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diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
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+++ b/docs/articles/FOCUS_D.html
@@ -31,7 +31,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span>
</span>
</div>
@@ -80,7 +80,7 @@
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -100,7 +100,7 @@
<h1 data-toc-skip>Example evaluation of FOCUS Example Dataset D</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2020-10-15</h4>
+ <h4 class="date">2021-02-03</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/FOCUS_D.rmd"><code>vignettes/FOCUS_D.rmd</code></a></small>
<div class="hidden name"><code>FOCUS_D.rmd</code></div>
@@ -110,9 +110,9 @@
<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">
-<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></pre></div>
+<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
@@ -160,37 +160,35 @@
## 44 m1 120 33.31</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>$diffs</code> of the <code>mkinmod</code> object. If a C compiler (gcc) is installed and functional, the differential equation model will be compiled from auto-generated C code.</p>
-<div class="sourceCode" id="cb3"><pre class="downlit">
-<span class="va">SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></pre></div>
-<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
-<div class="sourceCode" id="cb5"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">SFO_SFO</span><span class="op">$</span><span class="va">diffs</span><span class="op">)</span></pre></div>
+<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>
+<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>
<p>We do the fitting without progress report (<code>quiet = TRUE</code>).</p>
-<div class="sourceCode" id="cb7"><pre class="downlit">
-<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></pre></div>
+<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>
-<pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Shapiro-Wilk test for
-## standardized residuals: p = 0.0165</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="cb10"><pre class="downlit">
-<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></pre></div>
+<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>
<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="cb11"><pre class="downlit">
-<span class="fu"><a href="../reference/mkinparplot.html">mkinparplot</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></pre></div>
+<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>
<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="cb12"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></pre></div>
-<pre><code>## mkin version used for fitting: 0.9.50.3
+<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></code></pre></div>
+<pre><code>## mkin version used for fitting: 1.0.0
## R version used for fitting: 4.0.3
-## Date of fit: Thu Oct 15 12:42:00 2020
-## Date of summary: Thu Oct 15 12:42:00 2020
+## Date of fit: Wed Feb 3 17:32:13 2021
+## Date of summary: Wed Feb 3 17:32:14 2021
##
## Equations:
## d_parent/dt = - k_parent * parent
@@ -198,7 +196,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 421 model solutions performed in 0.172 s
+## Fitted using 401 model solutions performed in 0.161 s
##
## Error model: Constant variance
##
@@ -212,11 +210,11 @@
## 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_ilr_1 0.000000 -Inf Inf
+## 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
@@ -225,7 +223,6 @@
##
## Warning(s):
## Observations with value of zero were removed from the data
-## Shapiro-Wilk test for standardized residuals: p = 0.0165
##
## Results:
##
@@ -233,20 +230,20 @@
## 204.4486 212.6365 -97.22429
##
## Optimised, transformed parameters with symmetric confidence intervals:
-## Estimate Std. Error Lower Upper
-## parent_0 99.60000 1.57000 96.40000 102.8000
-## log_k_parent -2.31600 0.04087 -2.39900 -2.2330
-## log_k_m1 -5.24800 0.13320 -5.51800 -4.9770
-## f_parent_ilr_1 0.04096 0.06312 -0.08746 0.1694
-## sigma 3.12600 0.35850 2.39600 3.8550
+## 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_ilr_1 sigma
-## parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -3.214e-07
-## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 3.168e-07
-## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 -1.410e-07
-## f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 5.093e-10
-## sigma -3.214e-07 3.168e-07 -1.410e-07 5.093e-10 1.000e+00
+## parent_0 log_k_parent log_k_m1 f_parent_qlogis sigma
+## parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -1.171e-06
+## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 -8.481e-07
+## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 8.209e-07
+## f_parent_qlogis -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 1.305e-06
+## sigma -1.171e-06 -8.481e-07 8.209e-07 1.305e-06 1.000e+00
##
## Backtransformed parameters:
## Confidence intervals for internally transformed parameters are asymmetric.
@@ -283,10 +280,10 @@
## 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 49.91206 2.408e+00
-## 7 parent 55.13 49.91206 5.218e+00
-## 14 parent 27.27 25.01257 2.257e+00
-## 14 parent 26.64 25.01257 1.627e+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
@@ -294,25 +291,25 @@
## 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 -7.381e-04
+## 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 36.69002 5.000e+00
-## 14 m1 33.21 36.69002 -3.480e+00
+## 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 43.31312 -2.093e+00
-## 35 m1 37.95 43.31312 -5.363e+00
-## 50 m1 41.19 41.21831 -2.831e-02
-## 50 m1 40.01 41.21831 -1.208e+00
-## 75 m1 40.09 36.44703 3.643e+00
-## 75 m1 33.85 36.44703 -2.597e+00
-## 100 m1 31.04 31.98163 -9.416e-01
-## 100 m1 33.13 31.98163 1.148e+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>
</div>

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