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-rw-r--r--docs/dev/reference/aw.html202
-rw-r--r--docs/dev/reference/dimethenamid_2018.html6
-rw-r--r--docs/dev/reference/index.html22
-rw-r--r--docs/dev/reference/mkinfit.html17
-rw-r--r--docs/dev/reference/multistart.html195
-rw-r--r--docs/dev/reference/parms.html366
-rw-r--r--docs/dev/reference/saem.html18
-rw-r--r--docs/dev/reference/summary.mkinfit.html6
-rw-r--r--docs/dev/reference/summary.mmkin.html2
-rw-r--r--docs/dev/reference/summary.saem.mmkin.html6
10 files changed, 474 insertions, 366 deletions
diff --git a/docs/dev/reference/aw.html b/docs/dev/reference/aw.html
index 3b06f2a6..57dfa06c 100644
--- a/docs/dev/reference/aw.html
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expected Kullback-Leibler information as specified
-by Burnham and Anderson (2004)." />
-
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-<meta name="robots" content="noindex">
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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+by Burnham and Anderson (2004)."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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- <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">1.1.2</span>
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@@ -100,6 +43,9 @@ by Burnham and Anderson (2004)." />
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
+ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+ </li>
+ <li>
<a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
</li>
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@@ -114,34 +60,27 @@ by Burnham and Anderson (2004)." />
<li>
<a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
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<h1>Calculate Akaike weights for model averaging</h1>
- <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/aw.R'><code>R/aw.R</code></a></small>
+ <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/aw.R" class="external-link"><code>R/aw.R</code></a></small>
<div class="hidden name"><code>aw.Rd</code></div>
</div>
@@ -151,76 +90,85 @@ expected Kullback-Leibler information as specified
by Burnham and Anderson (2004).</p>
</div>
- <pre class="usage"><span class='fu'>aw</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span>
-
-<span class='co'># S3 method for mkinfit</span>
-<span class='fu'>aw</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span>
-
-<span class='co'># S3 method for mmkin</span>
-<span class='fu'>aw</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre>
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">aw</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for mkinfit</span></span>
+<span><span class="fu">aw</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for mmkin</span></span>
+<span><span class="fu">aw</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for mixed.mmkin</span></span>
+<span><span class="fu">aw</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for multistart</span></span>
+<span><span class="fu">aw</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
+ </div>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>object</th>
- <td><p>An <a href='mmkin.html'>mmkin</a> column object, containing two or more
-<a href='mkinfit.html'>mkinfit</a> models that have been fitted to the same data,
+ <div id="arguments">
+ <h2>Arguments</h2>
+ <dl><dt>object</dt>
+<dd><p>An <a href="mmkin.html">mmkin</a> column object, containing two or more
+<a href="mkinfit.html">mkinfit</a> models that have been fitted to the same data,
or an mkinfit object. In the latter case, further mkinfit
objects fitted to the same data should be specified
-as dots arguments.</p></td>
- </tr>
- <tr>
- <th>...</th>
- <td><p>Not used in the method for <a href='mmkin.html'>mmkin</a> column objects,
-further <a href='mkinfit.html'>mkinfit</a> objects in the method for mkinfit objects.</p></td>
- </tr>
- </table>
+as dots arguments.</p></dd>
+
- <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+<dt>...</dt>
+<dd><p>Not used in the method for <a href="mmkin.html">mmkin</a> column objects,
+further <a href="mkinfit.html">mkinfit</a> objects in the method for mkinfit objects.</p></dd>
+</dl></div>
+ <div id="references">
+ <h2>References</h2>
<p>Burnham KP and Anderson DR (2004) Multimodel
Inference: Understanding AIC and BIC in Model Selection.
