2.466989</span></span>
+<span><span class="co">## k_Z1        0.478305   0.028258 16.9266 6.2418e-22  0.424708   0.538666</span></span>
+<span><span class="co">## k_Z2        0.451627   0.042139 10.7176 1.6314e-14  0.374339   0.544872</span></span>
+<span><span class="co">## k_Z3        0.058692   0.015245  3.8499 1.7803e-04  0.034808   0.098965</span></span>
+<span><span class="co">## f_Z2_to_Z3  0.471502   0.058351  8.0805 9.6608e-11  0.357769   0.588274</span></span>
+<span><span class="co">## sigma       3.984431   0.383402 10.3923 4.5575e-14  3.213126   4.755736</span></span></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>
-<pre><code>## $ff
-##   Z2_Z3 Z2_sink 
-##  0.4715  0.5285 
-## 
-## $distimes
-##        DT50    DT90
-## Z0  0.31288  1.0394
-## Z1  1.44917  4.8141
-## Z2  1.53478  5.0984
-## Z3 11.80986 39.2315</code></pre>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## $ff</span></span>
+<span><span class="co">##   Z2_Z3 Z2_sink </span></span>
+<span><span class="co">##  0.4715  0.5285 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $distimes</span></span>
+<span><span class="co">##        DT50    DT90</span></span>
+<span><span class="co">## Z0  0.31288  1.0394</span></span>
+<span><span class="co">## Z1  1.44917  4.8141</span></span>
+<span><span class="co">## Z2  1.53478  5.0984</span></span>
+<span><span class="co">## Z3 11.80986 39.2315</span></span></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">
-<h1 class="hasAnchor">
-<a href="#using-the-sforb-model" class="anchor"></a>Using the SFORB model</h1>
+<div class="section level2">
+<h2 id="using-the-sforb-model">Using the SFORB model<a class="anchor" aria-label="anchor" href="#using-the-sforb-model"></a>
+</h2>
 <p>As the FOCUS report states, there is a certain tailing of the time course of metabolite Z3. Also, the time course of the parent compound is not fitted very well using the SFO model, as residues at a certain low level remain.</p>
 <p>Therefore, an additional model is offered here, using the single first-order reversible binding (SFORB) model for metabolite Z3. As expected, the <span class="math inline">\(\chi^2\)</span> error level is lower for metabolite Z3 using this model and the graphical fit for Z3 is improved. However, the covariance matrix is not returned.</p>
 <div class="sourceCode" id="cb38"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">Z.mkin.1</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-                    Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-                    Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,
-                    Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
-<pre><code>## Temporary DLL for differentials generated and loaded</code></pre>
+<code class="sourceCode R"><span><span class="va">Z.mkin.1</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>                    Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>                    Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,</span>
+<span>                    Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre>
 <div class="sourceCode" id="cb40"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">m.Z.mkin.1</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.1</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
-<pre><code>## Warning in mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
-## value of zero were removed from the data</code></pre>
+<code class="sourceCode R"><span><span class="va">m.Z.mkin.1</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.1</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Warning in mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span>
+<span><span class="co">## value of zero were removed from the data</span></span></code></pre>
 <div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.1</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.1</span><span class="op">)</span></span></code></pre></div>
 <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png" width="700"></p>
 <div class="sourceCode" id="cb43"><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.mkin.1</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">cov.unscaled</span></code></pre></div>
-<pre><code>## NULL</code></pre>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.mkin.1</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">cov.unscaled</span></span></code></pre></div>
+<pre><code><span><span class="co">## NULL</span></span></code></pre>
 <p>Therefore, a further stepwise model building is performed starting from the stage of parent and two metabolites, starting from the assumption that the model fit for the parent compound can be improved by using the SFORB model.</p>
 <div class="sourceCode" id="cb45"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">Z.mkin.3</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-                    Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-                    Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
-<pre><code>## Temporary DLL for differentials generated and loaded</code></pre>
+<code class="sourceCode R"><span><span class="va">Z.mkin.3</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>                    Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>                    Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre>
 <div class="sourceCode" id="cb47"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">m.Z.mkin.3</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.3</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
-<pre><code>## Warning in mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
-## value of zero were removed from the data</code></pre>
+<code class="sourceCode R"><span><span class="va">m.Z.mkin.3</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.3</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Warning in mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span>
+<span><span class="co">## value of zero were removed from the data</span></span></code></pre>
 <div class="sourceCode" id="cb49"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.3</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.3</span><span class="op">)</span></span></code></pre></div>
 <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png" width="700"></p>
 <p>This results in a much better representation of the behaviour of the parent compound Z0.</p>
 <p>Finally, Z3 is added as well. These models appear overparameterised (no covariance matrix returned) if the sink for Z1 is left in the models.</p>
 <div class="sourceCode" id="cb50"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">Z.mkin.4</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-                    Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-                    Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,
-                    Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
-<pre><code>## Temporary DLL for differentials generated and loaded</code></pre>
+<code class="sourceCode R"><span><span class="va">Z.mkin.4</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>                    Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>                    Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,</span>
+<span>                    Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre>
 <div class="sourceCode" id="cb52"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">m.Z.mkin.4</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.4</span>, <span class="va">FOCUS_2006_Z_mkin</span>,
-                      parms.ini <span class="op">=</span> <span class="va">m.Z.mkin.3</span><span class="op">$</span><span class="va">bparms.ode</span>,
-                      quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
-<pre><code>## Warning in mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, parms.ini = m.Z.mkin.
-## 3$bparms.ode, : Observations with value of zero were removed from the data</code></pre>
+<code class="sourceCode R"><span><span class="va">m.Z.mkin.4</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.4</span>, <span class="va">FOCUS_2006_Z_mkin</span>,</span>
+<span>                      parms.ini <span class="op">=</span> <span class="va">m.Z.mkin.3</span><span class="op">$</span><span class="va">bparms.ode</span>,</span>
+<span>                      quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Warning in mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, parms.ini =</span></span>
+<span><span class="co">## m.Z.mkin.3$bparms.ode, : Observations with value of zero were removed from the</span></span>
+<span><span class="co">## data</span></span></code></pre>
 <div class="sourceCode" id="cb54"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.4</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.4</span><span class="op">)</span></span></code></pre></div>
 <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png" width="700"></p>
 <p>The error level of the fit, but especially of metabolite Z3, can be improved if the SFORB model is chosen for this metabolite, as this model is capable of representing the tailing of the metabolite decline phase.</p>
 <div class="sourceCode" id="cb55"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">Z.mkin.5</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-                    Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
-                    Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,
-                    Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
-<pre><code>## Temporary DLL for differentials generated and loaded</code></pre>
+<code class="sourceCode R"><span><span class="va">Z.mkin.5</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>                    Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>                    Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,</span>
+<span>                    Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre>
 <div class="sourceCode" id="cb57"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">m.Z.mkin.5</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>,
-                      parms.ini <span class="op">=</span> <span class="va">m.Z.mkin.4</span><span class="op">$</span><span class="va">bparms.ode</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">4</span><span class="op">]</span>,
-                      quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
-<pre><code>## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = m.Z.mkin.
-## 4$bparms.ode[1:4], : Observations with value of zero were removed from the data</code></pre>
+<code class="sourceCode R"><span><span class="va">m.Z.mkin.5</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>,</span>
+<span>                      parms.ini <span class="op">=</span> <span class="va">m.Z.mkin.4</span><span class="op">$</span><span class="va">bparms.ode</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">4</span><span class="op">]</span>,</span>
+<span>                      quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini =</span></span>
+<span><span class="co">## m.Z.mkin.4$bparms.ode[1:4], : Observations with value of zero were removed from</span></span>
+<span><span class="co">## the data</span></span></code></pre>
 <div class="sourceCode" id="cb59"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.5</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.5</span><span class="op">)</span></span></code></pre></div>
 <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png" width="700"></p>
 <p>The summary view of the backtransformed parameters shows that we get no confidence intervals due to overparameterisation. As the optimized  is excessively small, it seems reasonable to fix it to zero.</p>
 <div class="sourceCode" id="cb60"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">m.Z.mkin.5a</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>,
-                       parms.ini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="va">m.Z.mkin.5</span><span class="op">$</span><span class="va">bparms.ode</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">7</span><span class="op">]</span>,
-                                     k_Z3_bound_free <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,
-                       fixed_parms <span class="op">=</span> <span class="st">"k_Z3_bound_free"</span>,
-                       quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
-<pre><code>## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = c(m.Z.mkin.
-## 5$bparms.ode[1:7], : Observations with value of zero were removed from the data</code></pre>
+<code class="sourceCode R"><span><span class="va">m.Z.mkin.5a</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>,</span>
+<span>                       parms.ini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">m.Z.mkin.5</span><span class="op">$</span><span class="va">bparms.ode</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">7</span><span class="op">]</span>,</span>
+<span>                                     k_Z3_bound_free <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span>
+<span>                       fixed_parms <span class="op">=</span> <span class="st">"k_Z3_bound_free"</span>,</span>
+<span>                       quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini =</span></span>
+<span><span class="co">## c(m.Z.mkin.5$bparms.ode[1:7], : Observations with value of zero were removed</span></span>
+<span><span class="co">## from the data</span></span></code></pre>
 <div class="sourceCode" id="cb62"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></span></code></pre></div>
 <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png" width="700"></p>
 <p>As expected, the residual plots for Z0 and Z3 are more random than in the case of the all SFO model for which they were shown above. In conclusion, the model  is proposed as the best-fit model for the dataset from Appendix 7 of the FOCUS report.</p>
 <p>A graphical representation of the confidence intervals can finally be obtained.</p>
 <div class="sourceCode" id="cb63"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="../../reference/mkinparplot.html">mkinparplot</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="../../reference/mkinparplot.html">mkinparplot</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></span></code></pre></div>
 <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png" width="700"></p>
 <p>The endpoints obtained with this model are</p>
 <div class="sourceCode" id="cb64"><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.mkin.5a</span><span class="op">)</span></code></pre></div>
-<pre><code>## $ff
-## Z0_free   Z2_Z3 Z2_sink Z3_free 
-## 1.00000 0.53656 0.46344 1.00000 
-## 
-## $SFORB
-##     Z0_b1     Z0_b2     Z3_b1     Z3_b2 
-## 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     92.266         NA         NA
-## Z1 1.5148 5.0320       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>
+<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## $ff</span></span>
+<span><span class="co">## Z0_free   Z2_Z3 Z2_sink Z3_free </span></span>
+<span><span class="co">## 1.00000 0.53656 0.46344 1.00000 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $SFORB</span></span>
+<span><span class="co">##     Z0_b1     Z0_b2      Z0_g     Z3_b1     Z3_b2      Z3_g </span></span>
+<span><span class="co">## 2.4471322 0.0075125 0.9519862 0.0800069 0.0000000 0.9347820 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $distimes</span></span>
+<span><span class="co">##      DT50   DT90 DT50back DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2</span></span>
+<span><span class="co">## Z0 0.3043 1.1848  0.35666    0.28325     92.266         NA         NA</span></span>
+<span><span class="co">## Z1 1.5148 5.0320       NA         NA         NA         NA         NA</span></span>
+<span><span class="co">## Z2 1.6414 5.4526       NA         NA         NA         NA         NA</span></span>
+<span><span class="co">## Z3     NA     NA       NA         NA         NA     8.6636        Inf</span></span></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>
-<div id="references" class="section level1">
-<h1 class="hasAnchor">
-<a href="#references" class="anchor"></a>References</h1>
+<div class="section level2">
+<h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
+</h2>
 <!-- vim: set foldmethod=syntax: -->
 <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">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" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p>
 </div>
 </div>
 </div>
@@ -385,11 +399,13 @@
 
