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1 files changed, 12 insertions, 12 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index e01fd46d..fabb567a 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -88,7 +88,7 @@ <h1>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-02-26</h4> + <h4 class="date">2019-03-04</h4> <div class="hidden name"><code>FOCUS_D.Rmd</code></div> @@ -98,8 +98,8 @@ <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"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(mkin, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(FOCUS_<span class="dv">2006</span>_D)</a></code></pre></div> +<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(mkin, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb1-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(FOCUS_<span class="dv">2006</span>_D)</a></code></pre></div> <pre><code>## name time value ## 1 parent 0 99.46 ## 2 parent 0 102.04 @@ -147,27 +147,27 @@ ## 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>$diffs</code> of the <code>mkinmod</code> object. If a C compiler (gcc) is installed and functional, the differential equation model will be compiled from auto-generated C code.</p> -<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1">SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>), <span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>), <span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(SFO_SFO<span class="op">$</span>diffs)</a></code></pre></div> +<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(SFO_SFO<span class="op">$</span>diffs)</a></code></pre></div> <pre><code>## parent ## "d_parent = - k_parent_sink * parent - k_parent_m1 * parent" ## m1 ## "d_m1 = + k_parent_m1 * parent - k_m1_sink * m1"</code></pre> <p>We do the fitting without progress report (<code>quiet = TRUE</code>).</p> -<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">fit <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">fit <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> <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="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(fit, <span class="dt">lpos =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(fit, <span class="dt">lpos =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>))</a></code></pre></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="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1"><span class="kw"><a href="../reference/mkinparplot.html">mkinparplot</a></span>(fit)</a></code></pre></div> +<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1"><span class="kw"><a href="../reference/mkinparplot.html">mkinparplot</a></span>(fit)</a></code></pre></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="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(fit)</a></code></pre></div> +<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(fit)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.48.1 ## R version used for fitting: 3.5.2 -## Date of fit: Tue Feb 26 21:09:15 2019 -## Date of summary: Tue Feb 26 21:09:15 2019 +## Date of fit: Mon Mar 4 10:09:33 2019 +## Date of summary: Mon Mar 4 10:09:33 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -175,7 +175,7 @@ ## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 0.712 s +## Fitted with method Port using 153 model solutions performed in 0.687 s ## ## Weighting: none ## |