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| author | Johannes Ranke <jranke@uni-bremen.de> | 2016-10-26 23:18:20 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2016-10-26 23:18:20 +0200 |
| commit | 8f38147e145c66ebd27f5d9fcc6f00172c25872f (patch) | |
| tree | 35123308ef781f6ad4b83b6d421d5e0e35d2e574 /docs/articles/FOCUS_L.html | |
| parent | d106bebafe070cb803dd7205b1581b20eaf61cb5 (diff) | |
Static documentation rebuilt by pkgdown::build_site()
Diffstat (limited to 'docs/articles/FOCUS_L.html')
| -rw-r--r-- | docs/articles/FOCUS_L.html | 100 |
1 files changed, 55 insertions, 45 deletions
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 5d586799..cb3096e0 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -1,10 +1,10 @@ <!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 Laboratory Data L1 to L3. 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" 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="../pkgdown.js"></script><!-- mathjax --><script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<!-- 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 Laboratory Data L1 to L3 • 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"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -30,6 +30,7 @@ </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header><div class="row"> <div class="col-md-9"> @@ -37,13 +38,14 @@ <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-10-06</h4> + <h4 class="date">2016-10-26</h4> </div> +<div class="contents"> <div id="laboratory-data-l1" class="section level1"> -<h1>Laboratory Data L1</h1> +<h1 class="hasAnchor"><html><body><a href="#laboratory-data-l1" class="anchor"> </a></body></html>Laboratory Data L1</h1> <p>The following code defines example dataset L1 from the FOCUS kinetics report, p. 284:</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>) FOCUS_2006_L1 =<span class="st"> </span><span class="kw">data.frame</span>( @@ -58,15 +60,15 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re <span class="kw">summary</span>(m.L1.SFO)</code></pre></div> <pre><code>## mkin version: 0.9.44.9000 ## R version: 3.3.1 -## Date of fit: Thu Oct 6 08:54:05 2016 -## Date of summary: Thu Oct 6 08:54:05 2016 +## Date of fit: Wed Oct 26 23:18:11 2016 +## Date of summary: Wed Oct 26 23:18:11 2016 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.087 s +## Fitted with method Port using 37 model solutions performed in 0.089 s ## ## Weighting: none ## @@ -138,21 +140,21 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re ## 30 parent 4.0 5.251 -1.2513</code></pre> <p>A plot of the fit is obtained with the plot function for mkinfit objects.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plot</span>(m.L1.SFO, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L1 - SFO"</span>)</code></pre></div> -<p><img src="/home/jranke/git/mkin/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-4-1.png" width="576"></p> +<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-4-1.png" width="576"></p> <p>The residual plot can be easily obtained by</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/mkinresplot.html">mkinresplot</a></span>(m.L1.SFO, <span class="dt">ylab =</span> <span class="st">"Observed"</span>, <span class="dt">xlab =</span> <span class="st">"Time"</span>)</code></pre></div> -<p><img src="/home/jranke/git/mkin/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-5-1.png" width="576"></p> +<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-5-1.png" width="576"></p> <p>For comparison, the FOMC model is fitted as well, and the <span class="math inline">\(\chi^2\)</span> error level is checked.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.L1.FOMC <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"FOMC"</span>, FOCUS_2006_L1_mkin, <span class="dt">quiet=</span><span class="ot">TRUE</span>)</code></pre></div> <pre><code>## Warning in mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet = TRUE): Optimisation by method Port did not converge. ## Convergence code is 1</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plot</span>(m.L1.FOMC, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L1 - FOMC"</span>)</code></pre></div> -<p><img src="/home/jranke/git/mkin/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png" width="576"></p> +<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-6-1.png" width="576"></p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> <pre><code>## mkin version: 0.9.44.9000 ## R version: 3.3.1 -## Date of fit: Thu Oct 6 08:54:06 2016 -## Date of summary: Thu Oct 6 08:54:06 2016 +## Date of fit: Wed Oct 26 23:18:12 2016 +## Date of summary: Wed Oct 26 23:18:12 2016 ## ## ## Warning: Optimisation by method Port did not converge. @@ -164,7 +166,7 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 188 model solutions performed in 0.437 s +## Fitted with method Port using 188 model solutions performed in 0.434 s ## ## Weighting: none ## @@ -219,7 +221,7 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re <p>The <span class="math inline">\(\chi^2\)</span> error levels reported in Appendix 3 and Appendix 7 to the FOCUS kinetics report are rounded to integer percentages and partly deviate by one percentage point from the results calculated by mkin. The reason for this is not known. However, mkin gives the same <span class="math inline">\(\chi^2\)</span> error levels as the kinfit package and the calculation routines of the kinfit package have been extensively compared to the results obtained by the KinGUI software, as documented in the kinfit package vignette. KinGUI was the first widely used standard package in this field. Also, the calculation of <span class="math inline">\(\chi^2\)</span> error levels was compared with KinGUII, CAKE and DegKin manager in a project sponsored by the German Umweltbundesamt <span class="citation">(Ranke, n.d.)</span>.</p> </div> <div id="laboratory-data-l2" class="section level1"> -<h1>Laboratory Data L2</h1> +<h1 class="hasAnchor"><html><body><a href="#laboratory-data-l2" class="anchor"> </a></body></html>Laboratory Data L2</h1> <p>The following code defines example dataset L2 from the FOCUS kinetics report, p. 287:</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">FOCUS_2006_L2 =<span class="st"> </span><span class="kw">data.frame</span>( <span class="dt">t =</span> <span class="kw">rep</span>(<span class="kw">c</span>(<span class="dv">0</span>, <span class="dv">1</span>, <span class="dv">3</span>, <span class="dv">7</span>, <span class="dv">14</span>, <span class="dv">28</span>), <span class="dt">each =</span> <span class="dv">2</span>), @@ -228,35 +230,35 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re <span class="fl">2.6</span>, <span class="fl">1.2</span>, <span class="fl">0.3</span>, <span class="fl">0.6</span>)) FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_2006_L2)</code></pre></div> <div id="sfo-fit-for-l2" class="section level2"> -<h2>SFO fit for L2</h2> +<h2 class="hasAnchor"><html><body><a href="#sfo-fit-for-l2" class="anchor"> </a></body></html>SFO fit for L2</h2> <p>Again, the SFO model is fitted and the result is plotted. The residual plot can be obtained simply by adding the argument <code>show_residuals</code> to the plot command.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.L2.SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"SFO"</span>, FOCUS_2006_L2_mkin, <span class="dt">quiet=</span><span class="ot">TRUE</span>) <span class="kw">plot</span>(m.L2.SFO, <span class="dt">show_residuals =</span> <span class="ot">TRUE</span>, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L2 - SFO"</span>)</code></pre></div> -<p><img src="/home/jranke/git/mkin/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png" width="672"></p> +<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-8-1.png" width="672"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 14% suggests that the model does not fit very well. This is also obvious from the plots of the fit, in which we have included the residual plot.</p> <p>In the FOCUS kinetics report, it is stated that there is no apparent systematic error observed from the residual plot up to the measured DT90 (approximately at day 5), and there is an underestimation beyond that point.</p> <p>We may add that it is difficult to judge the random nature of the residuals just from the three samplings at days 0, 1 and 3. Also, it is not clear <em>a priori</em> why a consistent underestimation after the approximate DT90 should be irrelevant. However, this can be rationalised by the fact that the FOCUS fate models generally only implement SFO kinetics.</p> </div> <div id="fomc-fit-for-l2" class="section level2"> -<h2>FOMC fit for L2</h2> +<h2 class="hasAnchor"><html><body><a href="#fomc-fit-for-l2" class="anchor"> </a></body></html>FOMC fit for L2</h2> <p>For comparison, the FOMC model is fitted as well, and the <span class="math inline">\(\chi^2\)</span> error level is checked.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.L2.FOMC <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"FOMC"</span>, FOCUS_2006_L2_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw">plot</span>(m.L2.FOMC, <span class="dt">show_residuals =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L2 - FOMC"</span>)</code></pre></div> -<p><img src="/home/jranke/git/mkin/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p> +<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> <pre><code>## mkin version: 0.9.44.9000 ## R version: 3.3.1 -## Date of fit: Thu Oct 6 08:54:07 2016 -## Date of summary: Thu Oct 6 08:54:07 2016 +## Date of fit: Wed Oct 26 23:18:12 2016 +## Date of summary: Wed Oct 26 23:18:12 2016 ## ## Equations: ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 81 model solutions performed in 0.19 s +## Fitted with method Port using 81 model solutions performed in 0.191 s ## ## Weighting: none ## @@ -309,17 +311,17 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re <p>The error level at which the <span class="math inline">\(\chi^2\)</span> test passes is much lower in this case. Therefore, the FOMC model provides a better description of the data, as less experimental error has to be assumed in order to explain the data.