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diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index a9345c8e..d8114300 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -1,6 +1,6 @@
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+<html lang="en">
<head>
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@@ -9,17 +9,17 @@
<title>Function to set up a kinetic model with one or more state variables — mkinmod • mkin</title>
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@@ -43,7 +43,8 @@ For the definition of model types and their parameters, the equations given
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@@ -59,14 +60,15 @@ For the definition of model types and their parameters, the equations given
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
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- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.47.6</span>
</span>
</div>
@@ -215,51 +217,28 @@ For the definition of model types and their parameters, the equations given
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span>
-<span class='no'>SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))
-
+<span class='no'>SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='error'>Error in mkinmod(parent = list(type = "SFO")): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'>
<span class='co'># One parent compound, one metabolite, both single first order</span>
<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
- <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='error'>Error in mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'>
</div><div class='input'><span class='co'># The above model used to be specified like this, before the advent of mkinsub()</span>
<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(
- <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>),
- <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+ <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>),
+ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='error'>Error in mkinmod(parent = list(type = "SFO", to = "m1"), m1 = list(type = "SFO")): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'>
<span class='co'># Show details of creating the C function</span>
<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
- <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; Compilation argument:
-#&gt; /usr/lib/R/bin/R CMD SHLIB file5bb92cd04f44.c 2&gt; file5bb92cd04f44.c.err.txt
-#&gt; Program source:
-#&gt; 1: #include &lt;R.h&gt;
-#&gt; 2:
-#&gt; 3:
-#&gt; 4: static double parms [3];
-#&gt; 5: #define k_parent_sink parms[0]
-#&gt; 6: #define k_parent_m1 parms[1]
-#&gt; 7: #define k_m1_sink parms[2]
-#&gt; 8:
-#&gt; 9: void initpar(void (* odeparms)(int *, double *)) {
-#&gt; 10: int N = 3;
-#&gt; 11: odeparms(&amp;N, parms);
-#&gt; 12: }
-#&gt; 13:
-#&gt; 14:
-#&gt; 15: void func ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) {
-#&gt; 16:
-#&gt; 17: f[0] = - k_parent_sink * y[0] - k_parent_m1 * y[0];
-#&gt; 18: f[1] = + k_parent_m1 * y[0] - k_m1_sink * y[1];
-#&gt; 19: }</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='error'>Error in mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), verbose = TRUE): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'>
<span class='co'># If we have several parallel metabolites </span>
<span class='co'># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span>
-<span class='no'>m_synth_DFOP_par</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"DFOP"</span>, <span class='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)),
+<span class='no'>m_synth_DFOP_par</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"DFOP"</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)),
<span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>),
<span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>),
- <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-
+ <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='error'>Error in mkinmod(parent = mkinsub("DFOP", c("M1", "M2")), M1 = mkinsub("SFO"), M2 = mkinsub("SFO"), use_of_ff = "max", quiet = TRUE): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'>
<span class='no'>fit_DFOP_par_c</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_DFOP_par</span>,
<span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>12</span>]]$<span class='no'>data</span>,
- <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div></pre>
+ <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='error'>Error in mkinfit(m_synth_DFOP_par, synthetic_data_for_UBA_2014[[12]]$data, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div></pre>
</div>
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<h2>Contents</h2>
@@ -276,9 +255,7 @@ For the definition of model types and their parameters, the equations given
</ul>
<h2>Author</h2>
-
- Johannes Ranke
-
+ <p>Johannes Ranke</p>
</div>
</div>
@@ -288,9 +265,8 @@ For the definition of model types and their parameters, the equations given
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