 
       <footer><div class="copyright">
-  <p>Developed by Johannes Ranke.</p>
+  <p></p>
+<p>Developed by Johannes Ranke.</p>
 </div>
 
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-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <p></p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
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@@ -398,5 +414,7 @@
   
 
 
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diff --git a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png
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diff --git a/docs/dev/articles/web_only/NAFTA_examples.html b/docs/dev/articles/web_only/NAFTA_examples.html
index b9784415..a054d4a1 100644
--- a/docs/dev/articles/web_only/NAFTA_examples.html
+++ b/docs/dev/articles/web_only/NAFTA_examples.html
@@ -20,6 +20,8 @@
 <![endif]-->
 </head>
 <body data-spy="scroll" data-target="#toc">
+    
+
     <div class="container template-article">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
@@ -32,7 +34,7 @@
       </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">1.0.3.9000</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
       </span>
     </div>
 
@@ -42,7 +44,7 @@
   <a href="../../reference/index.html">Functions and data</a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
     Articles
      
     <span class="caret"></span>
@@ -58,19 +60,28 @@
       <a href="../../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
     </li>
     <li>
-      <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+      <a href="../../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+    </li>
+    <li>
+      <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a>
     </li>
     <li>
       <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
     </li>
     <li>
+      <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+    </li>
+    <li>
       <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
     </li>
     <li>
       <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
     <li>
-      <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a>
+      <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+    </li>
+    <li>
+      <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
   </ul>
 </li>
@@ -80,7 +91,7 @@
       </ul>
 <ul class="nav navbar-nav navbar-right">
 <li>
-  <a href="https://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/" class="external-link">
     <span class="fab fa-github fa-lg"></span>
      
   </a>
@@ -95,908 +106,908 @@
 
       
 
-      </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">
+      </header><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 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 class="date">26 February 2019 (rebuilt 2021-02-15)</h4>
+            <h4 data-toc-skip class="date">26 February 2019 (rebuilt 2022-11-24)</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>
+      <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/NAFTA_examples.rmd" class="external-link"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small>
       <div class="hidden name"><code>NAFTA_examples.rmd</code></div>
 
     </div>
 
     
     
