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diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index cb3096e0..55caa22e 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -16,13 +16,16 @@ </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin"> + <a href="http://github.com/jranke/mkin"> <span class="fa fa-github fa-lg"></span> </a> @@ -38,7 +41,7 @@ <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-10-26</h4> + <h4 class="date">2016-11-03</h4> </div> @@ -59,16 +62,16 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.L1.SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"SFO"</span>, FOCUS_2006_L1_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <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: Wed Oct 26 23:18:11 2016 -## Date of summary: Wed Oct 26 23:18:11 2016 +## R version: 3.3.2 +## Date of fit: Thu Nov 3 17:47:48 2016 +## Date of summary: Thu Nov 3 17:47:48 2016 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.089 s +## Fitted with method Port using 37 model solutions performed in 0.093 s ## ## Weighting: none ## @@ -152,9 +155,9 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re <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: Wed Oct 26 23:18:12 2016 -## Date of summary: Wed Oct 26 23:18:12 2016 +## R version: 3.3.2 +## Date of fit: Thu Nov 3 17:47:49 2016 +## Date of summary: Thu Nov 3 17:47:49 2016 ## ## ## Warning: Optimisation by method Port did not converge. @@ -166,7 +169,7 @@ 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 0.434 s +## Fitted with method Port using 188 model solutions performed in 0.447 s ## ## Weighting: none ## @@ -249,16 +252,16 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re <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: Wed Oct 26 23:18:12 2016 -## Date of summary: Wed Oct 26 23:18:12 2016 +## R version: 3.3.2 +## Date of fit: Thu Nov 3 17:47:49 2016 +## Date of summary: Thu Nov 3 17:47:49 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 0.191 s +## Fitted with method Port using 81 model solutions performed in 0.189 s ## ## Weighting: none ## @@ -319,9 +322,9 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re <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: Wed Oct 26 23:18:13 2016 -## Date of summary: Wed Oct 26 23:18:14 2016 +## R version: 3.3.2 +## Date of fit: Thu Nov 3 17:47:50 2016 +## Date of summary: Thu Nov 3 17:47:50 2016 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -330,7 +333,7 @@ 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 0.803 s +## Fitted with method Port using 336 model solutions performed in 0.836 s ## ## Weighting: none ## @@ -392,8 +395,8 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re <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 class="hasAnchor"><html><body><a href="#use-mmkin-to-fit-multiple-models" class="anchor"> </a></body></html>Use mmkin to fit multiple models</h2> +<div id="fit-multiple-models" class="section level2"> +<h2 class="hasAnchor"><html><body><a href="#fit-multiple-models" class="anchor"> </a></body></html>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>, @@ -402,15 +405,15 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <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 class="hasAnchor"><html><body><a href="#accessing-elements-of-mmkin-objects" class="anchor"> </a></body></html>Accessing elements of mmkin objects</h2> +<div id="accessing-mmkin-objects" class="section level2"> +<h2 class="hasAnchor"><html><body><a href="#accessing-mmkin-objects" class="anchor"> </a></body></html>Accessing 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: Wed Oct 26 23:18:15 2016 -## Date of summary: Wed Oct 26 23:18:15 2016 +## R version: 3.3.2 +## Date of fit: Thu Nov 3 17:47:51 2016 +## Date of summary: Thu Nov 3 17:47:52 2016 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -419,7 +422,7 @@ 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 0.323 s +## Fitted with method Port using 137 model solutions performed in 0.328 s ## ## Weighting: none ## @@ -508,16 +511,16 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <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: Wed Oct 26 23:18:15 2016 -## Date of summary: Wed Oct 26 23:18:16 2016 +## R version: 3.3.2 +## Date of fit: Thu Nov 3 17:47:52 2016 +## Date of summary: Thu Nov 3 17:47:52 2016 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.108 s +## Fitted with method Port using 46 model solutions performed in 0.107 s ## ## Weighting: none ## @@ -568,16 +571,16 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin ## parent 106 352</code></pre> <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: Wed Oct 26 23:18:16 2016 -## Date of summary: Wed Oct 26 23:18:16 2016 +## R version: 3.3.2 +## Date of fit: Thu Nov 3 17:47:52 2016 +## Date of summary: Thu Nov 3 17:47:52 2016 ## ## Equations: ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 66 model solutions performed in 0.151 s +## Fitted with method Port using 66 model solutions performed in 0.148 s ## ## Weighting: none ## @@ -647,8 +650,8 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <li><a href="#fomc-fit-for-l2">FOMC fit for L2</a></li> <li><a href="#dfop-fit-for-l2">DFOP fit for L2</a></li> </ul></li> - <li><a href="#laboratory-data-l3">Laboratory Data L3</a><ul class="nav nav-pills nav-stacked"><li><a href="#use-mmkin-to-fit-multiple-models">Use mmkin to fit multiple models</a></li> - <li><a href="#accessing-elements-of-mmkin-objects">Accessing elements of mmkin objects</a></li> + <li><a href="#laboratory-data-l3">Laboratory Data L3</a><ul class="nav nav-pills nav-stacked"><li><a href="#fit-multiple-models">Fit multiple models</a></li> + <li><a href="#accessing-mmkin-objects">Accessing mmkin objects</a></li> </ul></li> <li><a href="#laboratory-data-l4">Laboratory Data L4</a></li> <li><a href="#references">References</a></li> @@ -659,7 +662,7 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <footer><div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> |