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diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index b89c7b20..7cef7abd 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -62,14 +62,7 @@ <a href="../news/index.html">News</a> </li> </ul> -<ul class="nav navbar-nav navbar-right"> -<li> - <a href="http://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> - </ul> +<ul class="nav navbar-nav navbar-right"></ul> </div> <!--/.nav-collapse --> </div> @@ -84,7 +77,7 @@ <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2017-09-14</h4> + <h4 class="date">2017-11-16</h4> </div> @@ -105,17 +98,17 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re <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_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: 0.9.46.1 -## R version: 3.4.1 -## Date of fit: Thu Sep 14 12:15:03 2017 -## Date of summary: Thu Sep 14 12:15:03 2017 +<pre><code>## mkin version: 0.9.46.2 +## R version: 3.4.2 +## Date of fit: Thu Nov 16 17:12:46 2017 +## Date of summary: Thu Nov 16 17:12:46 2017 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.255 s +## Fitted with method Port using 37 model solutions performed in 0.253 s ## ## Weighting: none ## @@ -198,10 +191,10 @@ 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"><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: 0.9.46.1 -## R version: 3.4.1 -## Date of fit: Thu Sep 14 12:15:05 2017 -## Date of summary: Thu Sep 14 12:15:05 2017 +<pre><code>## mkin version: 0.9.46.2 +## R version: 3.4.2 +## Date of fit: Thu Nov 16 17:12:47 2017 +## Date of summary: Thu Nov 16 17:12:47 2017 ## ## ## Warning: Optimisation by method Port did not converge. @@ -213,7 +206,7 @@ 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 155 model solutions performed in 0.458 s +## Fitted with method Port using 155 model solutions performed in 0.485 s ## ## Weighting: none ## @@ -298,17 +291,17 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re <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: 0.9.46.1 -## R version: 3.4.1 -## Date of fit: Thu Sep 14 12:15:06 2017 -## Date of summary: Thu Sep 14 12:15:06 2017 +<pre><code>## mkin version: 0.9.46.2 +## R version: 3.4.2 +## Date of fit: Thu Nov 16 17:12:48 2017 +## Date of summary: Thu Nov 16 17:12:48 2017 ## ## 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 0.176 s +## Fitted with method Port using 81 model solutions performed in 0.183 s ## ## Weighting: none ## @@ -369,10 +362,10 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re <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: 0.9.46.1 -## R version: 3.4.1 -## Date of fit: Thu Sep 14 12:15:07 2017 -## Date of summary: Thu Sep 14 12:15:07 2017 +<pre><code>## mkin version: 0.9.46.2 +## R version: 3.4.2 +## Date of fit: Thu Nov 16 17:12:49 2017 +## Date of summary: Thu Nov 16 17:12:49 2017 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -381,7 +374,7 @@ 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 0.821 s +## Fitted with method Port using 336 model solutions performed in 0.84 s ## ## Weighting: none ## @@ -461,10 +454,10 @@ 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: 0.9.46.1 -## R version: 3.4.1 -## Date of fit: Thu Sep 14 12:15:08 2017 -## Date of summary: Thu Sep 14 12:15:08 2017 +<pre><code>## mkin version: 0.9.46.2 +## R version: 3.4.2 +## Date of fit: Thu Nov 16 17:12:50 2017 +## Date of summary: Thu Nov 16 17:12:50 2017 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -473,7 +466,7 @@ 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 0.302 s +## Fitted with method Port using 137 model solutions performed in 0.309 s ## ## Weighting: none ## @@ -562,10 +555,10 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <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: 0.9.46.1 -## R version: 3.4.1 -## Date of fit: Thu Sep 14 12:15:08 2017 -## Date of summary: Thu Sep 14 12:15:09 2017 +<pre><code>## mkin version: 0.9.46.2 +## R version: 3.4.2 +## Date of fit: Thu Nov 16 17:12:50 2017 +## Date of summary: Thu Nov 16 17:12:51 2017 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent @@ -622,17 +615,17 @@ 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: 0.9.46.1 -## R version: 3.4.1 -## Date of fit: Thu Sep 14 12:15:08 2017 -## Date of summary: Thu Sep 14 12:15:09 2017 +<pre><code>## mkin version: 0.9.46.2 +## R version: 3.4.2 +## Date of fit: Thu Nov 16 17:12:51 2017 +## Date of summary: Thu Nov 16 17:12:51 2017 ## ## 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 0.151 s +## Fitted with method Port using 66 model solutions performed in 0.136 s ## ## Weighting: none ## |