-<div id="introduction" class="section level1">
-<h1 class="hasAnchor">
-<a href="#introduction" class="anchor"></a>Introduction</h1>
+<div class="section level2">
+<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
+</h2>
 <p>In this document, the example evaluations provided in Attachment 1 to the SOP of US EPA for using the NAFTA guidance <span class="citation">(US EPA 2015)</span> are repeated using mkin. The original evaluations reported in the attachment were performed using PestDF in version 0.8.4. Note that PestDF 0.8.13 is the version distributed at the US EPA website today (2019-02-26).</p>
 <p>The datasets are now distributed with the mkin package.</p>
 </div>
-<div id="examples-where-dfop-did-not-converge-with-pestdf-0-8-4" class="section level1">
-<h1 class="hasAnchor">
-<a href="#examples-where-dfop-did-not-converge-with-pestdf-0-8-4" class="anchor"></a>Examples where DFOP did not converge with PestDF 0.8.4</h1>
+<div class="section level2">
+<h2 id="examples-where-dfop-did-not-converge-with-pestdf-0-8-4">Examples where DFOP did not converge with PestDF 0.8.4<a class="anchor" aria-label="anchor" href="#examples-where-dfop-did-not-converge-with-pestdf-0-8-4"></a>
+</h2>
 <p>In attachment 1, it is reported that the DFOP model does not converge for these datasets when PestDF 0.8.4 was used. For all four datasets, the DFOP model can be fitted with mkin (see below). The negative half-life given by PestDF 0.8.4 for these fits appears to be the result of a bug. The results for the other two models (SFO and IORE) are the same.</p>
-<div id="example-on-page-5-upper-panel" class="section level2">
-<h2 class="hasAnchor">
-<a href="#example-on-page-5-upper-panel" class="anchor"></a>Example on page 5, upper panel</h2>
+<div class="section level3">
+<h3 id="example-on-page-5-upper-panel">Example on page 5, upper panel<a class="anchor" aria-label="anchor" href="#example-on-page-5-upper-panel"></a>
+</h3>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">p5a</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">"p5a"</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>
+<code class="sourceCode R"><span><span class="va">p5a</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">"p5a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <div class="sourceCode" id="cb4"><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">p5a</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p5a-1.png" width="700"></p>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></code></pre></div>
-<pre><code>## Sums of squares:
-##       SFO      IORE      DFOP 
-## 465.21753  56.27506  32.06401 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 64.4304
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)  Lower   Upper
-## parent_0  95.8401 4.67e-21 92.245 99.4357
-## k_parent   0.0102 3.92e-12  0.009  0.0117
-## sigma      4.8230 3.81e-06  3.214  6.4318
-## 
-## $IORE
-##                Estimate Pr(&gt;t)    Lower    Upper
-## parent_0       1.01e+02     NA 9.91e+01 1.02e+02
-## k__iore_parent 1.54e-05     NA 4.08e-06 5.84e-05
-## N_parent       2.57e+00     NA 2.25e+00 2.89e+00
-## sigma          1.68e+00     NA 1.12e+00 2.24e+00
-## 
-## $DFOP
-##          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       2.26e-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
-## 
-## 
-## DTx values:
-##      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 5.59e+11 3.07e+11
-## 
-## Representative half-life:
-## [1] 321.51</code></pre>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##       SFO      IORE      DFOP </span></span>
+<span><span class="co">## 465.21753  56.27506  32.06401 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 64.4304</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)  Lower   Upper</span></span>
+<span><span class="co">## parent_0  95.8401 4.67e-21 92.245 99.4357</span></span>
+<span><span class="co">## k_parent   0.0102 3.92e-12  0.009  0.0117</span></span>
+<span><span class="co">## sigma      4.8230 3.81e-06  3.214  6.4318</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0       1.01e+02     NA 9.91e+01 1.02e+02</span></span>
+<span><span class="co">## k__iore_parent 1.54e-05     NA 4.08e-06 5.84e-05</span></span>
+<span><span class="co">## N_parent       2.57e+00     NA 2.25e+00 2.89e+00</span></span>
+<span><span class="co">## sigma          1.68e+00     NA 1.12e+00 2.24e+00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)   Lower    Upper</span></span>
+<span><span class="co">## parent_0 9.99e+01 1.41e-26 98.8116 101.0810</span></span>
+<span><span class="co">## k1       2.67e-02 5.05e-06  0.0243   0.0295</span></span>
+<span><span class="co">## k2       2.26e-12 5.00e-01  0.0000      Inf</span></span>
+<span><span class="co">## g        6.47e-01 3.67e-06  0.6248   0.6677</span></span>
+<span><span class="co">## sigma    1.27e+00 8.91e-06  0.8395   1.6929</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50     DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  67.7 2.25e+02 6.77e+01</span></span>
+<span><span class="co">## IORE 58.2 1.07e+03 3.22e+02</span></span>
+<span><span class="co">## DFOP 55.5 5.59e+11 3.07e+11</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 321.51</span></span></code></pre>
 </div>
-<div id="example-on-page-5-lower-panel" class="section level2">
-<h2 class="hasAnchor">
-<a href="#example-on-page-5-lower-panel" class="anchor"></a>Example on page 5, lower panel</h2>
+<div class="section level3">
+<h3 id="example-on-page-5-lower-panel">Example on page 5, lower panel<a class="anchor" aria-label="anchor" href="#example-on-page-5-lower-panel"></a>
+</h3>
 <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">p5b</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">"p5b"</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>
+<code class="sourceCode R"><span><span class="va">p5b</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">"p5b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <div class="sourceCode" id="cb10"><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">p5b</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p5b-1.png" width="700"></p>
 <div class="sourceCode" id="cb11"><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">p5b</span><span class="op">)</span></code></pre></div>
-<pre><code>## Sums of squares:
-##      SFO     IORE     DFOP 
-## 94.81123 10.10936  7.55871 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 11.77879
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0   96.497 2.32e-24 94.85271 98.14155
-## k_parent    0.008 3.42e-14  0.00737  0.00869
-## sigma       2.295 1.22e-05  1.47976  3.11036
-## 
-## $IORE
-##                Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0       9.85e+01 1.17e-28 9.79e+01 9.92e+01
-## k__iore_parent 1.53e-04 6.50e-03 7.21e-05 3.26e-04
-## N_parent       1.94e+00 5.88e-13 1.76e+00 2.12e+00
-## sigma          7.49e-01 1.63e-05 4.82e-01 1.02e+00
-## 
-## $DFOP
-##          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       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
-## 
-## 
-## DTx values:
-##      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 1.32e+11 8.04e+10
-## 
-## Representative half-life:
-## [1] 215.87</code></pre>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##      SFO     IORE     DFOP </span></span>
+<span><span class="co">## 94.81123 10.10936  7.55871 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 11.77879</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0   96.497 2.32e-24 94.85271 98.14155</span></span>
+<span><span class="co">## k_parent    0.008 3.42e-14  0.00737  0.00869</span></span>
+<span><span class="co">## sigma       2.295 1.22e-05  1.47976  3.11036</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0       9.85e+01 1.17e-28 9.79e+01 9.92e+01</span></span>
+<span><span class="co">## k__iore_parent 1.53e-04 6.50e-03 7.21e-05 3.26e-04</span></span>
+<span><span class="co">## N_parent       1.94e+00 5.88e-13 1.76e+00 2.12e+00</span></span>
+<span><span class="co">## sigma          7.49e-01 1.63e-05 4.82e-01 1.02e+00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)   Lower   Upper</span></span>
+<span><span class="co">## parent_0 9.84e+01 1.24e-27 97.8078 98.9187</span></span>
+<span><span class="co">## k1       1.55e-02 4.10e-04  0.0143  0.0167</span></span>
+<span><span class="co">## k2       8.63e-12 5.00e-01  0.0000     Inf</span></span>
+<span><span class="co">## g        6.89e-01 2.92e-03  0.6626  0.7142</span></span>
+<span><span class="co">## sigma    6.48e-01 2.38e-05  0.4147  0.8813</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50     DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  86.6 2.88e+02 8.66e+01</span></span>
+<span><span class="co">## IORE 85.5 7.17e+02 2.16e+02</span></span>
+<span><span class="co">## DFOP 83.6 1.32e+11 8.04e+10</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 215.87</span></span></code></pre>
 </div>
-<div id="example-on-page-6" class="section level2">
-<h2 class="hasAnchor">
-<a href="#example-on-page-6" class="anchor"></a>Example on page 6</h2>
+<div class="section level3">
+<h3 id="example-on-page-6">Example on page 6<a class="anchor" aria-label="anchor" href="#example-on-page-6"></a>
+</h3>
 <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">p6</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">"p6"</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>
+<code class="sourceCode R"><span><span class="va">p6</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">"p6"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <div class="sourceCode" id="cb16"><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">p6</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p6-1.png" width="700"></p>
 <div class="sourceCode" id="cb17"><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">p6</span><span class="op">)</span></code></pre></div>
-<pre><code>## Sums of squares:
-##       SFO      IORE      DFOP 
-## 188.45361  51.00699  42.46931 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 58.39888
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)   Lower   Upper
-## parent_0  94.7759 7.29e-24 92.3478 97.2039
-## k_parent   0.0179 8.02e-16  0.0166  0.0194
-## sigma      3.0696 3.81e-06  2.0456  4.0936
-## 
-## $IORE
-##                Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0       97.12446 2.63e-26 95.62461 98.62431
-## k__iore_parent  0.00252 1.95e-03  0.00134  0.00472
-## N_parent        1.49587 4.07e-13  1.33896  1.65279
-## sigma           1.59698 5.05e-06  1.06169  2.13227
-## 
-## $DFOP
-##          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       3.22e-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
-## 
-## 
-## DTx values:
-##      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 1.01e+10 2.15e+10
-## 
-## Representative half-life:
-## [1] 53.17</code></pre>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##       SFO      IORE      DFOP </span></span>
+<span><span class="co">## 188.45361  51.00699  42.46931 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 58.39888</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)   Lower   Upper</span></span>
+<span><span class="co">## parent_0  94.7759 7.29e-24 92.3478 97.2039</span></span>
+<span><span class="co">## k_parent   0.0179 8.02e-16  0.0166  0.0194</span></span>
+<span><span class="co">## sigma      3.0696 3.81e-06  2.0456  4.0936</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0       97.12446 2.63e-26 95.62461 98.62431</span></span>
+<span><span class="co">## k__iore_parent  0.00252 1.95e-03  0.00134  0.00472</span></span>
+<span><span class="co">## N_parent        1.49587 4.07e-13  1.33896  1.65279</span></span>
+<span><span class="co">## sigma           1.59698 5.05e-06  1.06169  2.13227</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)   Lower   Upper</span></span>
+<span><span class="co">## parent_0 9.66e+01 1.57e-25 95.3476 97.8979</span></span>
+<span><span class="co">## k1       2.55e-02 7.33e-06  0.0233  0.0278</span></span>
+<span><span class="co">## k2       3.22e-11 5.00e-01  0.0000     Inf</span></span>
+<span><span class="co">## g        8.61e-01 7.55e-06  0.8314  0.8867</span></span>
+<span><span class="co">## sigma    1.46e+00 6.93e-06  0.9661  1.9483</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50     DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  38.6 1.28e+02 3.86e+01</span></span>
+<span><span class="co">## IORE 34.0 1.77e+02 5.32e+01</span></span>
+<span><span class="co">## DFOP 34.1 1.01e+10 2.15e+10</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 53.17</span></span></code></pre>
 </div>
-<div id="example-on-page-7" class="section level2">
-<h2 class="hasAnchor">
-<a href="#example-on-page-7" class="anchor"></a>Example on page 7</h2>
+<div class="section level3">
+<h3 id="example-on-page-7">Example on page 7<a class="anchor" aria-label="anchor" href="#example-on-page-7"></a>
+</h3>
 <div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">p7</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">"p7"</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>
+<code class="sourceCode R"><span><span class="va">p7</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">"p7"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <div class="sourceCode" id="cb22"><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">p7</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p7-1.png" width="700"></p>
 <div class="sourceCode" id="cb23"><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">p7</span><span class="op">)</span></code></pre></div>
-<pre><code>## Sums of squares:
-##      SFO     IORE     DFOP 
-## 3661.661 3195.030 3174.145 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 3334.194
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0 96.41796 4.80e-53 93.32245 99.51347
-## k_parent  0.00735 7.64e-21  0.00641  0.00843
-## sigma     7.94557 1.83e-15  6.46713  9.42401
-## 
-## $IORE
-##                Estimate Pr(&gt;t)    Lower    Upper
-## parent_0       9.92e+01     NA 9.55e+01 1.03e+02
-## k__iore_parent 1.60e-05     NA 1.45e-07 1.77e-03
-## N_parent       2.45e+00     NA 1.35e+00 3.54e+00
-## sigma          7.42e+00     NA 6.04e+00 8.80e+00
-## 
-## $DFOP
-##          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       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
-## 
-## 
-## DTx values:
-##      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 3.77e+09 1.91e+09
-## 
-## Representative half-life:
-## [1] 454.55</code></pre>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##      SFO     IORE     DFOP </span></span>
+<span><span class="co">## 3661.661 3195.030 3174.145 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 3334.194</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0 96.41796 4.80e-53 93.32245 99.51347</span></span>
+<span><span class="co">## k_parent  0.00735 7.64e-21  0.00641  0.00843</span></span>
+<span><span class="co">## sigma     7.94557 1.83e-15  6.46713  9.42401</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0       9.92e+01     NA 9.55e+01 1.03e+02</span></span>
+<span><span class="co">## k__iore_parent 1.60e-05     NA 1.45e-07 1.77e-03</span></span>
+<span><span class="co">## N_parent       2.45e+00     NA 1.35e+00 3.54e+00</span></span>
+<span><span class="co">## sigma          7.42e+00     NA 6.04e+00 8.80e+00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)   Lower    Upper</span></span>
+<span><span class="co">## parent_0 9.89e+01 9.44e-49 95.4640 102.2573</span></span>
+<span><span class="co">## k1       1.81e-02 1.75e-01  0.0116   0.0281</span></span>
+<span><span class="co">## k2       3.63e-10 5.00e-01  0.0000      Inf</span></span>
+<span><span class="co">## g        6.06e-01 2.19e-01  0.4826   0.7178</span></span>
