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authorJohannes Ranke <jranke@uni-bremen.de>2018-06-06 01:24:15 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2018-06-06 01:24:15 +0200
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<title>Example evaluation of FOCUS Example Dataset D • mkin</title>
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- <a class="navbar-brand" href="../index.html">mkin</a>
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+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span>
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<h1>Example evaluation of FOCUS Example Dataset D</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-03-21</h4>
- </div>
+ <h4 class="date">2018-06-06</h4>
+
+
+ <div class="hidden name"><code>FOCUS_D.Rmd</code></div>
+
+ </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="dt">quietly =</span> <span class="ot">TRUE</span>)
<span class="kw">print</span>(FOCUS_<span class="dv">2006</span>_D)</code></pre></div>
@@ -153,10 +160,10 @@
<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"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(fit)</code></pre></div>
-<pre><code>## mkin version: 0.9.46.3
-## R version: 3.4.3
-## Date of fit: Sun Mar 11 22:11:56 2018
-## Date of summary: Sun Mar 11 22:11:57 2018
+<pre><code>## mkin version used for fitting: 0.9.47.1
+## R version used for fitting: 3.5.0
+## Date of fit: Wed Jun 6 01:21:49 2018
+## Date of summary: Wed Jun 6 01:21:50 2018
##
## Equations:
## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -164,7 +171,7 @@
##
## Model predictions using solution type deSolve
##
-## Fitted with method Port using 153 model solutions performed in 0.984 s
+## Fitted with method Port using 153 model solutions performed in 0.633 s
##
## Weighting: none
##
@@ -231,51 +238,46 @@
##
## Data:
## time variable observed predicted residual
-## 0 parent 99.46 9.960e+01 -1.385e-01
-## 0 parent 102.04 9.960e+01 2.442e+00
-## 1 parent 93.50 9.024e+01 3.262e+00
-## 1 parent 92.50 9.024e+01 2.262e+00
-## 3 parent 63.23 7.407e+01 -1.084e+01
-## 3 parent 68.99 7.407e+01 -5.083e+00
-## 7 parent 52.32 4.991e+01 2.408e+00
-## 7 parent 55.13 4.991e+01 5.218e+00
-## 14 parent 27.27 2.501e+01 2.257e+00
-## 14 parent 26.64 2.501e+01 1.627e+00
-## 21 parent 11.50 1.253e+01 -1.035e+00
-## 21 parent 11.64 1.253e+01 -8.946e-01
-## 35 parent 2.85 3.148e+00 -2.979e-01
-## 35 parent 2.91 3.148e+00 -2.379e-01
-## 50 parent 0.69 7.162e-01 -2.624e-02
-## 50 parent 0.63 7.162e-01 -8.624e-02
-## 75 parent 0.05 6.074e-02 -1.074e-02
-## 75 parent 0.06 6.074e-02 -7.382e-04
-## 100 parent NA 5.151e-03 NA
-## 100 parent NA 5.151e-03 NA
-## 120 parent NA 7.155e-04 NA
-## 120 parent NA 7.155e-04 NA
-## 0 m1 0.00 0.000e+00 0.000e+00
-## 0 m1 0.00 0.000e+00 0.000e+00
-## 1 m1 4.84 4.803e+00 3.704e-02
-## 1 m1 5.64 4.803e+00 8.370e-01
-## 3 m1 12.91 1.302e+01 -1.140e-01
-## 3 m1 12.96 1.302e+01 -6.400e-02
-## 7 m1 22.97 2.504e+01 -2.075e+00
-## 7 m1 24.47 2.504e+01 -5.748e-01
-## 14 m1 41.69 3.669e+01 5.000e+00
-## 14 m1 33.21 3.669e+01 -3.480e+00
-## 21 m1 44.37 4.165e+01 2.717e+00
-## 21 m1 46.44 4.165e+01 4.787e+00
-## 35 m1 41.22 4.331e+01 -2.093e+00
-## 35 m1 37.95 4.331e+01 -5.363e+00
-## 50 m1 41.19 4.122e+01 -2.831e-02
-## 50 m1 40.01 4.122e+01 -1.208e+00
-## 75 m1 40.09 3.645e+01 3.643e+00
-## 75 m1 33.85 3.645e+01 -2.597e+00
-## 100 m1 31.04 3.198e+01 -9.416e-01
-## 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>
-</div>
+## 0 parent 99.46 99.59848 -1.385e-01
+## 0 parent 102.04 99.59848 2.442e+00
+## 1 parent 93.50 90.23787 3.262e+00
+## 1 parent 92.50 90.23787 2.262e+00
+## 3 parent 63.23 74.07320 -1.084e+01
+## 3 parent 68.99 74.07320 -5.083e+00
+## 7 parent 52.32 49.91207 2.408e+00
+## 7 parent 55.13 49.91207 5.218e+00
+## 14 parent 27.27 25.01257 2.257e+00
+## 14 parent 26.64 25.01257 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
+## 35 parent 2.91 3.14787 -2.379e-01
+## 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 -7.382e-04
+## 0 m1 0.00 0.00000 0.000e+00
+## 0 m1 0.00 0.00000 0.000e+00
+## 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
+## 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 36.44704 3.643e+00
+## 75 m1 33.85 36.44704 -2.597e+00
+## 100 m1 31.04 31.98163 -9.416e-01
+## 100 m1 33.13 31.98163 1.148e+00
+## 120 m1 25.15 28.78984 -3.640e+00
+## 120 m1 33.31 28.78984 4.520e+00</code></pre>
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