<em>Sociological Methods &amp; Research</em> <strong>33</strong>(2) 261-304</p>
+ </div>
- <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='co'># \dontrun{</span>
-<span class='va'>f_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-<span class='va'>f_dfop</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-<span class='va'>aw_sfo_dfop</span> <span class='op'>&lt;-</span> <span class='fu'>aw</span><span class='op'>(</span><span class='va'>f_sfo</span>, <span class='va'>f_dfop</span><span class='op'>)</span>
-<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='va'>aw_sfo_dfop</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; [1] 1</div><div class='input'><span class='va'>aw_sfo_dfop</span> <span class='co'># SFO gets more weight as it has less parameters and a similar fit</span>
-</div><div class='output co'>#&gt; [1] 0.5970258 0.4029742</div><div class='input'><span class='va'>f</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"FOCUS D"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_D</span><span class='op'>)</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-<span class='fu'>aw</span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; [1] 0.4808722 0.1945539 0.3245740</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='fu'>aw</span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; [1] 1</div><div class='input'><span class='fu'>aw</span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; [1] 0.5970258 0.4029742</div><div class='input'><span class='co'># }</span>
-</div></pre>
+ <div id="ref-examples">
+ <h2>Examples</h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span><span class="va">f_sfo</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">f_dfop</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">aw_sfo_dfop</span> <span class="op">&lt;-</span> <span class="fu">aw</span><span class="op">(</span><span class="va">f_sfo</span>, <span class="va">f_dfop</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">aw_sfo_dfop</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1</span>
+<span class="r-in"><span><span class="va">aw_sfo_dfop</span> <span class="co"># SFO gets more weight as it has less parameters and a similar fit</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5970258 0.4029742</span>
+<span class="r-in"><span><span class="va">f</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS D"</span> <span class="op">=</span> <span class="va">FOCUS_2006_D</span><span class="op">)</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">aw</span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.4808722 0.1945539 0.3245740</span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="fu">aw</span><span class="op">(</span><span class="va">f</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1</span>
+<span class="r-in"><span><span class="fu">aw</span><span class="op">(</span><span class="va">f</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"DFOP"</span><span class="op">)</span><span class="op">]</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5970258 0.4029742</span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
+</code></pre></div>
+ </div>
</div>
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- <h2 data-toc-skip>Contents</h2>
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+
+ </body></html>
diff --git a/docs/dev/reference/dimethenamid_2018.html b/docs/dev/reference/dimethenamid_2018.html
index 7a356284..2454a609 100644
--- a/docs/dev/reference/dimethenamid_2018.html
+++ b/docs/dev/reference/dimethenamid_2018.html
@@ -203,8 +203,8 @@ specific pieces of information in the comments.</p>
<span class="r-out co"><span class="r-pr">#&gt;</span> saemix version used for fitting: 3.1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting: 1.1.2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting: 4.2.1 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit: Wed Aug 10 15:24:12 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Wed Aug 10 15:24:12 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit: Fri Sep 16 10:29:07 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Fri Sep 16 10:29:07 2022 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> d_DMTA/dt = - k_DMTA * DMTA</span>
@@ -217,7 +217,7 @@ specific pieces of information in the comments.</p>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type deSolve </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 791.863 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 797.539 s</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Using 300, 100 iterations and 9 chains</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Variance model: Two-component variance function </span>
diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html
index 98f170b6..3372a69a 100644
--- a/docs/dev/reference/index.html
+++ b/docs/dev/reference/index.html
@@ -107,6 +107,10 @@ degradation models and one or more error models</p></td>
<p class="section-desc"></p><p>Generic functions introduced by the package</p>
</th>
</tr></tbody><tbody><tr><td>
+ <p><code><a href="parms.html">parms()</a></code> </p>
+ </td>
+ <td><p>Extract model parameters</p></td>
+ </tr><tr><td>
<p><code><a href="convergence.html">convergence()</a></code> <code><a href="convergence.html">print(<i>&lt;convergence.mmkin&gt;</i>)</a></code> </p>
</td>
<td><p>Method to get convergence information</p></td>
@@ -119,6 +123,10 @@ degradation models and one or more error models</p></td>
</td>
<td><p>Function to calculate endpoints for further use from kinetic models fitted
with mkinfit</p></td>
+ </tr><tr><td>
+ <p><code><a href="aw.html">aw()</a></code> </p>
