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authorJohannes Ranke <jranke@uni-bremen.de>2020-05-27 06:06:08 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-05-27 06:06:08 +0200
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+ <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>
+
+ <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>
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+
+<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>
+<pre><code>## name time value
+## 1 parent 0 99.46
+## 2 parent 0 102.04
+## 3 parent 1 93.50
+## 4 parent 1 92.50
+## 5 parent 3 63.23
+## 6 parent 3 68.99
+## 7 parent 7 52.32
+## 8 parent 7 55.13
+## 9 parent 14 27.27
+## 10 parent 14 26.64
+## 11 parent 21 11.50
+## 12 parent 21 11.64
+## 13 parent 35 2.85
+## 14 parent 35 2.91
+## 15 parent 50 0.69
+## 16 parent 50 0.63
+## 17 parent 75 0.05
+## 18 parent 75 0.06
+## 19 parent 100 NA
+## 20 parent 100 NA
+## 21 parent 120 NA
+## 22 parent 120 NA
+## 23 m1 0 0.00
+## 24 m1 0 0.00
+## 25 m1 1 4.84
+## 26 m1 1 5.64
+## 27 m1 3 12.91
+## 28 m1 3 12.96
+## 29 m1 7 22.97
+## 30 m1 7 24.47
+## 31 m1 14 41.69
+## 32 m1 14 33.21
+## 33 m1 21 44.37
+## 34 m1 21 46.44
+## 35 m1 35 41.22
+## 36 m1 35 37.95
+## 37 m1 50 41.19
+## 38 m1 50 40.01
+## 39 m1 75 40.09
+## 40 m1 75 33.85
+## 41 m1 100 31.04
+## 42 m1 100 33.13
+## 43 m1 120 25.15
+## 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>$diffs</code> of the <code>mkinmod</code> object. If a C compiler (gcc) is installed and functional, the differential equation model will be compiled from auto-generated C code.</p>
+<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">SFO_SFO</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>), <span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</pre></body></html></div>
+<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
+<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">SFO_SFO</span>$<span class="no">diffs</span>)</pre></body></html></div>
+<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">&lt;-</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>
+<pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with value
+## of zero were removed from the data</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>
+<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>
+<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: 0.9.50.3
+## R version used for fitting: 4.0.0
+## Date of fit: Wed May 27 06:02:21 2020
+## Date of summary: Wed May 27 06:02:21 2020
+##
+## Equations:
+## d_parent/dt = - k_parent * parent
+## d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
+##
+## Model predictions using solution type analytical
+##
+## Fitted using 421 model solutions performed in 0.177 s
+##
+## Error model: Constant variance
+##
+## Error model algorithm: OLS
+##
+## Starting values for parameters to be optimised:
+## value type
+## parent_0 100.7500 state
+## k_parent 0.1000 deparm
+## k_m1 0.1001 deparm
+## 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
+##
+## Fixed parameter values:
+## value type
+## m1_0 0 state
+##
+## Results:
+##
+## AIC BIC logLik
+## 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
+##
+## 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
+## 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
+##
+## Backtransformed parameters:
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
+## Estimate t value Pr(&gt;t) Lower Upper
+## parent_0 99.600000 63.430 2.298e-36 96.400000 1.028e+02
+## k_parent 0.098700 24.470 4.955e-23 0.090820 1.073e-01
+## k_m1 0.005261 7.510 6.165e-09 0.004012 6.898e-03
+## f_parent_to_m1 0.514500 23.070 3.104e-22 0.469100 5.596e-01
+## sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00
+##
+## FOCUS Chi2 error levels in percent:
+## err.min n.optim df
+## All data 6.398 4 15
+## parent 6.459 2 7
+## m1 4.690 2 8
+##
+## Resulting formation fractions:
+## ff
+## parent_m1 0.5145
+## parent_sink 0.4855
+##
+## Estimated disappearance times:
+## DT50 DT90
+## parent 7.023 23.33
+## m1 131.761 437.70
+##
+## Data:
+## time variable observed predicted residual
+## 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 74.07319 -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
+## 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 -7.381e-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
+## 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
+## 120 m1 25.15 28.78984 -3.640e+00
+## 120 m1 33.31 28.78984 4.520e+00</code></pre>
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