</p> </div> <div id="dfop-fit-for-l2" class="section level2"> -<h2>DFOP fit for L2</h2> +<h2 class="hasAnchor"><html><body><a href="#dfop-fit-for-l2" class="anchor"> </a></body></html>DFOP fit for L2</h2> <p>Fitting the four parameter DFOP model further reduces the <span class="math inline">\(\chi^2\)</span> error level.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.L2.DFOP <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"DFOP"</span>, FOCUS_2006_L2_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw">plot</span>(m.L2.DFOP, <span class="dt">show_residuals =</span> <span class="ot">TRUE</span>, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L2 - DFOP"</span>)</code></pre></div> -<p><img src="/home/jranke/git/mkin/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p> +<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> <pre><code>## mkin version: 0.9.44.9000 ## R version: 3.3.1 -## Date of fit: Thu Oct 6 08:54:08 2016 -## Date of summary: Thu Oct 6 08:54:08 2016 +## Date of fit: Wed Oct 26 23:18:13 2016 +## Date of summary: Wed Oct 26 23:18:14 2016 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -328,7 +330,7 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.804 s +## Fitted with method Port using 336 model solutions performed in 0.803 s ## ## Weighting: none ## @@ -384,31 +386,31 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re </div> </div> <div id="laboratory-data-l3" class="section level1"> -<h1>Laboratory Data L3</h1> +<h1 class="hasAnchor"><html><body><a href="#laboratory-data-l3" class="anchor"> </a></body></html>Laboratory Data L3</h1> <p>The following code defines example dataset L3 from the FOCUS kinetics report, p. 290.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">FOCUS_2006_L3 =<span class="st"> </span><span class="kw">data.frame</span>( <span class="dt">t =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="dv">3</span>, <span class="dv">7</span>, <span class="dv">14</span>, <span class="dv">30</span>, <span class="dv">60</span>, <span class="dv">91</span>, <span class="dv">120</span>), <span class="dt">parent =</span> <span class="kw">c</span>(<span class="fl">97.8</span>, <span class="dv">60</span>, <span class="dv">51</span>, <span class="dv">43</span>, <span class="dv">35</span>, <span class="dv">22</span>, <span class="dv">15</span>, <span class="dv">12</span>)) FOCUS_2006_L3_mkin <-<span class="st"> </span><span class="kw"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_2006_L3)</code></pre></div> <div id="use-mmkin-to-fit-multiple-models" class="section level2"> -<h2>Use mmkin to fit multiple models</h2> +<h2 class="hasAnchor"><html><body><a href="#use-mmkin-to-fit-multiple-models" class="anchor"> </a></body></html>Use mmkin to fit multiple models</h2> <p>As of mkin version 0.9-39 (June 2015), we can fit several models to one or more datasets in one call to the function <code>mmkin</code>. The datasets have to be passed in a list, in this case a named list holding only the L3 dataset prepared above.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Only use one core here, not to offend the CRAN checks</span> mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin.html">mmkin</a></span>(<span class="kw">c</span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>), <span class="dt">cores =</span> <span class="dv">1</span>, <span class="kw">list</span>(<span class="st">"FOCUS L3"</span> =<span class="st"> </span>FOCUS_2006_L3_mkin), <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw">plot</span>(mm.L3)</code></pre></div> -<p><img src="/home/jranke/git/mkin/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png" width="672"></p> +<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-12-1.png" width="672"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 21% as well as the plot suggest that the SFO model does not fit very well. The FOMC model performs better, with an error level at which the <span class="math inline">\(\chi^2\)</span> test passes of 7%. Fitting the four parameter DFOP model further reduces the <span class="math inline">\(\chi^2\)</span> error level considerably.</p> </div> <div id="accessing-elements-of-mmkin-objects" class="section level2"> -<h2>Accessing elements of mmkin objects</h2> +<h2 class="hasAnchor"><html><body><a href="#accessing-elements-of-mmkin-objects" class="anchor"> </a></body></html>Accessing elements of mmkin objects</h2> <p>The objects returned by mmkin are arranged like a matrix, with models as a row index and datasets as a column index.