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      <h1>Example evaluation of FOCUS Example Dataset D</h1>
                        <h4 class="author">Johannes Ranke</h4>
            
            <h4 class="date">2019-04-10</h4>
      
      
      <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"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(mkin, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb1-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(FOCUS_<span class="dv">2006</span>_D)</a></code></pre></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>$diffs</code> of the <code>mkinmod</code> object. If a C compiler (gcc) is installed and functional, the differential equation model will be compiled from auto-generated C code.</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>), <span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(SFO_SFO<span class="op">$</span>diffs)</a></code></pre></div>
<pre><code>##                                                       parent 
## "d_parent = - k_parent_sink * parent - k_parent_m1 * parent" 
##                                                           m1 
##             "d_m1 = + k_parent_m1 * parent - k_m1_sink * m1"</code></pre>
<p>We do the fitting without progress report (<code>quiet = TRUE</code>).</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">fit &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></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>
<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"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(fit, <span class="dt">lpos =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>))</a></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="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1"><span class="kw"><a href="../reference/mkinparplot.html">mkinparplot</a></span>(fit)</a></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="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(fit)</a></code></pre></div>
<pre><code>## mkin version used for fitting:    0.9.49.4 
## R version used for fitting:       3.5.3 
## Date of fit:     Wed Apr 10 10:11:31 2019 
## Date of summary: Wed Apr 10 10:11:31 2019 
## 
## Equations:
## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
## d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1
## 
## Model predictions using solution type deSolve 
## 
## Fitted with method using 396 model solutions performed in 1.048 s
## 
## Error model:
## NULL
## 
## Starting values for parameters to be optimised:
##                    value   type
## parent_0      100.750000  state
## k_parent_sink   0.100000 deparm
## k_parent_m1     0.100100 deparm
## k_m1_sink       0.100200 deparm
## sigma           3.125504  error
## 
## Starting values for the transformed parameters actually optimised:
##                        value lower upper
## parent_0          100.750000  -Inf   Inf
## log_k_parent_sink  -2.302585  -Inf   Inf
## log_k_parent_m1    -2.301586  -Inf   Inf
## log_k_m1_sink      -2.300587  -Inf   Inf
## sigma               3.125504     0   Inf
## 
## Fixed parameter values:
##      value  type
## m1_0     0 state
## 
## Optimised, transformed parameters with symmetric confidence intervals:
##                   Estimate Std. Error  Lower   Upper
## parent_0            99.600    1.57000 96.400 102.800
## log_k_parent_sink   -3.038    0.07626 -3.193  -2.883
## log_k_parent_m1     -2.980    0.04033 -3.062  -2.898
## log_k_m1_sink       -5.248    0.13320 -5.518  -4.977
## sigma                3.126    0.35850  2.396   3.855
## 
## Parameter correlation:
##                     parent_0 log_k_parent_sink log_k_parent_m1
## parent_0           1.000e+00         6.067e-01      -6.372e-02
## log_k_parent_sink  6.067e-01         1.000e+00      -8.550e-02
## log_k_parent_m1   -6.372e-02        -8.550e-02       1.000e+00
## log_k_m1_sink     -1.688e-01        -6.252e-01       4.731e-01
## sigma             -3.368e-07         3.365e-08       8.420e-07
##                   log_k_m1_sink      sigma
## parent_0             -1.688e-01 -3.368e-07
## log_k_parent_sink    -6.252e-01  3.365e-08
## log_k_parent_m1       4.731e-01  8.420e-07
## log_k_m1_sink         1.000e+00  1.958e-08
## sigma                 1.958e-08  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_sink  0.047920  13.110 6.126e-15  0.041030 5.596e-02
## k_parent_m1    0.050780  24.800 3.269e-23  0.046780 5.512e-02
## k_m1_sink      0.005261   7.510 6.165e-09  0.004012 6.898e-03
## sigma          3.126000   8.718 2.235e-10  2.396000 3.855e+00
## 
## Chi2 error levels in percent:
##          err.min n.optim df
## All data   6.398       4 15
## parent     6.827       3  6
## m1         4.490       1  9
## 
## Resulting formation fractions:
##                 ff
## parent_sink 0.4855
## parent_m1   0.5145
## m1_sink     1.0000
## 
## 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  36.69003  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  41.21832 -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  31.98163 -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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