From 5b1179f0daff9077e1370065f9b9f03a2d0e0450 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 15 Oct 2020 12:53:23 +0200
Subject: Update online docs for release version
---
docs/articles/FOCUS_D.html | 63 +++++++++++++++++++++++++++++-----------------
1 file changed, 40 insertions(+), 23 deletions(-)
(limited to 'docs/articles/FOCUS_D.html')
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index cdd85f43..dd5fe08e 100644
--- a/docs/articles/FOCUS_D.html
+++ 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">0.9.50.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.3</span>
</span>
</div>
@@ -68,6 +68,9 @@
<li>
<a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
</li>
+ <li>
+ <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+ </li>
</ul>
</li>
<li>
@@ -76,7 +79,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
- <a href="http://github.com/jranke/mkin/">
+ <a href="https://github.com/jranke/mkin/">
<span class="fab fa fab fa-github fa-lg"></span>
</a>
@@ -97,18 +100,19 @@
<h1 data-toc-skip>Example evaluation of FOCUS Example Dataset D</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2020-05-27</h4>
+ <h4 class="date">2020-10-15</h4>
- <small class="dont-index">Source: <a href="http://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>
+ <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>
</div>
<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"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">mkin</span>, <span class="kw">quietly</span> <span class="kw">=</span> <span class="fl">TRUE</span>)
-<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">FOCUS_2006_D</span>)</pre></body></html></div>
+<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>
<pre><code>## name time value
## 1 parent 0 99.46
## 2 parent 0 102.04
@@ -156,29 +160,37 @@
## 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>$diffs</code> of the <code>mkinmod</code> object. If a C compiler (gcc) is installed and functional, the differential equation model will be compiled from auto-generated C code.</p>
-<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">SFO_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>), <span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</pre></body></html></div>
+<div class="sourceCode" id="cb3"><pre class="downlit">
+<span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></pre></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
-<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">SFO_SFO</span>$<span class="no">diffs</span>)</pre></body></html></div>
+<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>
<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"><html><body><pre class="r"><span class="no">fit</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOCUS_2006_D</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div>
+<div class="sourceCode" id="cb7"><pre class="downlit">
+<span class="va">fit</span> <span class="op"><-</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>
<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="cb9"><html><body><pre class="r"><span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">fit</span>, <span class="kw">lpos</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>))</pre></body></html></div>
+<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>
<p><img src="FOCUS_D_files/figure-html/plot-1.png" width="768"></p>
<p>Confidence intervals for the parameter estimates are obtained using the <code>mkinparplot</code> function.</p>
-<div class="sourceCode" id="cb10"><html><body><pre class="r"><span class="fu"><a href="../reference/mkinparplot.html">mkinparplot</a></span>(<span class="no">fit</span>)</pre></body></html></div>
+<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>
<p><img src="FOCUS_D_files/figure-html/plot_2-1.png" width="768"></p>
<p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code> objects.</p>
-<div class="sourceCode" id="cb11"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">fit</span>)</pre></body></html></div>
-<pre><code>## mkin version used for fitting: 0.9.50.2
-## R version used for fitting: 4.0.0
-## Date of fit: Wed May 27 07:05:33 2020
-## Date of summary: Wed May 27 07:05:34 2020
+<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
+## 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
##
## Equations:
## d_parent/dt = - k_parent * parent
@@ -186,7 +198,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 421 model solutions performed in 0.166 s
+## Fitted using 421 model solutions performed in 0.172 s
##
## Error model: Constant variance
##
@@ -210,6 +222,11 @@
## value type
## m1_0 0 state
##
+##
+## Warning(s):
+## Observations with value of zero were removed from the data
+## Shapiro-Wilk test for standardized residuals: p = 0.0165
+##
## Results:
##
## AIC BIC logLik
@@ -225,11 +242,11 @@
##
## 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 -3.190e-07
+## 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 -1.406e-07
-## f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 -1.587e-10
-## sigma -3.190e-07 3.168e-07 -1.406e-07 -1.587e-10 1.000e+00
+## 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
##
## Backtransformed parameters:
## Confidence intervals for internally transformed parameters are asymmetric.
@@ -313,7 +330,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
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