+ </td>
+ <td><p>Calculate Akaike weights for model averaging</p></td>
</tr></tbody><tbody><tr><th colspan="2">
<h2 id="show-results">Show results <a href="#show-results" class="anchor" aria-hidden="true"></a></h2>
<p class="section-desc"></p><p>Functions working with mkinfit objects</p>
@@ -132,10 +140,6 @@ with mkinfit</p></td>
</td>
<td><p>Summary method for class "mkinfit"</p></td>
</tr><tr><td>
- <p><code><a href="parms.html">parms()</a></code> </p>
- </td>
- <td><p>Extract model parameters from mkinfit models</p></td>
- </tr><tr><td>
<p><code><a href="confint.mkinfit.html">confint(<i>&lt;mkinfit&gt;</i>)</a></code> </p>
</td>
<td><p>Confidence intervals for parameters of mkinfit objects</p></td>
@@ -156,10 +160,6 @@ with mkinfit</p></td>
</td>
<td><p>Calculate the minimum error to assume in order to pass the variance test</p></td>
</tr><tr><td>
- <p><code><a href="aw.html">aw()</a></code> </p>
- </td>
- <td><p>Calculate Akaike weights for model averaging</p></td>
- </tr><tr><td>
<p><code><a href="CAKE_export.html">CAKE_export()</a></code> </p>
</td>
<td><p>Export a list of datasets format to a CAKE study file</p></td>
@@ -193,7 +193,7 @@ of an mmkin object</p></td>
</td>
<td><p>Create an nlme model for an mmkin row object</p></td>
</tr><tr><td>
- <p><code><a href="saem.html">saem()</a></code> <code><a href="saem.html">print(<i>&lt;saem.mmkin&gt;</i>)</a></code> <code><a href="saem.html">saemix_model()</a></code> <code><a href="saem.html">saemix_data()</a></code> </p>
+ <p><code><a href="saem.html">saem()</a></code> <code><a href="saem.html">print(<i>&lt;saem.mmkin&gt;</i>)</a></code> <code><a href="saem.html">saemix_model()</a></code> <code><a href="saem.html">saemix_data()</a></code> <code><a href="saem.html">parms(<i>&lt;saem.mmkin&gt;</i>)</a></code> </p>
</td>
<td><p>Fit nonlinear mixed models with SAEM</p></td>
</tr><tr><td>
@@ -233,6 +233,10 @@ degradation models and one or more error models</p></td>
<p><code><a href="intervals.saem.mmkin.html">intervals(<i>&lt;saem.mmkin&gt;</i>)</a></code> </p>
</td>
<td><p>Confidence intervals for parameters in saem.mmkin objects</p></td>
+ </tr><tr><td>
+ <p><code><a href="multistart.html">multistart()</a></code> <code><a href="multistart.html">print(<i>&lt;multistart&gt;</i>)</a></code> <code><a href="multistart.html">parms(<i>&lt;multistart&gt;</i>)</a></code> <code><a href="multistart.html">parhist()</a></code> <code><a href="multistart.html">llhist()</a></code> </p>
+ </td>
+ <td><p>Perform a hierarchical model fit with multiple starting values</p></td>
</tr></tbody><tbody><tr><th colspan="2">
<h2 id="datasets-and-known-results">Datasets and known results <a href="#datasets-and-known-results" class="anchor" aria-hidden="true"></a></h2>
<p class="section-desc"></p>
diff --git a/docs/dev/reference/mkinfit.html b/docs/dev/reference/mkinfit.html
index a00a0458..bcc86ded 100644
--- a/docs/dev/reference/mkinfit.html
+++ b/docs/dev/reference/mkinfit.html
@@ -380,8 +380,8 @@ Degradation Data. <em>Environments</em> 6(12) 124
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for fitting: 1.1.2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting: 4.2.1 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit: Wed Aug 10 15:24:16 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Wed Aug 10 15:24:16 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit: Fri Sep 16 10:29:10 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Fri Sep 16 10:29:10 2022 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span>
@@ -528,10 +528,11 @@ Degradation Data. <em>Environments</em> 6(12) 124
<span class="r-in"><span> analytical <span class="op">=</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span></span>
<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: rbenchmark</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> test relative elapsed</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3 analytical 1.000 0.605</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1 deSolve_compiled 1.448 0.876</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2 eigen 2.479 1.500</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3 analytical 1.000 0.577</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 deSolve_compiled 1.537 0.887</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2 eigen 2.551 1.472</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span></span></span>
@@ -560,8 +561,8 @@ Degradation Data. <em>Environments</em> 6(12) 124
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>diag(.) had 0 or NA entries; non-finite result is doubtful</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for fitting: 1.1.2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting: 4.2.1 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit: Wed Aug 10 15:24:27 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Wed Aug 10 15:24:27 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit: Fri Sep 16 10:29:21 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Fri Sep 16 10:29:21 2022 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span>
@@ -570,7 +571,7 @@ Degradation Data. <em>Environments</em> 6(12) 124
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type deSolve </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted using 3729 model solutions performed in 2.475 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted using 3729 model solutions performed in 2.48 s</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Error model: Two-component variance function </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
diff --git a/docs/dev/reference/multistart.html b/docs/dev/reference/multistart.html