</p> <p>We can extract the summary and plot for <em>e.g.</em> the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</code></pre></div> <pre><code>## mkin version: 0.9.44.9000 ## R version: 3.3.1 -## Date of fit: Thu Oct 6 08:54:09 2016 -## Date of summary: Thu Oct 6 08:54:09 2016 +## Date of fit: Wed Oct 26 23:18:15 2016 +## Date of summary: Wed Oct 26 23:18:15 2016 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -417,7 +419,7 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 137 model solutions performed in 0.319 s +## Fitted with method Port using 137 model solutions performed in 0.323 s ## ## Weighting: none ## @@ -484,13 +486,13 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin ## 91 parent 15.0 15.18 -0.18181 ## 120 parent 12.0 10.19 1.81395</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plot</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]], <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>)</code></pre></div> -<p><img src="/home/jranke/git/mkin/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png" width="672"></p> +<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-13-1.png" width="672"></p> <p>Here, a look to the model plot, the confidence intervals of the parameters and the correlation matrix suggest that the parameter estimates are reliable, and the DFOP model can be used as the best-fit model based on the <span class="math inline">\(\chi^2\)</span> error level criterion for laboratory data L3.</p> <p>This is also an example where the standard t-test for the parameter <code>g_ilr</code> is misleading, as it tests for a significant difference from zero. In this case, zero appears to be the correct value for this parameter, and the confidence interval for the backtransformed parameter <code>g</code> is quite narrow.</p> </div> </div> <div id="laboratory-data-l4" class="section level1"> -<h1>Laboratory Data L4</h1> +<h1 class="hasAnchor"><html><body><a href="#laboratory-data-l4" class="anchor"> </a></body></html>Laboratory Data L4</h1> <p>The following code defines example dataset L4 from the FOCUS kinetics report, p. 293:</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">FOCUS_2006_L4 =<span class="st"> </span><span class="kw">data.frame</span>( <span class="dt">t =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="dv">3</span>, <span class="dv">7</span>, <span class="dv">14</span>, <span class="dv">30</span>, <span class="dv">60</span>, <span class="dv">91</span>, <span class="dv">120</span>), @@ -502,20 +504,20 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <span class="kw">list</span>(<span class="st">"FOCUS L4"</span> =<span class="st"> </span>FOCUS_2006_L4_mkin), <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw">plot</span>(mm.L4)</code></pre></div> -<p><img src="/home/jranke/git/mkin/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png" width="672"></p> +<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-15-1.png" width="672"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the <span class="math inline">\(\chi^2\)</span> test passes is slightly lower for the FOMC model. However, the difference appears negligible.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> <pre><code>## mkin version: 0.9.44.9000 ## R version: 3.3.1 -## Date of fit: Thu Oct 6 08:54:10 2016 -## Date of summary: Thu Oct 6 08:54:10 2016 +## Date of fit: Wed Oct 26 23:18:15 2016 +## Date of summary: Wed Oct 26 23:18:16 2016 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.158 s +## Fitted with method Port using 46 model solutions performed in 0.108 s ## ## Weighting: none ## @@ -567,8 +569,8 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> <pre><code>## mkin version: 0.9.44.9000 ## R version: 3.3.1 -## Date of fit: Thu Oct 6 08:54:10 2016 -## Date of summary: Thu Oct 6 08:54:10 2016 +## Date of fit: Wed Oct 26 23:18:16 2016 +## Date of summary: Wed Oct 26 23:18:16 2016 ## ## Equations: ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -627,16 +629,17 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin ## parent 108.9 1644 494.9</code></pre> </div> <div id="references" class="section level1 unnumbered"> -<h1>References</h1> +<h1 class="hasAnchor"><html><body><a href="#references" class="anchor"> </a></body></html>References</h1> <div id="refs" class="references"> <div id="ref-ranke2014"> <p>Ranke, Johannes. n.d. “Prüfung und Validierung von Modellierungssoftware als Alternative zu ModelMaker 4.0.” Umweltbundesamt Projektnummer 27452.</p> </div> </div> </div> +</div> </div> - <div class="col-md-3 hidden-xs"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div id="tocnav"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"><li><a href="#laboratory-data-l1">Laboratory Data L1</a></li> @@ -655,7 +658,14 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin </div> - <footer><p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. 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