+<span><span class="co">## sigma    7.40e+00 2.97e-15  6.0201   8.7754</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50     DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  94.3 3.13e+02 9.43e+01</span></span>
+<span><span class="co">## IORE 96.7 1.51e+03 4.55e+02</span></span>
+<span><span class="co">## DFOP 96.4 3.77e+09 1.91e+09</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 454.55</span></span></code></pre>
 </div>
 </div>
-<div id="examples-where-the-representative-half-life-deviates-from-the-observed-dt50" class="section level1">
-<h1 class="hasAnchor">
-<a href="#examples-where-the-representative-half-life-deviates-from-the-observed-dt50" class="anchor"></a>Examples where the representative half-life deviates from the observed DT50</h1>
-<div id="example-on-page-8" class="section level2">
-<h2 class="hasAnchor">
-<a href="#example-on-page-8" class="anchor"></a>Example on page 8</h2>
+<div class="section level2">
+<h2 id="examples-where-the-representative-half-life-deviates-from-the-observed-dt50">Examples where the representative half-life deviates from the observed DT50<a class="anchor" aria-label="anchor" href="#examples-where-the-representative-half-life-deviates-from-the-observed-dt50"></a>
+</h2>
+<div class="section level3">
+<h3 id="example-on-page-8">Example on page 8<a class="anchor" aria-label="anchor" href="#example-on-page-8"></a>
+</h3>
 <p>For this dataset, the IORE fit does not converge when the default starting values used by mkin for the IORE model are used. Therefore, a lower value for the rate constant is used here.</p>
 <div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">p8</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">"p8"</span><span class="op">]</span><span class="op">]</span>, parms.ini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span>k__iore_parent <span class="op">=</span> <span class="fl">1e-3</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>
+<code class="sourceCode R"><span><span class="va">p8</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">"p8"</span><span class="op">]</span><span class="op">]</span>, parms.ini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k__iore_parent <span class="op">=</span> <span class="fl">1e-3</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <div class="sourceCode" id="cb28"><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">p8</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p8-1.png" width="700"></p>
 <div class="sourceCode" id="cb29"><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">p8</span><span class="op">)</span></code></pre></div>
-<pre><code>## Sums of squares:
-##       SFO      IORE      DFOP 
-## 1996.9408  444.9237  547.5616 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 477.4924
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0 88.16549 6.53e-29 83.37344 92.95754
-## k_parent  0.00803 1.67e-13  0.00674  0.00957
-## sigma     7.44786 4.17e-10  5.66209  9.23363
-## 
-## $IORE
-##                Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0       9.77e+01 7.03e-35 9.44e+01 1.01e+02
-## k__iore_parent 6.14e-05 3.20e-02 2.12e-05 1.78e-04
-## N_parent       2.27e+00 4.23e-18 2.00e+00 2.54e+00
-## sigma          3.52e+00 5.36e-10 2.67e+00 4.36e+00
-## 
-## $DFOP
-##          Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0 95.70619 8.99e-32 91.87941 99.53298
-## k1        0.02500 5.25e-04  0.01422  0.04394
-## k2        0.00273 6.84e-03  0.00125  0.00597
-## g         0.58835 2.84e-06  0.36595  0.77970
-## sigma     3.90001 6.94e-10  2.96260  4.83741
-## 
-## 
-## DTx values:
-##      DT50 DT90 DT50_rep
-## SFO  86.3  287     86.3
-## IORE 53.4  668    201.0
-## DFOP 55.6  517    253.0
-## 
-## Representative half-life:
-## [1] 201.03</code></pre>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##       SFO      IORE      DFOP </span></span>
+<span><span class="co">## 1996.9408  444.9237  547.5616 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 477.4924</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0 88.16549 6.53e-29 83.37344 92.95754</span></span>
+<span><span class="co">## k_parent  0.00803 1.67e-13  0.00674  0.00957</span></span>
+<span><span class="co">## sigma     7.44786 4.17e-10  5.66209  9.23363</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0       9.77e+01 7.03e-35 9.44e+01 1.01e+02</span></span>
+<span><span class="co">## k__iore_parent 6.14e-05 3.20e-02 2.12e-05 1.78e-04</span></span>
+<span><span class="co">## N_parent       2.27e+00 4.23e-18 2.00e+00 2.54e+00</span></span>
+<span><span class="co">## sigma          3.52e+00 5.36e-10 2.67e+00 4.36e+00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0 95.70619 8.99e-32 91.87941 99.53298</span></span>
+<span><span class="co">## k1        0.02500 5.25e-04  0.01422  0.04394</span></span>
+<span><span class="co">## k2        0.00273 6.84e-03  0.00125  0.00597</span></span>
+<span><span class="co">## g         0.58835 2.84e-06  0.36595  0.77970</span></span>
+<span><span class="co">## sigma     3.90001 6.94e-10  2.96260  4.83741</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50 DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  86.3  287     86.3</span></span>
+<span><span class="co">## IORE 53.4  668    201.0</span></span>
+<span><span class="co">## DFOP 55.6  517    253.0</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 201.03</span></span></code></pre>
 </div>
 </div>
-<div id="examples-where-sfo-was-not-selected-for-an-abiotic-study" class="section level1">
-<h1 class="hasAnchor">
-<a href="#examples-where-sfo-was-not-selected-for-an-abiotic-study" class="anchor"></a>Examples where SFO was not selected for an abiotic study</h1>
-<div id="example-on-page-9-upper-panel" class="section level2">
-<h2 class="hasAnchor">
-<a href="#example-on-page-9-upper-panel" class="anchor"></a>Example on page 9, upper panel</h2>
+<div class="section level2">
+<h2 id="examples-where-sfo-was-not-selected-for-an-abiotic-study">Examples where SFO was not selected for an abiotic study<a class="anchor" aria-label="anchor" href="#examples-where-sfo-was-not-selected-for-an-abiotic-study"></a>
+</h2>
+<div class="section level3">
+<h3 id="example-on-page-9-upper-panel">Example on page 9, upper panel<a class="anchor" aria-label="anchor" href="#example-on-page-9-upper-panel"></a>
+</h3>
 <div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">p9a</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">"p9a"</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>
+<code class="sourceCode R"><span><span class="va">p9a</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">"p9a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <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/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p9a-1.png" width="700"></p>
 <div class="sourceCode" id="cb35"><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">p9a</span><span class="op">)</span></code></pre></div>
-<pre><code>## Sums of squares:
-##       SFO      IORE      DFOP 
-## 839.35238  88.57064   9.93363 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 105.5678
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)   Lower   Upper
-## parent_0  88.1933 3.06e-12 79.9447 96.4419
-## k_parent   0.0409 2.07e-07  0.0324  0.0516
-## sigma      7.2429 3.92e-05  4.4768 10.0090
-## 
-## $IORE
-##                Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0       9.89e+01 1.12e-16 9.54e+01 1.02e+02
-## k__iore_parent 1.93e-05 1.13e-01 3.49e-06 1.06e-04
-## N_parent       2.91e+00 1.45e-09 2.50e+00 3.32e+00
-## sigma          2.35e+00 5.31e-05 1.45e+00 3.26e+00
-## 
-## $DFOP
-##          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       9.02e-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
-## 
-## 
-## DTx values:
-##      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 7.69e+11
-## 
-## Representative half-life:
-## [1] 101.43</code></pre>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##       SFO      IORE      DFOP </span></span>
+<span><span class="co">## 839.35238  88.57064   9.93363 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 105.5678</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)   Lower   Upper</span></span>
+<span><span class="co">## parent_0  88.1933 3.06e-12 79.9447 96.4419</span></span>
+<span><span class="co">## k_parent   0.0409 2.07e-07  0.0324  0.0516</span></span>
+<span><span class="co">## sigma      7.2429 3.92e-05  4.4768 10.0090</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0       9.89e+01 1.12e-16 9.54e+01 1.02e+02</span></span>
+<span><span class="co">## k__iore_parent 1.93e-05 1.13e-01 3.49e-06 1.06e-04</span></span>
+<span><span class="co">## N_parent       2.91e+00 1.45e-09 2.50e+00 3.32e+00</span></span>
+<span><span class="co">## sigma          2.35e+00 5.31e-05 1.45e+00 3.26e+00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)  Lower  Upper</span></span>
+<span><span class="co">## parent_0 9.85e+01 2.54e-20 97.390 99.672</span></span>
+<span><span class="co">## k1       1.38e-01 3.52e-05  0.131  0.146</span></span>
+<span><span class="co">## k2       9.02e-13 5.00e-01  0.000    Inf</span></span>
+<span><span class="co">## g        6.52e-01 8.13e-06  0.642  0.661</span></span>
+<span><span class="co">## sigma    7.88e-01 6.13e-02  0.481  1.095</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50     DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  16.9 5.63e+01 1.69e+01</span></span>
+<span><span class="co">## IORE 11.6 3.37e+02 1.01e+02</span></span>
+<span><span class="co">## DFOP 10.5 1.38e+12 7.69e+11</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 101.43</span></span></code></pre>
 <p>In this example, the residuals of the SFO indicate a lack of fit of this model, so even if it was an abiotic experiment, the data do not suggest a simple exponential decline.</p>
 </div>
-<div id="example-on-page-9-lower-panel" class="section level2">
-<h2 class="hasAnchor">
-<a href="#example-on-page-9-lower-panel" class="anchor"></a>Example on page 9, lower panel</h2>
+<div class="section level3">
+<h3 id="example-on-page-9-lower-panel">Example on page 9, lower panel<a class="anchor" aria-label="anchor" href="#example-on-page-9-lower-panel"></a>
+</h3>
 <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>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span>
+<span><span class="co">## doubtful</span></span></code></pre>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <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>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p>
 <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 
-## 35.64867 23.22334 35.64867 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 28.54188
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)  Lower   Upper
-## parent_0  94.7123 2.15e-19 93.178 96.2464
-## k_parent   0.0389 4.47e-14  0.037  0.0408
-## sigma      1.5957 1.28e-04  0.932  2.2595
-## 
-## $IORE
-##                Estimate   Pr(&gt;t)   Lower  Upper
-## parent_0         93.863 2.32e-18 92.4565 95.269
-## k__iore_parent    0.127 1.85e-02  0.0504  0.321
-## N_parent          0.711 1.88e-05  0.4843  0.937
-## sigma             1.288 1.76e-04  0.7456  1.830
-## 
-## $DFOP
-##          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:
-##      DT50 DT90 DT50_rep
-## SFO  17.8 59.2     17.8
-## IORE 18.4 49.2     14.8
-## DFOP 17.8 59.2     17.8
-## 
-## Representative half-life:
-## [1] 14.8</code></pre>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##      SFO     IORE     DFOP </span></span>
+<span><span class="co">## 35.64867 23.22334 35.64867 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 28.54188</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)  Lower   Upper</span></span>
+<span><span class="co">## parent_0  94.7123 2.15e-19 93.178 96.2464</span></span>
+<span><span class="co">## k_parent   0.0389 4.47e-14  0.037  0.0408</span></span>
+<span><span class="co">## sigma      1.5957 1.28e-04  0.932  2.2595</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate   Pr(&gt;t)   Lower  Upper</span></span>
+<span><span class="co">## parent_0         93.863 2.32e-18 92.4565 95.269</span></span>
+<span><span class="co">## k__iore_parent    0.127 1.85e-02  0.0504  0.321</span></span>
+<span><span class="co">## N_parent          0.711 1.88e-05  0.4843  0.937</span></span>
+<span><span class="co">## sigma             1.288 1.76e-04  0.7456  1.830</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)   Lower   Upper</span></span>
+<span><span class="co">## parent_0  94.7123 1.61e-16 93.1355 96.2891</span></span>
+<span><span class="co">## k1         0.0389 1.08e-04  0.0266  0.0569</span></span>
+<span><span class="co">## k2         0.0389 2.23e-04  0.0255  0.0592</span></span>
+<span><span class="co">## g          0.5256      NaN      NA      NA</span></span>
+<span><span class="co">## sigma      1.5957 2.50e-04  0.9135  2.2779</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50 DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  17.8 59.2     17.8</span></span>
+<span><span class="co">## IORE 18.4 49.2     14.8</span></span>
+<span><span class="co">## DFOP 17.8 59.2     17.8</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 14.8</span></span></code></pre>
 <p>Here, mkin gives a longer slow DT50 for the DFOP model (17.8 days) than PestDF (13.5 days). Presumably, this is related to the fact that PestDF gives a negative value for the proportion of the fast degradation which should be between 0 and 1, inclusive. This parameter is called f in PestDF and g in mkin. In mkin, it is restricted to the interval from 0 to 1.</p>
 </div>
-<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="section level3">
+<h3 id="example-on-page-10">Example on page 10<a class="anchor" aria-label="anchor" href="#example-on-page-10"></a>
+</h3>
 <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)): 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>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span>
+<span><span class="co">## doubtful</span></span></code></pre>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <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>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p>
 <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 
-## 899.4089 336.4348 899.4089 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 413.4841
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)   Lower    Upper
-## parent_0 101.7315 6.42e-11 91.9259 111.5371
-## k_parent   0.0495 1.70e-07  0.0404   0.0607
-## sigma      8.0152 1.28e-04  4.6813  11.3491
-## 
-## $IORE
-##                Estimate   Pr(&gt;t)  Lower   Upper
-## parent_0          96.86 3.32e-12 90.848 102.863
-## k__iore_parent     2.96 7.91e-02  0.687  12.761
-## N_parent           0.00 5.00e-01 -0.372   0.372
-## sigma              4.90 1.77e-04  2.837   6.968
-## 
-## $DFOP
-##          Estimate   Pr(&gt;t)   Lower    Upper
-## parent_0 101.7315 1.41e-09 91.6534 111.8097
-## 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
-## 
-## 
-## DTx values:
-##      DT50 DT90 DT50_rep
-## SFO  14.0 46.5    14.00
-## IORE 16.4 29.4     8.86
-## DFOP 14.0 46.5    14.00
-## 
-## Representative half-life:
-## [1] 8.86</code></pre>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##      SFO     IORE     DFOP </span></span>
+<span><span class="co">## 899.4089 336.4348 899.4089 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 413.4841</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)   Lower    Upper</span></span>
+<span><span class="co">## parent_0 101.7315 6.42e-11 91.9259 111.5371</span></span>
+<span><span class="co">## k_parent   0.0495 1.70e-07  0.0404   0.0607</span></span>
+<span><span class="co">## sigma      8.0152 1.28e-04  4.6813  11.3491</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate   Pr(&gt;t)  Lower   Upper</span></span>