new file mode 100644
index 00000000..9f2d297e
--- /dev/null
+++ b/docs/dev/reference/multistart.html
@@ -0,0 +1,195 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Perform a hierarchical model fit with multiple starting values — multistart • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Perform a hierarchical model fit with multiple starting values — multistart"><meta property="og:description" content="The purpose of this method is to check if a certain algorithm for fitting
+nonlinear hierarchical models (also known as nonlinear mixed-effects models)
+will reliably yield results that are sufficiently similar to each other, if
+started with a certain range of reasonable starting parameters. It is
+inspired by the article on practical identifiabiliy in the frame of nonlinear
+mixed-effects models by Duchesne et al (2021)."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+<![endif]--></head><body data-spy="scroll" data-target="#toc">
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+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
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+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
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+ <a href="../reference/index.html">Functions and data</a>
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+ Articles
+
+ <span class="caret"></span>
+ </a>
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+ <a href="../articles/mkin.html">Introduction to mkin</a>
+ </li>
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+ <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+ </li>
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+ <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+ </li>
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+ <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+ </li>
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+ <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
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+
+
+
+ </header><div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Perform a hierarchical model fit with multiple starting values</h1>
+ <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/multistart.R" class="external-link"><code>R/multistart.R</code></a></small>
+ <div class="hidden name"><code>multistart.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>The purpose of this method is to check if a certain algorithm for fitting
+nonlinear hierarchical models (also known as nonlinear mixed-effects models)
+will reliably yield results that are sufficiently similar to each other, if
+started with a certain range of reasonable starting parameters. It is
+inspired by the article on practical identifiabiliy in the frame of nonlinear
+mixed-effects models by Duchesne et al (2021).</p>
+ </div>
+
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">multistart</span><span class="op">(</span><span class="va">object</span>, n <span class="op">=</span> <span class="fl">50</span>, cores <span class="op">=</span> <span class="fl">1</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for saem.mmkin</span></span>
+<span><span class="fu">multistart</span><span class="op">(</span><span class="va">object</span>, n <span class="op">=</span> <span class="fl">50</span>, cores <span class="op">=</span> <span class="fl">1</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for multistart</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for multistart</span></span>
+<span><span class="fu"><a href="parms.html">parms</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">parhist</span><span class="op">(</span><span class="va">object</span>, lpos <span class="op">=</span> <span class="st">"topleft"</span>, main <span class="op">=</span> <span class="st">""</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">llhist</span><span class="op">(</span><span class="va">object</span>, breaks <span class="op">=</span> <span class="st">"Sturges"</span>, lpos <span class="op">=</span> <span class="st">"topleft"</span>, main <span class="op">=</span> <span class="st">""</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
+ </div>
+
+ <div id="arguments">
+ <h2>Arguments</h2>
+ <dl><dt>object</dt>
+<dd><p>The fit object to work with</p></dd>
+
+
+<dt>n</dt>
+<dd><p>How many different combinations of starting parameters should be
+used?</p></dd>
+
+
+<dt>cores</dt>
+<dd><p>How many fits should be run in parallel?</p></dd>
+
+
+<dt>...</dt>
+<dd><p>Passed to the update function, or to the basic plotting
+function in the case of the graphical functions.</p></dd>
+
+
+<dt>x</dt>
+<dd><p>The multistart object to print</p></dd>
+
+
+<dt>lpos</dt>
+<dd><p>Positioning of the legend.</p></dd>
+
+
+<dt>main</dt>
+<dd><p>title of the plot</p></dd>
+
+
+<dt>breaks</dt>
+<dd><p>Passed to <a href="https://rdrr.io/r/graphics/hist.html" class="external-link">hist</a></p></dd>
+
+</dl></div>
+ <div id="value">
+ <h2>Value</h2>
+
+
+<p>A list of <a href="saem.html">saem.mmkin</a> objects, with class attributes
+'multistart.saem.mmkin' and 'multistart'.</p>
+ </div>
+ <div id="details">
+ <h2>Details</h2>
+ <p>Currently, parallel execution of the fits is only supported using
+<a href="https://rdrr.io/r/parallel/mclapply.html" class="external-link">parallel::mclapply</a>, i.e. not available on Windows.</p>
+ </div>
+ <div id="references">
+ <h2>References</h2>
+ <p>Duchesne R, Guillemin A, Gandrillon O, Crauste F. Practical
+identifiability in the frame of nonlinear mixed effects models: the example
+of the in vitro erythropoiesis. BMC Bioinformatics. 2021 Oct 4;22(1):478.
