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diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html new file mode 100644 index 00000000..df259e21 --- /dev/null +++ b/docs/articles/FOCUS_D.html @@ -0,0 +1,255 @@ +<!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/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" 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="../jquery.sticky-kit.min.js"></script><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]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--></head><body> + <div class="container template-vignette"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header><div class="row"> + <div class="col-md-9"> + <div class="page-header toc-ignore"> + <h1>Example evaluation of FOCUS Example Dataset D</h1> + <h4 class="author">Johannes Ranke</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> +<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>$diffs</code> of the <code>mkinmod</code> object. If a C compiler (gcc) is installed and functional, the differential equation model will be compiled from auto-generated C code.</p> +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>), <span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</code></pre></div> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">print</span>(SFO_SFO$diffs)</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"><pre class="sourceCode r"><code class="sourceCode r">fit <-<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="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="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: 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 +## d_m1 = + k_parent_m1 * parent - k_m1_sink * m1 +## +## Model predictions using solution type deSolve +## +## Fitted with method Port using 153 model solutions performed in 0.628 s +## +## Weighting: none +## +## Starting values for parameters to be optimised: +## value type +## parent_0 100.7500 state +## k_parent_sink 0.1000 deparm +## k_parent_m1 0.1001 deparm +## k_m1_sink 0.1002 deparm +## +## 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 +## +## 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 1.61400 96.330 102.900 +## log_k_parent_sink -3.038 0.07826 -3.197 -2.879 +## log_k_parent_m1 -2.980 0.04124 -3.064 -2.897 +## log_k_m1_sink -5.248 0.13610 -5.523 -4.972 +## +## Parameter correlation: +## parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +## parent_0 1.00000 0.6075 -0.06625 -0.1701 +## log_k_parent_sink 0.60752 1.0000 -0.08740 -0.6253 +## log_k_parent_m1 -0.06625 -0.0874 1.00000 0.4716 +## log_k_m1_sink -0.17006 -0.6253 0.47163 1.0000 +## +## Residual standard error: 3.211 on 36 degrees of freedom +## +## 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(>t) Lower Upper +## parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02 +## k_parent_sink 0.047920 12.780 3.050e-15 0.040890 5.616e-02 +## k_parent_m1 0.050780 24.250 3.407e-24 0.046700 5.521e-02 +## k_m1_sink 0.005261 7.349 5.758e-09 0.003992 6.933e-03 +## +## 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 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> + </div> + + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + </div> + +</div> + + + <footer><div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer></div> + + </body></html> |