+<span><span class="co">## parent_0          96.86 3.32e-12 90.848 102.863</span></span>
+<span><span class="co">## k__iore_parent     2.96 7.91e-02  0.687  12.761</span></span>
+<span><span class="co">## N_parent           0.00 5.00e-01 -0.372   0.372</span></span>
+<span><span class="co">## sigma              4.90 1.77e-04  2.837   6.968</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)   Lower    Upper</span></span>
+<span><span class="co">## parent_0 101.7315 1.41e-09 91.6534 111.8097</span></span>
+<span><span class="co">## k1         0.0495 6.58e-03  0.0303   0.0809</span></span>
+<span><span class="co">## k2         0.0495 2.60e-03  0.0410   0.0598</span></span>
+<span><span class="co">## g          0.4487 5.00e-01      NA       NA</span></span>
+<span><span class="co">## sigma      8.0152 2.50e-04  4.5886  11.4418</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50 DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  14.0 46.5    14.00</span></span>
+<span><span class="co">## IORE 16.4 29.4     8.86</span></span>
+<span><span class="co">## DFOP 14.0 46.5    14.00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 8.86</span></span></code></pre>
 <p>Here, a value below N is given for the IORE model, because the data suggests a faster decline towards the end of the experiment, which appears physically rather unlikely in the case of a photolysis study. It seems PestDF does not constrain N to values above zero, thus the slight difference in IORE model parameters between PestDF and mkin.</p>
 </div>
 </div>
-<div id="the-dt50-was-not-observed-during-the-study" class="section level1">
-<h1 class="hasAnchor">
-<a href="#the-dt50-was-not-observed-during-the-study" class="anchor"></a>The DT50 was not observed during the study</h1>
-<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="section level2">
+<h2 id="the-dt50-was-not-observed-during-the-study">The DT50 was not observed during the study<a class="anchor" aria-label="anchor" href="#the-dt50-was-not-observed-during-the-study"></a>
+</h2>
+<div class="section level3">
+<h3 id="example-on-page-11">Example on page 11<a class="anchor" aria-label="anchor" href="#example-on-page-11"></a>
+</h3>
 <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>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <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>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p>
 <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 
-## 579.6805 204.7932 144.7783 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 251.6944
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0 96.15820 4.83e-13 90.24934 1.02e+02
-## k_parent  0.00321 4.71e-05  0.00222 4.64e-03
-## sigma     6.43473 1.28e-04  3.75822 9.11e+00
-## 
-## $IORE
-##                Estimate Pr(&gt;t)    Lower    Upper
-## parent_0       1.05e+02     NA 9.90e+01 1.10e+02
-## k__iore_parent 3.11e-17     NA 1.35e-20 7.18e-14
-## N_parent       8.36e+00     NA 6.62e+00 1.01e+01
-## sigma          3.82e+00     NA 2.21e+00 5.44e+00
-## 
-## $DFOP
-##          Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0 1.05e+02 9.47e-13  99.9990 109.1224
-## k1       4.41e-02 5.95e-03   0.0296   0.0658
-## k2       9.94e-13 5.00e-01   0.0000      Inf
-## g        3.22e-01 1.45e-03   0.2814   0.3650
-## sigma    3.22e+00 3.52e-04   1.8410   4.5906
-## 
-## 
-## DTx values:
-##          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 6.98e+11
-## 
-## Representative half-life:
-## [1] 41148170</code></pre>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##      SFO     IORE     DFOP </span></span>
+<span><span class="co">## 579.6805 204.7932 144.7783 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 251.6944</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0 96.15820 4.83e-13 90.24934 1.02e+02</span></span>
+<span><span class="co">## k_parent  0.00321 4.71e-05  0.00222 4.64e-03</span></span>
+<span><span class="co">## sigma     6.43473 1.28e-04  3.75822 9.11e+00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0       1.05e+02     NA 9.90e+01 1.10e+02</span></span>
+<span><span class="co">## k__iore_parent 3.11e-17     NA 1.35e-20 7.18e-14</span></span>
+<span><span class="co">## N_parent       8.36e+00     NA 6.62e+00 1.01e+01</span></span>
+<span><span class="co">## sigma          3.82e+00     NA 2.21e+00 5.44e+00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0 1.05e+02 9.47e-13  99.9990 109.1224</span></span>
+<span><span class="co">## k1       4.41e-02 5.95e-03   0.0296   0.0658</span></span>
+<span><span class="co">## k2       9.94e-13 5.00e-01   0.0000      Inf</span></span>
+<span><span class="co">## g        3.22e-01 1.45e-03   0.2814   0.3650</span></span>
+<span><span class="co">## sigma    3.22e+00 3.52e-04   1.8410   4.5906</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##          DT50     DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  2.16e+02 7.18e+02 2.16e+02</span></span>
+<span><span class="co">## IORE 9.73e+02 1.37e+08 4.11e+07</span></span>
+<span><span class="co">## DFOP 3.07e+11 1.93e+12 6.98e+11</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 41148170</span></span></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>
-<div id="n-is-less-than-1-and-the-dfop-rate-constants-are-like-the-sfo-rate-constant" class="section level1">
-<h1 class="hasAnchor">
-<a href="#n-is-less-than-1-and-the-dfop-rate-constants-are-like-the-sfo-rate-constant" class="anchor"></a>N is less than 1 and the DFOP rate constants are like the SFO rate constant</h1>
+<div class="section level2">
+<h2 id="n-is-less-than-1-and-the-dfop-rate-constants-are-like-the-sfo-rate-constant">N is less than 1 and the DFOP rate constants are like the SFO rate constant<a class="anchor" aria-label="anchor" href="#n-is-less-than-1-and-the-dfop-rate-constants-are-like-the-sfo-rate-constant"></a>
+</h2>
 <p>In the following three examples, the same results are obtained with mkin as reported for PestDF. As in the case on page 10, the N values below 1 are deemed unrealistic and appear to be the result of an overparameterisation.</p>
-<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="section level3">
+<h3 id="example-on-page-12-upper-panel">Example on page 12, upper panel<a class="anchor" aria-label="anchor" href="#example-on-page-12-upper-panel"></a>
+</h3>
 <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</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>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance</span></span>
+<span><span class="co">## matrix</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span>
+<span><span class="co">## doubtful</span></span></code></pre>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <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>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p>
 <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 
-## 695.4440 220.0685 695.4440 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 270.4679
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)  Lower   Upper
-## parent_0  100.521 8.75e-12 92.461 108.581
-## k_parent    0.124 3.61e-08  0.104   0.148
-## sigma       7.048 1.28e-04  4.116   9.980
-## 
-## $IORE
-##                Estimate Pr(&gt;t) Lower Upper
-## parent_0         96.823     NA    NA    NA
-## k__iore_parent    2.436     NA    NA    NA
-## N_parent          0.263     NA    NA    NA
-## sigma             3.965     NA    NA    NA
-## 
-## $DFOP
-##          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:
-##      DT50 DT90 DT50_rep
-## SFO  5.58 18.5     5.58
-## IORE 6.49 13.2     3.99
-## DFOP 5.58 18.5     5.58
-## 
-## Representative half-life:
-## [1] 3.99</code></pre>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##      SFO     IORE     DFOP </span></span>
+<span><span class="co">## 695.4440 220.0685 695.4440 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 270.4679</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)  Lower   Upper</span></span>
+<span><span class="co">## parent_0  100.521 8.75e-12 92.461 108.581</span></span>
+<span><span class="co">## k_parent    0.124 3.61e-08  0.104   0.148</span></span>
+<span><span class="co">## sigma       7.048 1.28e-04  4.116   9.980</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate Pr(&gt;t) Lower Upper</span></span>
+<span><span class="co">## parent_0         96.823     NA    NA    NA</span></span>
+<span><span class="co">## k__iore_parent    2.436     NA    NA    NA</span></span>
+<span><span class="co">## N_parent          0.263     NA    NA    NA</span></span>
+<span><span class="co">## sigma             3.965     NA    NA    NA</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)   Lower   Upper</span></span>
+<span><span class="co">## parent_0  100.521 2.74e-10 92.2366 108.805</span></span>
+<span><span class="co">## k1          0.124 2.53e-05  0.0908   0.170</span></span>
+<span><span class="co">## k2          0.124 2.52e-02  0.0456   0.339</span></span>
+<span><span class="co">## g           0.793      NaN      NA      NA</span></span>
+<span><span class="co">## sigma       7.048 2.50e-04  4.0349  10.061</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50 DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  5.58 18.5     5.58</span></span>
+<span><span class="co">## IORE 6.49 13.2     3.99</span></span>
+<span><span class="co">## DFOP 5.58 18.5     5.58</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 3.99</span></span></code></pre>
 </div>
-<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="section level3">
+<h3 id="example-on-page-12-lower-panel">Example on page 12, lower panel<a class="anchor" aria-label="anchor" href="#example-on-page-12-lower-panel"></a>
+</h3>
 <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 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(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>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## Warning in qt(alpha/2, rdf): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in qt(1 - alpha/2, rdf): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <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>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p>
 <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 
-## 58.90242 19.06353 58.90242 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 51.51756
-## 
-## Parameters:
-## $SFO
-##          Estimate  Pr(&gt;t)   Lower    Upper
-## parent_0  97.6840 0.00039 85.9388 109.4292
-## k_parent   0.0589 0.00261  0.0431   0.0805
-## sigma      3.4323 0.04356 -1.2377   8.1023
-## 
-## $IORE
-##                Estimate Pr(&gt;t)     Lower  Upper
-## parent_0         95.523 0.0055 74.539157 116.51
-## k__iore_parent    0.333 0.1433  0.000717 154.57
-## N_parent          0.568 0.0677 -0.989464   2.13
-## sigma             1.953 0.0975 -5.893100   9.80
-## 
-## $DFOP
-##          Estimate Pr(&gt;t) Lower Upper
-## 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:
-##      DT50 DT90 DT50_rep
-## SFO  11.8 39.1    11.80
-## IORE 12.9 31.4     9.46
-## DFOP 11.8 39.1    11.80
-## 
-## Representative half-life:
-## [1] 9.46</code></pre>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##      SFO     IORE     DFOP </span></span>
+<span><span class="co">## 58.90242 19.06353 58.90242 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 51.51756</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate  Pr(&gt;t)   Lower    Upper</span></span>
+<span><span class="co">## parent_0  97.6840 0.00039 85.9388 109.4292</span></span>
+<span><span class="co">## k_parent   0.0589 0.00261  0.0431   0.0805</span></span>
+<span><span class="co">## sigma      3.4323 0.04356 -1.2377   8.1023</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate Pr(&gt;t)     Lower  Upper</span></span>
+<span><span class="co">## parent_0         95.523 0.0055 74.539157 116.51</span></span>
+<span><span class="co">## k__iore_parent    0.333 0.1433  0.000717 154.57</span></span>
+<span><span class="co">## N_parent          0.568 0.0677 -0.989464   2.13</span></span>
+<span><span class="co">## sigma             1.953 0.0975 -5.893100   9.80</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate Pr(&gt;t) Lower Upper</span></span>
+<span><span class="co">## parent_0  97.6840    NaN   NaN   NaN</span></span>
+<span><span class="co">## k1         0.0589    NaN    NA    NA</span></span>
+<span><span class="co">## k2         0.0589    NaN    NA    NA</span></span>
+<span><span class="co">## g          0.6473    NaN    NA    NA</span></span>
+<span><span class="co">## sigma      3.4323    NaN   NaN   NaN</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50 DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  11.8 39.1    11.80</span></span>
+<span><span class="co">## IORE 12.9 31.4     9.46</span></span>
+<span><span class="co">## DFOP 11.8 39.1    11.80</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 9.46</span></span></code></pre>
 </div>
-<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="section level3">
+<h3 id="example-on-page-13">Example on page 13<a class="anchor" aria-label="anchor" href="#example-on-page-13"></a>
+</h3>
 <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>## 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>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <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>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p>
 <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 
-## 174.5971 142.3951 174.5971 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 172.131
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0 92.73500 5.99e-17 89.61936 95.85065
-## k_parent  0.00258 2.42e-09  0.00223  0.00299
-## sigma     3.41172 7.07e-05  2.05455  4.76888
-## 
-## $IORE
-##                Estimate   Pr(&gt;t)    Lower  Upper
-## parent_0        91.6016 6.34e-16 88.53086 94.672
-## k__iore_parent   0.0396 2.36e-01  0.00207  0.759
-## N_parent         0.3541 1.46e-01 -0.35153  1.060
-## sigma            3.0811 9.64e-05  1.84296  4.319
-## 
-## $DFOP
-##          Estimate Pr(&gt;t)    Lower    Upper
-## parent_0 92.73500     NA 8.95e+01 95.92118
-## 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
-## 
-## 
-## DTx values:
-##      DT50 DT90 DT50_rep
-## SFO   269  892      269
-## IORE  261  560      169
-## DFOP  269  892      269
-## 
-## Representative half-life:
-## [1] 168.51</code></pre>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##      SFO     IORE     DFOP </span></span>
+<span><span class="co">## 174.5971 142.3951 174.5971 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 172.131</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0 92.73500 5.99e-17 89.61936 95.85065</span></span>
+<span><span class="co">## k_parent  0.00258 2.42e-09  0.00223  0.00299</span></span>
+<span><span class="co">## sigma     3.41172 7.07e-05  2.05455  4.76888</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate   Pr(&gt;t)    Lower  Upper</span></span>
+<span><span class="co">## parent_0        91.6016 6.34e-16 88.53086 94.672</span></span>
+<span><span class="co">## k__iore_parent   0.0396 2.36e-01  0.00207  0.759</span></span>
+<span><span class="co">## N_parent         0.3541 1.46e-01 -0.35153  1.060</span></span>
+<span><span class="co">## sigma            3.0811 9.64e-05  1.84296  4.319</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0 92.73500     NA 8.95e+01 95.92118</span></span>
+<span><span class="co">## k1        0.00258     NA 4.14e-04  0.01611</span></span>
+<span><span class="co">## k2        0.00258     NA 1.74e-03  0.00383</span></span>
+<span><span class="co">## g         0.16452     NA 0.00e+00  1.00000</span></span>
+<span><span class="co">## sigma     3.41172     NA 2.02e+00  4.79960</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50 DT90 DT50_rep</span></span>