+doi: 10.1186/s12859-021-04373-4.</p>
+ </div>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
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@@ -1,69 +1,14 @@
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+model parameters per default, in order to avoid working with a fitted model
+without considering the error structure that was assumed for the fit."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+
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-
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+ <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
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@@ -74,23 +19,21 @@ considering the error structure that was assumed for the fit." />
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<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span>
</span>
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- <ul class="nav navbar-nav">
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+ <ul class="nav navbar-nav"><li>
<a href="../reference/index.html">Functions and data</a>
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+ <ul class="dropdown-menu" role="menu"><li>
<a href="../articles/mkin.html">Introduction to mkin</a>
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<li>
@@ -100,6 +43,9 @@ considering the error structure that was assumed for the fit." />
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
+ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+ </li>
+ <li>
<a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
</li>
<li>
@@ -114,185 +60,191 @@ considering the error structure that was assumed for the fit." />
<li>
<a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
</li>
- </ul>
-</li>
+ </ul></li>
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<a href="../news/index.html">News</a>
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- </ul>
- <ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://github.com/jranke/mkin/">
+ </ul><ul class="nav navbar-nav navbar-right"><li>
+ <a href="https://github.com/jranke/mkin/" class="external-link">
<span class="fab fa-github fa-lg"></span>
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-
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+ </header><div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Extract model parameters from mkinfit models</h1>
- <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/parms.mkinfit.R'><code>R/parms.mkinfit.R</code></a></small>
+ <h1>Extract model parameters</h1>
+ <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parms.mkinfit.R" class="external-link"><code>R/parms.mkinfit.R</code></a></small>
<div class="hidden name"><code>parms.Rd</code></div>
</div>
<div class="ref-description">
- <p>This function always returns degradation model parameters as well as error
-model parameters, in order to avoid working with a fitted model without
-considering the error structure that was assumed for the fit.</p>
+ <p>This function returns degradation model parameters as well as error
+model parameters per default, in order to avoid working with a fitted model
+without considering the error structure that was assumed for the fit.</p>
+ </div>
+
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">parms</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for mkinfit</span></span>
+<span><span class="fu">parms</span><span class="op">(</span><span class="va">object</span>, transformed <span class="op">=</span> <span class="cn">FALSE</span>, errparms <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for mmkin</span></span>
+<span><span class="fu">parms</span><span class="op">(</span><span class="va">object</span>, transformed <span class="op">=</span> <span class="cn">FALSE</span>, errparms <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
</div>
- <pre class="usage"><span class='fu'>parms</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span>
+ <div id="arguments">
+ <h2>Arguments</h2>
+ <dl><dt>object</dt>
+<dd><p>A fitted model object.</p></dd>
+
+
+<dt>...</dt>
+<dd><p>Not used</p></dd>
-<span class='co'># S3 method for mkinfit</span>
-<span class='fu'>parms</span><span class='op'>(</span><span class='va'>object</span>, transformed <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span>
-<span class='co'># S3 method for mmkin</span>
-<span class='fu'>parms</span><span class='op'>(</span><span class='va'>object</span>, transformed <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span></pre>
+<dt>transformed</dt>
+<dd><p>Should the parameters be returned as used internally
+during the optimisation?</p></dd>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>object</th>
- <td><p>A fitted model object. Methods are implemented for
-<code><a href='mkinfit.html'>mkinfit()</a></code> objects and for <code><a href='mmkin.html'>mmkin()</a></code> objects.</p></td>
- </tr>
- <tr>
- <th>...</th>
- <td><p>Not used</p></td>
- </tr>
- <tr>
- <th>transformed</th>
- <td><p>Should the parameters be returned
-as used internally during the optimisation?</p></td>
- </tr>
- </table>
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+<dt>errparms</dt>
+<dd><p>Should the error model parameters be returned
+in addition to the degradation parameters?</p></dd>
- <p>For mkinfit objects, a numeric vector of fitted model parameters.
