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authorJohannes Ranke <jranke@uni-bremen.de>2016-10-26 23:18:20 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2016-10-26 23:18:20 +0200
commit8f38147e145c66ebd27f5d9fcc6f00172c25872f (patch)
tree35123308ef781f6ad4b83b6d421d5e0e35d2e574 /docs/articles/FOCUS_D.html
parentd106bebafe070cb803dd7205b1581b20eaf61cb5 (diff)
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<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html><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>Example evaluation of FOCUS Example Dataset D. mkin</title><!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
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<h1>Example evaluation of FOCUS Example Dataset D</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2016-10-06</h4>
+ <h4 class="date">2016-10-26</h4>
</div>
+<div class="contents">
<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 a 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"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(<span class="st">"mkin"</span>)
<span class="kw">print</span>(FOCUS_2006_D)</code></pre></div>
@@ -103,16 +105,16 @@
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">fit &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_2006_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</code></pre></div>
<p>A plot of the fit including a residual plot for both observed variables is obtained using the <code>plot</code> method for <code>mkinfit</code> objects.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plot</span>(fit, <span class="dt">show_residuals =</span> <span class="ot">TRUE</span>)</code></pre></div>
-<p><img src="/home/jranke/git/mkin/docs/articles/FOCUS_D_files/figure-html/unnamed-chunk-5-1.png" width="672"></p>
+<p><img src="FOCUS_D_files/figure-html/unnamed-chunk-5-1.png" width="672"></p>
<p>Confidence intervals for the parameter estimates are obtained using the <code>mkinparplot</code> function.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/mkinparplot.html">mkinparplot</a></span>(fit)</code></pre></div>
-<p><img src="/home/jranke/git/mkin/docs/articles/FOCUS_D_files/figure-html/unnamed-chunk-6-1.png" width="672"></p>
+<p><img src="FOCUS_D_files/figure-html/unnamed-chunk-6-1.png" width="672"></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"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(fit)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.1
-## Date of fit: Thu Oct 6 08:54:04 2016
-## Date of summary: Thu Oct 6 08:54:04 2016
+## Date of fit: Wed Oct 26 23:18:10 2016
+## Date of summary: Wed Oct 26 23:18:10 2016
##
## Equations:
## d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -120,7 +122,7 @@
##
## Model predictions using solution type deSolve
##
-## Fitted with method Port using 153 model solutions performed in 0.637 s
+## Fitted with method Port using 153 model solutions performed in 0.628 s
##
## Weighting: none
##
@@ -231,15 +233,23 @@
## 100 m1 33.13 3.198e+01 1.148e+00
## 120 m1 25.15 2.879e+01 -3.640e+00
## 120 m1 33.31 2.879e+01 4.520e+00</code></pre>
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