+<span><span class="co">## SFO   269  892      269</span></span>
+<span><span class="co">## IORE  261  560      169</span></span>
+<span><span class="co">## DFOP  269  892      269</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 168.51</span></span></code></pre>
 </div>
 </div>
-<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="section level2">
+<h2 id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf">DT50 not observed in the study and DFOP problems in PestDF<a class="anchor" aria-label="anchor" href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf"></a>
+</h2>
 <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>
-<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>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span>
+<span><span class="co">## doubtful</span></span></code></pre>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <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>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p>
 <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 
-## 48.43249 28.67746 27.26248 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 32.83337
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0 99.47124 2.06e-30 98.42254 1.01e+02
-## k_parent  0.00279 3.75e-15  0.00256 3.04e-03
-## sigma     1.55616 3.81e-06  1.03704 2.08e+00
-## 
-## $IORE
-##                Estimate Pr(&gt;t) Lower Upper
-## parent_0       1.00e+02     NA   NaN   NaN
-## k__iore_parent 9.44e-08     NA   NaN   NaN
-## N_parent       3.31e+00     NA   NaN   NaN
-## sigma          1.20e+00     NA 0.796   1.6
-## 
-## $DFOP
-##          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       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
-## 
-## 
-## DTx values:
-##          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 3.05e+10 2.95e+11 1.14e+11
-## 
-## Representative half-life:
-## [1] 6697.44</code></pre>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##      SFO     IORE     DFOP </span></span>
+<span><span class="co">## 48.43249 28.67746 27.26248 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 32.83337</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0 99.47124 2.06e-30 98.42254 1.01e+02</span></span>
+<span><span class="co">## k_parent  0.00279 3.75e-15  0.00256 3.04e-03</span></span>
+<span><span class="co">## sigma     1.55616 3.81e-06  1.03704 2.08e+00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate Pr(&gt;t) Lower Upper</span></span>
+<span><span class="co">## parent_0       1.00e+02     NA   NaN   NaN</span></span>
+<span><span class="co">## k__iore_parent 9.44e-08     NA   NaN   NaN</span></span>
+<span><span class="co">## N_parent       3.31e+00     NA   NaN   NaN</span></span>
+<span><span class="co">## sigma          1.20e+00     NA 0.796   1.6</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0 1.00e+02 2.96e-28 99.40280 101.2768</span></span>
+<span><span class="co">## k1       9.53e-03 1.20e-01  0.00638   0.0143</span></span>
+<span><span class="co">## k2       6.08e-12 5.00e-01  0.00000      Inf</span></span>
+<span><span class="co">## g        3.98e-01 2.19e-01  0.30481   0.4998</span></span>
+<span><span class="co">## sigma    1.17e+00 7.68e-06  0.77406   1.5610</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##          DT50     DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  2.48e+02 8.25e+02 2.48e+02</span></span>
+<span><span class="co">## IORE 4.34e+02 2.22e+04 6.70e+03</span></span>
+<span><span class="co">## DFOP 3.05e+10 2.95e+11 1.14e+11</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 6697.44</span></span></code></pre>
 <p>The slower rate constant reported by PestDF is negative, which is not physically realistic, and not possible in mkin. The other fits give the same results in mkin and PestDF.</p>
 </div>
-<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="section level2">
+<h2 id="n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero">N is less than 1 and DFOP fraction parameter is below zero<a class="anchor" aria-label="anchor" href="#n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero"></a>
+</h2>
 <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>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <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>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p>
 <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 
-## 245.5248 135.0132 245.5248 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 165.9335
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)    Lower   Upper
-## parent_0 97.96751 2.00e-15 94.32049 101.615
-## k_parent  0.00952 4.93e-09  0.00824   0.011
-## sigma     4.18778 1.28e-04  2.44588   5.930
-## 
-## $IORE
-##                Estimate   Pr(&gt;t)  Lower  Upper
-## parent_0         95.874 2.94e-15 92.937 98.811
-## k__iore_parent    0.629 2.11e-01  0.044  8.982
-## N_parent          0.000 5.00e-01 -0.642  0.642
-## sigma             3.105 1.78e-04  1.795  4.416
-## 
-## $DFOP
-##          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:
-##      DT50 DT90 DT50_rep
-## SFO  72.8  242     72.8
-## IORE 76.3  137     41.3
-## DFOP 72.8  242     72.8
-## 
-## Representative half-life:
-## [1] 41.33</code></pre>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##      SFO     IORE     DFOP </span></span>
+<span><span class="co">## 245.5248 135.0132 245.5248 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 165.9335</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)    Lower   Upper</span></span>
+<span><span class="co">## parent_0 97.96751 2.00e-15 94.32049 101.615</span></span>
+<span><span class="co">## k_parent  0.00952 4.93e-09  0.00824   0.011</span></span>
+<span><span class="co">## sigma     4.18778 1.28e-04  2.44588   5.930</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate   Pr(&gt;t)  Lower  Upper</span></span>
+<span><span class="co">## parent_0         95.874 2.94e-15 92.937 98.811</span></span>
+<span><span class="co">## k__iore_parent    0.629 2.11e-01  0.044  8.982</span></span>
+<span><span class="co">## N_parent          0.000 5.00e-01 -0.642  0.642</span></span>
+<span><span class="co">## sigma             3.105 1.78e-04  1.795  4.416</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0 97.96751 2.85e-13 94.21913 101.7159</span></span>
+<span><span class="co">## k1        0.00952 6.28e-02  0.00250   0.0363</span></span>
+<span><span class="co">## k2        0.00952 1.27e-04  0.00646   0.0140</span></span>
+<span><span class="co">## g         0.21241 5.00e-01  0.00000   1.0000</span></span>
+<span><span class="co">## sigma     4.18778 2.50e-04  2.39747   5.9781</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50 DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  72.8  242     72.8</span></span>
+<span><span class="co">## IORE 76.3  137     41.3</span></span>
+<span><span class="co">## DFOP 72.8  242     72.8</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 41.33</span></span></code></pre>
 <div class="sourceCode" id="cb104"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">p15b</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
-<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre>
-<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre>
-<pre><code>## Warning in cov2cor(ans$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>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span>
+<span><span class="co">## doubtful</span></span></code></pre>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <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>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p>
 <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 
-## 106.91629  68.55574 106.91629 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 84.25618
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0 1.01e+02 3.06e-17 98.31594 1.03e+02
-## k_parent 4.86e-03 2.48e-10  0.00435 5.42e-03
-## sigma    2.76e+00 1.28e-04  1.61402 3.91e+00
-## 
-## $IORE
-##                Estimate   Pr(&gt;t)    Lower  Upper
-## 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
-## 
-## $DFOP
-##          Estimate Pr(&gt;t)    Lower    Upper
-## parent_0 1.01e+02     NA 9.82e+01 1.04e+02
-## k1       4.86e-03     NA 8.63e-04 2.73e-02
-## k2       4.86e-03     NA 3.21e-03 7.35e-03
-## g        1.88e-01     NA       NA       NA
-## sigma    2.76e+00     NA 1.58e+00 3.94e+00
-## 
-## 
-## DTx values:
-##      DT50 DT90 DT50_rep
-## SFO   143  474    143.0
-## IORE  131  236     71.2
-## DFOP  143  474    143.0
-## 
-## Representative half-life:
-## [1] 71.18</code></pre>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##       SFO      IORE      DFOP </span></span>
+<span><span class="co">## 106.91629  68.55574 106.91629 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 84.25618</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0 1.01e+02 3.06e-17 98.31594 1.03e+02</span></span>
+<span><span class="co">## k_parent 4.86e-03 2.48e-10  0.00435 5.42e-03</span></span>
+<span><span class="co">## sigma    2.76e+00 1.28e-04  1.61402 3.91e+00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate   Pr(&gt;t)    Lower  Upper</span></span>
+<span><span class="co">## parent_0          99.83 1.81e-16 97.51349 102.14</span></span>
+<span><span class="co">## k__iore_parent     0.38 3.22e-01  0.00352  41.05</span></span>
+<span><span class="co">## N_parent           0.00 5.00e-01 -1.07696   1.08</span></span>
+<span><span class="co">## sigma              2.21 2.57e-04  1.23245   3.19</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0 1.01e+02     NA 9.82e+01 1.04e+02</span></span>
+<span><span class="co">## k1       4.86e-03     NA 8.63e-04 2.73e-02</span></span>
+<span><span class="co">## k2       4.86e-03     NA 3.21e-03 7.35e-03</span></span>
+<span><span class="co">## g        1.88e-01     NA       NA       NA</span></span>
+<span><span class="co">## sigma    2.76e+00     NA 1.58e+00 3.94e+00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50 DT90 DT50_rep</span></span>
+<span><span class="co">## SFO   143  474    143.0</span></span>
+<span><span class="co">## IORE  131  236     71.2</span></span>
+<span><span class="co">## DFOP  143  474    143.0</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 71.18</span></span></code></pre>
 <p>In mkin, only the IORE fit is affected (deemed unrealistic), as the fraction parameter of the DFOP model is restricted to the interval between 0 and 1 in mkin. The SFO fits give the same results for both mkin and PestDF.</p>
 </div>
-<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="section level2">
+<h2 id="the-dfop-fraction-parameter-is-greater-than-1">The DFOP fraction parameter is greater than 1<a class="anchor" aria-label="anchor" href="#the-dfop-fraction-parameter-is-greater-than-1"></a>
+</h2>
 <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>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The representative half-life of the IORE model is longer than the one corresponding</span></span></code></pre>
+<pre><code><span><span class="co">## to the terminal degradation rate found with the DFOP model.</span></span></code></pre>
+<pre><code><span><span class="co">## The representative half-life obtained from the DFOP model may be used</span></span></code></pre>
 <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>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></span></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p>
 <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 
-## 3831.804 2062.008 1550.980 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 2247.348
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)  Lower Upper
-## parent_0   71.953 2.33e-13 60.509 83.40
-## k_parent    0.159 4.86e-05  0.102  0.25
-## sigma      11.302 1.25e-08  8.308 14.30
-## 
-## $IORE
-##                Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0       8.74e+01 2.48e-16 7.72e+01 97.52972
-## k__iore_parent 4.55e-04 2.16e-01 3.48e-05  0.00595
-## N_parent       2.70e+00 1.21e-08 1.99e+00  3.40046
-## sigma          8.29e+00 1.61e-08 6.09e+00 10.49062
-## 
-## $DFOP
-##          Estimate   Pr(&gt;t)   Lower  Upper
-## parent_0  88.5333 7.40e-18 79.9836 97.083
-## k1        18.8461 5.00e-01  0.0000    Inf
-## k2         0.0776 1.41e-05  0.0518  0.116
-## g          0.4733 1.41e-09  0.3674  0.582
-## sigma      7.1902 2.11e-08  5.2785  9.102
-## 
-## 
-## DTx values:
-##      DT50 DT90 DT50_rep
-## SFO  4.35 14.4     4.35
-## IORE 1.48 32.1     9.67
-## DFOP 0.67 21.4     8.93
-## 
-## Representative half-life:
-## [1] 8.93</code></pre>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##      SFO     IORE     DFOP </span></span>
+<span><span class="co">## 3831.804 2062.008 1550.980 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 2247.348</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)  Lower Upper</span></span>
+<span><span class="co">## parent_0   71.953 2.33e-13 60.509 83.40</span></span>
+<span><span class="co">## k_parent    0.159 4.86e-05  0.102  0.25</span></span>
+<span><span class="co">## sigma      11.302 1.25e-08  8.308 14.30</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0       8.74e+01 2.48e-16 7.72e+01 97.52972</span></span>
+<span><span class="co">## k__iore_parent 4.55e-04 2.16e-01 3.48e-05  0.00595</span></span>
+<span><span class="co">## N_parent       2.70e+00 1.21e-08 1.99e+00  3.40046</span></span>
+<span><span class="co">## sigma          8.29e+00 1.61e-08 6.09e+00 10.49062</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)   Lower  Upper</span></span>
+<span><span class="co">## parent_0  88.5333 7.40e-18 79.9836 97.083</span></span>
+<span><span class="co">## k1        18.8461 5.00e-01  0.0000    Inf</span></span>
+<span><span class="co">## k2         0.0776 1.41e-05  0.0518  0.116</span></span>
+<span><span class="co">## g          0.4733 1.41e-09  0.3674  0.582</span></span>
+<span><span class="co">## sigma      7.1902 2.11e-08  5.2785  9.102</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50 DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  4.35 14.4     4.35</span></span>
+<span><span class="co">## IORE 1.48 32.1     9.67</span></span>
+<span><span class="co">## DFOP 0.67 21.4     8.93</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 8.93</span></span></code></pre>
 <p>In PestDF, the DFOP fit seems to have stuck in a local minimum, as mkin finds a solution with a much lower <span class="math inline">\(\chi^2\)</span> error level. As the half-life from the slower rate constant of the DFOP model is larger than the IORE derived half-life, the NAFTA recommendation obtained with mkin is to use the DFOP representative half-life of 8.9 days.</p>
 </div>
-<div id="conclusions" class="section level1">
-<h1 class="hasAnchor">
-<a href="#conclusions" class="anchor"></a>Conclusions</h1>
+<div class="section level2">
+<h2 id="conclusions">Conclusions<a class="anchor" aria-label="anchor" href="#conclusions"></a>
+</h2>
 <p>The results obtained with mkin deviate from the results obtained with PestDF either in cases where one of the interpretive rules would apply, i.e. the IORE parameter N is less than one or the DFOP k values obtained with PestDF are equal to the SFO k values, or in cases where the DFOP model did not converge, which often lead to negative rate constants returned by PestDF.</p>
 <p>Therefore, mkin appears to suitable for kinetic evaluations according to the NAFTA guidance.</p>
 </div>
-<div id="references" class="section level1 unnumbered">
-<h1 class="hasAnchor">
-<a href="#references" class="anchor"></a>References</h1>
+<div class="section level2">
+<h2 class="unnumbered" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
+</h2>
 <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>
@@ -1016,11 +1027,13 @@
 