-For mmkin row objects, a matrix with the parameters with a
-row for each dataset. If the mmkin object has more than one row, a list of
-such matrices is returned.</p>
+</dl></div>
+ <div id="value">
+ <h2>Value</h2>
+
- <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='co'># mkinfit objects</span>
-<span class='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-<span class='fu'>parms</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; parent_0 k_parent sigma
-#&gt; 82.4921598 0.3060633 4.6730124 </div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fit</span>, transformed <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; parent_0 log_k_parent sigma
-#&gt; 82.492160 -1.183963 4.673012 </div><div class='input'>
-<span class='co'># mmkin objects</span>
-<span class='va'>ds</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>,
- <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span><span class='op'>)</span>
-<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Dataset"</span>, <span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>)</span>
-<span class='co'># \dontrun{</span>
-<span class='va'>fits</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>
-<span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10
-#&gt; parent_0 88.52275400 82.666781678 86.8547308 91.7779306 82.14809450
-#&gt; k_parent 0.05794659 0.009647805 0.2102974 0.1232258 0.00720421
-#&gt; sigma 5.15274487 7.040168584 3.6769645 6.4669234 6.50457673</div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span>, <span class='fl'>2</span><span class='op'>]</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; $SFO
-#&gt; Dataset 7
-#&gt; parent_0 82.666781678
-#&gt; k_parent 0.009647805
-#&gt; sigma 7.040168584
-#&gt;
-#&gt; $FOMC
-#&gt; Dataset 7
-#&gt; parent_0 92.6837649
-#&gt; alpha 0.4967832
-#&gt; beta 14.1451255
-#&gt; sigma 1.9167519
-#&gt;
-#&gt; $DFOP
-#&gt; Dataset 7
-#&gt; parent_0 91.058971589
-#&gt; k1 0.044946770
-#&gt; k2 0.002868336
-#&gt; g 0.526942415
-#&gt; sigma 2.221302196
-#&gt; </div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; $SFO
-#&gt; Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10
-#&gt; parent_0 88.52275400 82.666781678 86.8547308 91.7779306 82.14809450
-#&gt; k_parent 0.05794659 0.009647805 0.2102974 0.1232258 0.00720421
-#&gt; sigma 5.15274487 7.040168584 3.6769645 6.4669234 6.50457673
-#&gt;
-#&gt; $FOMC
-#&gt; Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10
-#&gt; parent_0 95.558575 92.6837649 90.719787 98.383939 94.8481459
-#&gt; alpha 1.338667 0.4967832 1.639099 1.074460 0.2805272
-#&gt; beta 13.033315 14.1451255 5.007077 4.397126 6.9052224
-#&gt; sigma 1.847671 1.9167519 1.066063 3.146056 1.6222778
-#&gt;
-#&gt; $DFOP
-#&gt; Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10
-#&gt; parent_0 96.55213663 91.058971589 90.34509493 98.14858820 94.311323734
-#&gt; k1 0.21954588 0.044946770 0.41232288 0.31697588 0.080663857
-#&gt; k2 0.02957934 0.002868336 0.07581766 0.03260384 0.003425417
-#&gt; g 0.44845068 0.526942415 0.66091967 0.65322767 0.342652880
-#&gt; sigma 1.35690468 2.221302196 1.34169076 2.87159846 1.942067831
-#&gt; </div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span>, transformed <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; $SFO
-#&gt; Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10
-#&gt; parent_0 88.522754 82.666782 86.854731 91.777931 82.148094
-#&gt; log_k_parent -2.848234 -4.641025 -1.559232 -2.093737 -4.933090
-#&gt; sigma 5.152745 7.040169 3.676964 6.466923 6.504577
-#&gt;
-#&gt; $FOMC
-#&gt; Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10
-#&gt; parent_0 95.5585751 92.6837649 90.7197870 98.38393897 94.848146
-#&gt; log_alpha 0.2916741 -0.6996015 0.4941466 0.07181816 -1.271085
-#&gt; log_beta 2.5675088 2.6493701 1.6108523 1.48095106 1.932278
-#&gt; sigma 1.8476712 1.9167519 1.0660627 3.14605557 1.622278
-#&gt;
-#&gt; $DFOP
-#&gt; Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10
-#&gt; parent_0 96.5521366 91.0589716 90.3450949 98.1485882 94.3113237
-#&gt; log_k1 -1.5161940 -3.1022764 -0.8859486 -1.1489296 -2.5174647
-#&gt; log_k2 -3.5206791 -5.8540232 -2.5794240 -3.4233253 -5.6765322
-#&gt; g_qlogis -0.2069326 0.1078741 0.6673953 0.6332573 -0.6514943
-#&gt; sigma 1.3569047 2.2213022 1.3416908 2.8715985 1.9420678
-#&gt; </div><div class='input'><span class='co'># }</span>
-</div></pre>
+<p>Depending on the object, a numeric vector of fitted model parameters,
+a matrix (e.g. for mmkin row objects), or a list of matrices (e.g. for
+mmkin objects with more than one row).</p>
+ </div>
+ <div id="see-also">
+ <h2>See also</h2>
+ <div class="dont-index"><p><a href="saem.html">saem</a>, <a href="multistart.html">multistart</a></p></div>
+ </div>
+
+ <div id="ref-examples">
+ <h2>Examples</h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># mkinfit objects</span></span></span>
+<span class="r-in"><span><span class="va">fit</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 k_parent sigma </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 82.4921598 0.3060633 4.6730124 </span>
+<span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fit</span>, transformed <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 log_k_parent sigma </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 82.492160 -1.183963 4.673012 </span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># mmkin objects</span></span></span>
+<span class="r-in"><span><span class="va">ds</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
