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diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 08e144bd..fcd0719d 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -8,8 +8,8 @@ <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"> -<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Example evaluation of FOCUS Laboratory Data L1 to L3"> +<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script><meta property="og:title" content="Example evaluation of FOCUS Laboratory Data L1 to L3"> <meta property="og:description" content=""> <meta name="twitter:card" content="summary"> <!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> @@ -18,7 +18,7 @@ <![endif]--> </head> <body> - <div class="container template-vignette"> + <div class="container template-article"> <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> @@ -27,8 +27,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">mkin</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -75,17 +79,20 @@ </header><div class="row"> - <div class="col-md-9"> + <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-21</h4> - </div> + <h4 class="date">2018-06-06</h4> + + + <div class="hidden name"><code>FOCUS_L.Rmd</code></div> + + </div> -<div class="contents"> <div id="laboratory-data-l1" class="section level1"> <h1 class="hasAnchor"> <a href="#laboratory-data-l1" class="anchor"></a>Laboratory Data L1</h1> @@ -101,17 +108,17 @@ FOCUS_<span class="dv">2006</span>_L1_mkin <-<span class="st"> </span><span c <p>Since mkin version 0.9-32 (July 2014), we can use shorthand notation like <code>"SFO"</code> for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.</p> <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_<span class="dv">2006</span>_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: 0.9.46.3 -## R version: 3.4.4 -## Date of fit: Wed Mar 21 18:16:03 2018 -## Date of summary: Wed Mar 21 18:16:03 2018 +<pre><code>## mkin version used for fitting: 0.9.47.1 +## R version used for fitting: 3.5.0 +## Date of fit: Wed Jun 6 01:21:52 2018 +## Date of summary: Wed Jun 6 01:21:52 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.257 s +## Fitted with method Port using 37 model solutions performed in 0.094 s ## ## Weighting: none ## @@ -192,17 +199,17 @@ FOCUS_<span class="dv">2006</span>_L1_mkin <-<span class="st"> </span><span c <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="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: 0.9.46.3 -## R version: 3.4.4 -## Date of fit: Wed Mar 21 18:16:05 2018 -## Date of summary: Wed Mar 21 18:16:05 2018 +<pre><code>## mkin version used for fitting: 0.9.47.1 +## R version used for fitting: 3.5.0 +## Date of fit: Wed Jun 6 01:21:53 2018 +## Date of summary: Wed Jun 6 01:21:53 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 611 model solutions performed in 1.404 s +## Fitted with method Port using 611 model solutions performed in 1.369 s ## ## Weighting: none ## @@ -287,17 +294,17 @@ FOCUS_<span class="dv">2006</span>_L2_mkin <-<span class="st"> </span><span c <span class="dt">main =</span> <span class="st">"FOCUS L2 - FOMC"</span>)</code></pre></div> <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: 0.9.46.3 -## R version: 3.4.4 -## Date of fit: Wed Mar 21 18:16:06 2018 -## Date of summary: Wed Mar 21 18:16:06 2018 +<pre><code>## mkin version used for fitting: 0.9.47.1 +## R version used for fitting: 3.5.0 +## Date of fit: Wed Jun 6 01:21:54 2018 +## Date of summary: Wed Jun 6 01:21:54 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 81 model solutions performed in 0.168 s +## Fitted with method Port using 81 model solutions performed in 0.173 s ## ## Weighting: none ## @@ -358,10 +365,10 @@ FOCUS_<span class="dv">2006</span>_L2_mkin <-<span class="st"> </span><span c <span class="dt">main =</span> <span class="st">"FOCUS L2 - DFOP"</span>)</code></pre></div> <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: 0.9.46.3 -## R version: 3.4.4 -## Date of fit: Wed Mar 21 18:16:06 2018 -## Date of summary: Wed Mar 21 18:16:06 2018 +<pre><code>## mkin version used for fitting: 0.9.47.1 +## R version used for fitting: 3.5.0 +## Date of fit: Wed Jun 6 01:21:55 2018 +## Date of summary: Wed Jun 6 01:21:55 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -370,7 +377,7 @@ FOCUS_<span class="dv">2006</span>_L2_mkin <-<span class="st"> </span><span c ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.719 s +## Fitted with method Port using 336 model solutions performed in 0.76 s ## ## Weighting: none ## @@ -441,7 +448,7 @@ FOCUS_<span class="dv">2006</span>_L3_mkin <-<span class="st"> </span><span c 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_<span class="dv">2006</span>_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="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="700"></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-mmkin-objects" class="section level2"> @@ -450,10 +457,10 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <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: 0.9.46.3 -## R version: 3.4.4 -## Date of fit: Wed Mar 21 18:16:07 2018 -## Date of summary: Wed Mar 21 18:16:07 2018 +<pre><code>## mkin version used for fitting: 0.9.47.1 +## R version used for fitting: 3.5.0 +## Date of fit: Wed Jun 6 01:21:56 2018 +## Date of summary: Wed Jun 6 01:21:56 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -462,7 +469,7 @@ 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 0.283 s +## Fitted with method Port using 137 model solutions performed in 0.33 s ## ## Weighting: none ## @@ -529,7 +536,7 @@ 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="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="700"></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> @@ -548,20 +555,20 @@ 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_<span class="dv">2006</span>_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="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="700"></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: 0.9.46.3 -## R version: 3.4.4 -## Date of fit: Wed Mar 21 18:16:08 2018 -## Date of summary: Wed Mar 21 18:16:08 2018 +<pre><code>## mkin version used for fitting: 0.9.47.1 +## R version used for fitting: 3.5.0 +## Date of fit: Wed Jun 6 01:21:56 2018 +## Date of summary: Wed Jun 6 01:21:57 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.092 s +## Fitted with method Port using 46 model solutions performed in 0.099 s ## ## Weighting: none ## @@ -611,17 +618,17 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin ## DT50 DT90 ## 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: 0.9.46.3 -## R version: 3.4.4 -## Date of fit: Wed Mar 21 18:16:08 2018 -## Date of summary: Wed Mar 21 18:16:08 2018 +<pre><code>## mkin version used for fitting: 0.9.47.1 +## R version used for fitting: 3.5.0 +## Date of fit: Wed Jun 6 01:21:57 2018 +## Date of summary: Wed Jun 6 01:21:57 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 66 model solutions performed in 0.138 s +## Fitted with method Port using 66 model solutions performed in 0.146 s ## ## Weighting: none ## @@ -681,7 +688,6 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin </div> </div> </div> -</div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -723,5 +729,7 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin </footer> </div> + + </body> </html> |