 
       <footer><div class="copyright">
-  <p>Developed by Johannes Ranke.</p>
+  <p></p>
+<p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <p></p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer>
@@ -1029,5 +1042,7 @@
   
 
 
+  
+
   </body>
 </html>
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+++ b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png
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+++ b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png
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index ca1f29be..ae4d83a4 100644
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+++ b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p14-1.png
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index 71fcd257..6b9ba98c 100644
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+++ b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png
diff --git a/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p16-1.png b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p16-1.png
index 820501a3..72df855b 100644
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+++ b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p16-1.png
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+++ b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png
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index 3ce13a97..61359ea6 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 e2cf2f83..85790b1e 100644
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+++ b/docs/dev/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png
diff --git a/docs/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html
index 5c7aa3dc..b37ac926 100644
--- a/docs/dev/articles/web_only/benchmarks.html
+++ b/docs/dev/articles/web_only/benchmarks.html
@@ -34,7 +34,7 @@
       </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">1.2.0</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
       </span>
     </div>
 
@@ -112,7 +112,7 @@
       <h1 data-toc-skip>Benchmark timings for mkin</h1>
                         <h4 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 data-toc-skip class="date">Last change 14 July 2022 (rebuilt 2022-11-15)</h4>
+            <h4 data-toc-skip class="date">Last change 14 July 2022 (rebuilt 2022-11-24)</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/benchmarks.rmd" class="external-link"><code>vignettes/web_only/benchmarks.rmd</code></a></small>
       <div class="hidden name"><code>benchmarks.rmd</code></div>
@@ -351,8 +351,16 @@
 <td align="left">Ryzen 7 1700</td>
 <td align="left">4.2.2</td>
 <td align="left">1.2.0</td>
-<td align="right">2.129</td>
-<td align="right">3.784</td>
+<td align="right">2.140</td>
+<td align="right">3.774</td>
+</tr>
+<tr class="odd">
+<td align="left">Linux</td>
+<td align="left">Ryzen 7 1700</td>
+<td align="left">4.2.2</td>
+<td align="left">1.2.2</td>
+<td align="right">2.187</td>
+<td align="right">3.851</td>
 </tr>
 </tbody>
 </table>
@@ -530,9 +538,18 @@
 <td align="left">Ryzen 7 1700</td>
 <td align="left">4.2.2</td>
 <td align="left">1.2.0</td>
-<td align="right">1.559</td>
-<td align="right">6.097</td>
-<td align="right">2.841</td>
+<td align="right">1.554</td>
+<td align="right">6.193</td>
+<td align="right">2.843</td>
+</tr>
+<tr class="odd">
+<td align="left">Linux</td>
+<td align="left">Ryzen 7 1700</td>
+<td align="left">4.2.2</td>
+<td align="left">1.2.2</td>
+<td align="right">1.585</td>
+<td align="right">6.335</td>
+<td align="right">3.003</td>
 </tr>
 </tbody>
 </table>
@@ -764,12 +781,24 @@
 <td align="left">Ryzen 7 1700</td>
 <td align="left">4.2.2</td>
 <td align="left">1.2.0</td>
-<td align="right">0.911</td>
-<td align="right">1.328</td>
-<td align="right">1.519</td>
-<td align="right">2.986</td>
-<td align="right">1.957</td>
-<td align="right">2.769</td>
+<td align="right">0.913</td>
+<td align="right">1.345</td>
+<td align="right">1.539</td>
+<td align="right">3.011</td>
+<td align="right">1.987</td>
+<td align="right">2.802</td>
+</tr>
+<tr class="odd">
+<td align="left">Linux</td>
+<td align="left">Ryzen 7 1700</td>
+<td align="left">4.2.2</td>
+<td align="left">1.2.2</td>
+<td align="right">0.935</td>
+<td align="right">1.381</td>
+<td align="right">1.551</td>
+<td align="right">3.209</td>
+<td align="right">1.976</td>
+<td align="right">3.013</td>
 </tr>
 </tbody>
 </table>
diff --git a/docs/dev/articles/web_only/compiled_models.html b/docs/dev/articles/web_only/compiled_models.html
index ade86bc5..e9d80420 100644
--- a/docs/dev/articles/web_only/compiled_models.html
+++ b/docs/dev/articles/web_only/compiled_models.html
@@ -34,7 +34,7 @@
       </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">1.2.0</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
       </span>
     </div>
 
@@ -78,7 +78,10 @@
       <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
     <li>
-      <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a>
+      <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+    </li>
+    <li>
+      <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
   </ul>
 </li>
@@ -109,7 +112,7 @@
       <h1 data-toc-skip>Performance benefit by using compiled model definitions in mkin</h1>
                         <h4 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 data-toc-skip class="date">2022-11-01</h4>
+            <h4 data-toc-skip class="date">2022-11-24</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/compiled_models.rmd" class="external-link"><code>vignettes/web_only/compiled_models.rmd</code></a></small>
       <div class="hidden name"><code>compiled_models.rmd</code></div>
@@ -167,10 +170,10 @@
 <span>  <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="st">"R package rbenchmark is not available"</span><span class="op">)</span></span>
 <span><span class="op">}</span></span></code></pre></div>
 <pre><code><span><span class="co">##                    test replications relative elapsed</span></span>
-<span><span class="co">## 4            analytical            1    1.000   0.186</span></span>
-<span><span class="co">## 3     deSolve, compiled            1    1.656   0.308</span></span>
-<span><span class="co">## 2      Eigenvalue based            1    2.102   0.391</span></span>
-<span><span class="co">## 1 deSolve, not compiled            1   38.968   7.248</span></span></code></pre>
+<span><span class="co">## 4            analytical            1    1.000   0.221</span></span>
+<span><span class="co">## 3     deSolve, compiled            1    1.561   0.345</span></span>
+<span><span class="co">## 2      Eigenvalue based            1    1.932   0.427</span></span>
+<span><span class="co">## 1 deSolve, not compiled            1   33.629   7.432</span></span></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 class="section level2">
@@ -197,10 +200,10 @@
 <span><span class="op">}</span></span></code></pre></div>
 <pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre>
 <pre><code><span><span class="co">##                    test replications relative elapsed</span></span>
-<span><span class="co">## 2     deSolve, compiled            1    1.000   0.452</span></span>
-<span><span class="co">## 1 deSolve, not compiled            1   29.431  13.303</span></span></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 1.2.0 on</p>
+<span><span class="co">## 2     deSolve, compiled            1    1.000   0.482</span></span>
+<span><span class="co">## 1 deSolve, not compiled            1   27.865  13.431</span></span></code></pre>
+<p>Here we get a performance benefit of a factor of 28 using the version of the differential equation model compiled from C code!</p>
+<p>This vignette was built with mkin 1.2.2 on</p>
 <pre><code><span><span class="co">## R version 4.2.2 (2022-10-31)</span></span>
 <span><span class="co">## Platform: x86_64-pc-linux-gnu (64-bit)</span></span>
 <span><span class="co">## Running under: Debian GNU/Linux 11 (bullseye)</span></span></code></pre>
diff --git a/docs/dev/articles/web_only/dimethenamid_2018.html b/docs/dev/articles/web_only/dimethenamid_2018.html
index 60f1ab5a..ec7f54d8 100644
--- a/docs/dev/articles/web_only/dimethenamid_2018.html
+++ b/docs/dev/articles/web_only/dimethenamid_2018.html
@@ -34,7 +34,7 @@
       </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">1.1.2</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
       </span>
     </div>
 
@@ -63,19 +63,25 @@
       <a href="../../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
     </li>
     <li>
-      <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+      <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a>
     </li>
     <li>
       <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
     </li>
     <li>
+      <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+    </li>
+    <li>
       <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
     </li>
     <li>
       <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
     <li>
-      <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a>
+      <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+    </li>
+    <li>
+      <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
   </ul>
 </li>
@@ -106,7 +112,7 @@
       <h1 data-toc-skip>Example evaluations of the dimethenamid data from 2018</h1>
                         <h4 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 data-toc-skip class="date">Last change 1 July 2022, built on 16 Sep 2022</h4>
+            <h4 data-toc-skip class="date">Last change 1 July 2022, built on 24 Nov 2022</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/dimethenamid_2018.rmd" class="external-link"><code>vignettes/web_only/dimethenamid_2018.rmd</code></a></small>
       <div class="hidden name"><code>dimethenamid_2018.rmd</code></div>
@@ -366,7 +372,7 @@ DFOP tc more iterations 665.88 663.80</code></pre>
 <span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">AIC_parent_saemix_methods_defaults</span><span class="op">)</span></span></code></pre></div>
 <pre><code>    is     gq    lin 
-668.27 718.36 666.49 </code></pre>
+669.77 669.36 670.95 </code></pre>
 </div>
 </div>
 <div class="section level3">
@@ -437,7 +443,7 @@ DFOP tc more iterations 665.88 663.80</code></pre>
 </h2>
 <div class="sourceCode" id="cb32"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
-<pre><code>R version 4.2.1 (2022-06-23)
+<pre><code>R version 4.2.2 (2022-10-31)
 Platform: x86_64-pc-linux-gnu (64-bit)
 Running under: Debian GNU/Linux 11 (bullseye)
 
