From a77a10ea6c607346778ba0700b3b66ac393101a2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke <jranke@uni-bremen.de> Date: Wed, 27 May 2020 06:06:08 +0200 Subject: Create up to date pkgdown docs in development mode --- docs/dev/articles/FOCUS_D.html | 330 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 330 insertions(+) create mode 100644 docs/dev/articles/FOCUS_D.html (limited to 'docs/dev/articles/FOCUS_D.html') diff --git a/docs/dev/articles/FOCUS_D.html b/docs/dev/articles/FOCUS_D.html new file mode 100644 index 00000000..0b3ae03a --- /dev/null +++ b/docs/dev/articles/FOCUS_D.html @@ -0,0 +1,330 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"> +<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> 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class="col-md-9 contents"> + <div class="page-header toc-ignore"> + <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> + + </div> + + + +<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>$diffs</code> of the <code>mkinmod</code> object. If a C compiler (gcc) is installed and functional, the differential equation model will be compiled from auto-generated C code.</p> +<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">SFO_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>), <span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</pre></body></html></div> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> +<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">SFO_SFO</span>$<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"><-</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(>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> + </div> + + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + + </div> + +</div> + + + + <footer><div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> +</div> + + </footer> +</div> + + + + + </body> +</html> -- cgit v1.2.1