+<span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"name"</span>, <span class="st">"time"</span>, <span class="st">"value"</span><span class="op">)</span><span class="op">]</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span><span class="va">fits</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 88.52275400 82.666781678 86.8547308 91.7779306 82.14809450</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent 0.05794659 0.009647805 0.2102974 0.1232258 0.00720421</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 5.15274487 7.040168584 3.6769645 6.4669234 6.50457673</span>
+<span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span><span class="op">[</span>, <span class="fl">2</span><span class="op">]</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $SFO</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Dataset 7</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 82.666781678</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent 0.009647805</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 7.040168584</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $FOMC</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Dataset 7</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 92.6837649</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> alpha 0.4967832</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> beta 14.1451255</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 1.9167519</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $DFOP</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Dataset 7</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 91.058971589</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k1 0.044946770</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k2 0.002868336</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> g 0.526942415</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 2.221302196</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $SFO</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 88.52275400 82.666781678 86.8547308 91.7779306 82.14809450</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent 0.05794659 0.009647805 0.2102974 0.1232258 0.00720421</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 5.15274487 7.040168584 3.6769645 6.4669234 6.50457673</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $FOMC</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 95.558575 92.6837649 90.719787 98.383939 94.8481459</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> alpha 1.338667 0.4967832 1.639099 1.074460 0.2805272</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> beta 13.033315 14.1451255 5.007077 4.397126 6.9052224</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 1.847671 1.9167519 1.066063 3.146056 1.6222778</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $DFOP</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 96.55213663 91.058971589 90.34509493 98.14858820 94.311323734</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k1 0.21954588 0.044946770 0.41232288 0.31697588 0.080663857</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k2 0.02957934 0.002868336 0.07581766 0.03260384 0.003425417</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> g 0.44845068 0.526942415 0.66091967 0.65322767 0.342652880</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 1.35690468 2.221302196 1.34169076 2.87159846 1.942067831</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span>, transformed <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $SFO</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 88.522754 82.666782 86.854731 91.777931 82.148094</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_parent -2.848234 -4.641025 -1.559232 -2.093737 -4.933090</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 5.152745 7.040169 3.676964 6.466923 6.504577</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $FOMC</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 95.5585751 92.6837649 90.7197870 98.38393897 94.848146</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_alpha 0.2916741 -0.6996015 0.4941466 0.07181816 -1.271085</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_beta 2.5675088 2.6493701 1.6108523 1.48095106 1.932278</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 1.8476712 1.9167519 1.0660627 3.14605557 1.622278</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $DFOP</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 96.5521366 91.0589716 90.3450949 98.1485882 94.3113237</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k1 -1.5161940 -3.1022764 -0.8859486 -1.1489296 -2.5174647</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k2 -3.5206791 -5.8540232 -2.5794240 -3.4233253 -5.6765322</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> g_qlogis -0.2069326 0.1078741 0.6673953 0.6332573 -0.6514943</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 1.3569047 2.2213022 1.3416908 2.8715985 1.9420678</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
+</code></pre></div>
+ </div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
- <nav id="toc" data-toggle="toc" class="sticky-top">
- <h2 data-toc-skip>Contents</h2>
- </nav>
- </div>
+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+ </nav></div>
</div>
- <footer>
- <div class="copyright">
- <p>Developed by Johannes Ranke.</p>
+ <footer><div class="copyright">
+ <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>
- </div>
+ </footer></div>
- </body>
-</html>
+
+ </body></html>
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html
index b55f29a8..ce3d428c 100644
--- a/docs/dev/reference/saem.html
+++ b/docs/dev/reference/saem.html
@@ -124,7 +124,10 @@ Expectation Maximisation algorithm (SAEM).</p>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