@@ -457,24 +463,24 @@ attached base packages:
 [1] stats     graphics  grDevices utils     datasets  methods   base     
 
 other attached packages:
-[1] nlme_3.1-158 mkin_1.1.2   knitr_1.39  
+[1] saemix_3.2   npde_3.2     nlme_3.1-160 mkin_1.2.2   knitr_1.41  
 
 loaded via a namespace (and not attached):
- [1] deSolve_1.33       zoo_1.8-10         tidyselect_1.1.2   xfun_0.31         
- [5] bslib_0.4.0        purrr_0.3.4        lattice_0.20-45    colorspace_2.0-3  
- [9] vctrs_0.4.1        generics_0.1.3     htmltools_0.5.3    yaml_2.3.5        
-[13] utf8_1.2.2         rlang_1.0.4        pkgdown_2.0.6      saemix_3.1        
-[17] jquerylib_0.1.4    pillar_1.8.0       glue_1.6.2         DBI_1.1.3         
-[21] lifecycle_1.0.1    stringr_1.4.0      munsell_0.5.0      gtable_0.3.0      
-[25] ragg_1.2.2         memoise_2.0.1      evaluate_0.15      npde_3.2          
-[29] fastmap_1.1.0      lmtest_0.9-40      parallel_4.2.1     fansi_1.0.3       
-[33] highr_0.9          KernSmooth_2.23-20 scales_1.2.0       cachem_1.0.6      
-[37] desc_1.4.1         jsonlite_1.8.0     systemfonts_1.0.4  fs_1.5.2          
-[41] textshaping_0.3.6  gridExtra_2.3      ggplot2_3.3.6      digest_0.6.29     
-[45] stringi_1.7.8      dplyr_1.0.9        grid_4.2.1         rprojroot_2.0.3   
-[49] cli_3.3.0          tools_4.2.1        magrittr_2.0.3     sass_0.4.2        
-[53] tibble_3.1.8       pkgconfig_2.0.3    assertthat_0.2.1   rmarkdown_2.14.3  
-[57] mclust_5.4.10      R6_2.5.1           compiler_4.2.1    </code></pre>
+ [1] deSolve_1.34      zoo_1.8-11        tidyselect_1.2.0  xfun_0.35        
+ [5] bslib_0.4.1       purrr_0.3.5       lattice_0.20-45   colorspace_2.0-3 
+ [9] vctrs_0.5.1       generics_0.1.3    htmltools_0.5.3   yaml_2.3.6       
+[13] utf8_1.2.2        rlang_1.0.6       pkgdown_2.0.6     jquerylib_0.1.4  
+[17] pillar_1.8.1      glue_1.6.2        DBI_1.1.3         lifecycle_1.0.3  
+[21] stringr_1.4.1     munsell_0.5.0     gtable_0.3.1      ragg_1.2.4       
+[25] codetools_0.2-18  memoise_2.0.1     evaluate_0.18     fastmap_1.1.0    
+[29] lmtest_0.9-40     parallel_4.2.2    fansi_1.0.3       highr_0.9        
+[33] scales_1.2.1      cachem_1.0.6      desc_1.4.2        jsonlite_1.8.3   
+[37] systemfonts_1.0.4 fs_1.5.2          textshaping_0.3.6 gridExtra_2.3    
+[41] ggplot2_3.4.0     digest_0.6.30     stringi_1.7.8     dplyr_1.0.10     
+[45] grid_4.2.2        rprojroot_2.0.3   cli_3.4.1         tools_4.2.2      
+[49] magrittr_2.0.3    sass_0.4.3        tibble_3.1.8      pkgconfig_2.0.3  
+[53] assertthat_0.2.1  rmarkdown_2.18    R6_2.5.1          mclust_6.0.0     
+[57] compiler_4.2.2   </code></pre>
 </div>
 <div class="section level2">
 <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
diff --git a/docs/dev/articles/web_only/multistart.html b/docs/dev/articles/web_only/multistart.html
index 50a57d1b..fd05f340 100644
--- a/docs/dev/articles/web_only/multistart.html
+++ b/docs/dev/articles/web_only/multistart.html
@@ -34,7 +34,7 @@
       </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">1.2.0</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
       </span>
     </div>
 
@@ -78,7 +78,10 @@
       <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
     <li>
-      <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a>
+      <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+    </li>
+    <li>
+      <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
   </ul>
 </li>
@@ -109,7 +112,7 @@
       <h1 data-toc-skip>Short demo of the multistart method</h1>
                         <h4 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 data-toc-skip class="date">Last change 26 September 2022 (rebuilt 2022-11-01)</h4>
+            <h4 data-toc-skip class="date">Last change 26 September 2022 (rebuilt 2022-11-24)</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/multistart.rmd" class="external-link"><code>vignettes/web_only/multistart.rmd</code></a></small>
       <div class="hidden name"><code>multistart.rmd</code></div>
@@ -163,8 +166,8 @@
 <pre><code><span><span class="co">## Data: 155 observations of 1 variable(s) grouped in 6 datasets</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">##                            npar    AIC    BIC     Lik Chisq Df Pr(&gt;Chisq)</span></span>
-<span><span class="co">## best(f_saem_reduced_multi)    9 663.64 661.77 -322.82                    </span></span>
-<span><span class="co">## f_saem_full                  10 668.27 666.19 -324.13     0  1          1</span></span></code></pre>
+<span><span class="co">## best(f_saem_reduced_multi)    9 663.69 661.82 -322.85                    </span></span>
+<span><span class="co">## f_saem_full                  10 669.77 667.69 -324.89     0  1          1</span></span></code></pre>
 <p>While AIC and BIC are lower for the reduced model, the likelihood ratio test does not indicate a significant difference between the fits.</p>
   </div>
 
diff --git a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png
index 79543765..13bdb94b 100644
--- a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png
+++ b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png
diff --git a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png
index 4466d437..56147ae2 100644
--- a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png
+++ b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png
diff --git a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png
index 3dd36f91..f0b89dba 100644
--- a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png
+++ b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png
diff --git a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-6-1.png b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-6-1.png
index 3963e993..c57c247f 100644
--- a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-6-1.png
+++ b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-6-1.png
diff --git a/docs/dev/articles/web_only/saem_benchmarks.html b/docs/dev/articles/web_only/saem_benchmarks.html
index afff038f..66f4b075 100644
--- a/docs/dev/articles/web_only/saem_benchmarks.html
+++ b/docs/dev/articles/web_only/saem_benchmarks.html
@@ -34,7 +34,7 @@
       </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">1.2.0</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
       </span>
     </div>
 
@@ -112,7 +112,7 @@
       <h1 data-toc-skip>Benchmark timings for saem.mmkin</h1>
                         <h4 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 data-toc-skip class="date">Last change 14 November 2022 (rebuilt 2022-11-16)</h4>
+            <h4 data-toc-skip class="date">Last change 14 November 2022 (rebuilt 2022-11-24)</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/saem_benchmarks.rmd" class="external-link"><code>vignettes/web_only/saem_benchmarks.rmd</code></a></small>
       <div class="hidden name"><code>saem_benchmarks.rmd</code></div>
@@ -304,16 +304,28 @@
 <th align="right">t3</th>
 <th align="right">t4</th>
 </tr></thead>
-<tbody><tr class="odd">
+<tbody>
+<tr class="odd">
 <td align="left">Ryzen 7 1700</td>
 <td align="left">Linux</td>
 <td align="left">1.2.0</td>
 <td align="left">3.2</td>
-<td align="right">2.156</td>
-<td align="right">4.647</td>
-<td align="right">4.296</td>
-<td align="right">4.951</td>
-</tr></tbody>
+<td align="right">2.140</td>
+<td align="right">4.626</td>
+<td align="right">4.328</td>
+<td align="right">4.998</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 7 1700</td>
+<td align="left">Linux</td>
+<td align="left">1.2.2</td>
+<td align="left">3.2</td>
+<td align="right">2.427</td>
+<td align="right">4.550</td>
+<td align="right">4.217</td>
+<td align="right">4.851</td>
+</tr>
+</tbody>
 </table>
 <p>Two-component error fits for SFO, DFOP, SFORB and HS.</p>
 <table class="table">
@@ -327,16 +339,28 @@
 <th align="right">t7</th>
 <th align="right">t8</th>
 </tr></thead>
-<tbody><tr class="odd">
+<tbody>
+<tr class="odd">
 <td align="left">Ryzen 7 1700</td>
 <td align="left">Linux</td>
 <td align="left">1.2.0</td>
 <td align="left">3.2</td>
-<td align="right">5.645</td>
-<td align="right">7.415</td>
-<td align="right">7.848</td>
-<td align="right">7.967</td>
-</tr></tbody>
+<td align="right">5.678</td>
+<td align="right">7.441</td>
+<td align="right">8.000</td>
+<td align="right">7.980</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 7 1700</td>
+<td align="left">Linux</td>
+<td align="left">1.2.2</td>
+<td align="left">3.2</td>
+<td align="right">5.352</td>
+<td align="right">7.201</td>
+<td align="right">8.174</td>
+<td align="right">8.401</td>
+</tr>
+</tbody>
 </table>
 </div>
 <div class="section level3">
@@ -352,14 +376,24 @@
 <th align="right">t9</th>
 <th align="right">t10</th>
 </tr></thead>
-<tbody><tr class="odd">
+<tbody>
+<tr class="odd">
 <td align="left">Ryzen 7 1700</td>
 <td align="left">Linux</td>
 <td align="left">1.2.0</td>
 <td align="left">3.2</td>
-<td align="right">24.182</td>
-<td align="right">783.932</td>
-</tr></tbody>
+<td align="right">24.465</td>
+<td align="right">800.266</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 7 1700</td>
+<td align="left">Linux</td>
+<td align="left">1.2.2</td>
+<td align="left">3.2</td>
+<td align="right">25.193</td>
+<td align="right">798.580</td>
+</tr>
+</tbody>
 </table>
 </div>
 <div class="section level3">
@@ -374,13 +408,22 @@
 <th align="left">saemix</th>
 <th align="right">t11</th>
 </tr></thead>
-<tbody><tr class="odd">
+<tbody>
+<tr class="odd">
 <td align="left">Ryzen 7 1700</td>
 <td align="left">Linux</td>
 <td align="left">1.2.0</td>
 <td align="left">3.2</td>
-<td align="right">1322.5</td>
-</tr></tbody>
+<td align="right">1289.198</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 7 1700</td>
+<td align="left">Linux</td>
+<td align="left">1.2.2</td>
+<td align="left">3.2</td>
+<td align="right">1312.445</td>
+</tr>
+</tbody>
 </table>
 </div>
 </div>
author	Johannes Ranke <jranke@uni-bremen.de>	2022-11-24 09:02:26 +0100
committer	Johannes Ranke <jranke@uni-bremen.de>	2022-11-24 09:02:26 +0100
commit	af7c6de4db9981ac814362c441fbac22c8faa2d7 (patch)
tree	33c2963936ce6c38abe6533afcce3994a08d4ba9 /docs/dev/articles
parent	8e953c409e0020ea7e7c2a5121019c42cb66dde4 (diff)