-<span><span class="fu">saemix_data</span><span class="op">(</span><span class="va">object</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
+<span><span class="fu">saemix_data</span><span class="op">(</span><span class="va">object</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for saem.mmkin</span></span>
+<span><span class="fu"><a href="parms.html">parms</a></span><span class="op">(</span><span class="va">object</span>, ci <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
</div>
<div id="arguments">
@@ -199,6 +202,11 @@ and the end of the optimisation process?</p></dd>
<dt>digits</dt>
<dd><p>Number of digits to use for printing</p></dd>
+
+<dt>ci</dt>
+<dd><p>Should a matrix with estimates and confidence interval boundaries
+be returned? If FALSE (default), a vector of estimates is returned.</p></dd>
+
</dl></div>
<div id="value">
<h2>Value</h2>
@@ -304,7 +312,7 @@ using <a href="mmkin.html">mmkin</a>.</p>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Likelihoods calculated by importance sampling</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> AIC BIC</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 467.8664 465.1324</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2 469.9096 466.7851</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2 469.8018 466.6773</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">sfo_sfo</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span>
@@ -365,8 +373,8 @@ using <a href="mmkin.html">mmkin</a>.</p>
<span class="r-out co"><span class="r-pr">#&gt;</span> saemix version used for fitting: 3.1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting: 1.1.2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting: 4.2.1 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit: Wed Aug 10 15:27:26 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Wed Aug 10 15:27:26 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit: Fri Sep 16 10:30:47 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Fri Sep 16 10:30:47 2022 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span>
@@ -381,7 +389,7 @@ using <a href="mmkin.html">mmkin</a>.</p>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type analytical </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 9.438 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 9.651 s</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Using 300, 100 iterations and 10 chains</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Variance model: Constant variance </span>
diff --git a/docs/dev/reference/summary.mkinfit.html b/docs/dev/reference/summary.mkinfit.html
index 3a31bfe7..c58fffbb 100644
--- a/docs/dev/reference/summary.mkinfit.html
+++ b/docs/dev/reference/summary.mkinfit.html
@@ -209,15 +209,15 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_A</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for fitting: 1.1.2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting: 4.2.1 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit: Wed Aug 10 15:27:28 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Wed Aug 10 15:27:28 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit: Fri Sep 16 10:30:48 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Fri Sep 16 10:30:48 2022 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - k_parent * parent</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type analytical </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted using 131 model solutions performed in 0.029 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted using 131 model solutions performed in 0.028 s</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Error model: Constant variance </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
diff --git a/docs/dev/reference/summary.mmkin.html b/docs/dev/reference/summary.mmkin.html
index e916ba24..e440e4a9 100644
--- a/docs/dev/reference/summary.mmkin.html
+++ b/docs/dev/reference/summary.mmkin.html
@@ -129,7 +129,7 @@ and gives an overview of ill-defined parameters calculated by <a href="illparms.
<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Error model: Constant variance </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 0.802 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 0.81 s</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Convergence:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> dataset</span>
diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html
index 6cab9c5f..1a6da753 100644
--- a/docs/dev/reference/summary.saem.mmkin.html
+++ b/docs/dev/reference/summary.saem.mmkin.html
@@ -289,8 +289,8 @@ saemix authors for the parts inherited from saemix.</p>
<span class="r-out co"><span class="r-pr">#&gt;</span> saemix version used for fitting: 3.1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting: 1.1.2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting: 4.2.1 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit: Wed Aug 10 15:28:15 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Wed Aug 10 15:28:15 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit: Fri Sep 16 10:31:33 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Fri Sep 16 10:31:33 2022 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span>
@@ -305,7 +305,7 @@ saemix authors for the parts inherited from saemix.</p>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type analytical </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 27.674 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 27.615 s</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Using 300, 100 iterations and 10 chains</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Variance model: Two-component variance function </span>

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