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authorJohannes Ranke <jranke@uni-bremen.de>2019-01-31 15:35:31 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2019-01-31 15:40:09 +0100
commitde040ca33f6b13ef89be89718510f30631b67903 (patch)
tree049ba22116371b4f578c0b315da15371c093ce51 /docs/articles/web_only
parent47030f0342b66b1520b8a20844a0569d492d188e (diff)
Static documentation rebuilt by pkgdown
Diffstat (limited to 'docs/articles/web_only')
-rw-r--r--docs/articles/web_only/FOCUS_Z.html46
-rw-r--r--docs/articles/web_only/compiled_models.html58
2 files changed, 52 insertions, 52 deletions
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index 6ebe3c73..84bd971f 100644
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@@ -1,18 +1,18 @@
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- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
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@@ -84,7 +85,7 @@
<h1>Example evaluation of FOCUS dataset Z</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-11-26</h4>
+ <h4 class="date">2019-01-31</h4>
<div class="hidden name"><code>FOCUS_Z.Rmd</code></div>
@@ -98,18 +99,18 @@
<h1 class="hasAnchor">
<a href="#the-data" class="anchor"></a>The data</h1>
<p>The following code defines the example dataset from Appendix 7 to the FOCUS kinetics report <span class="citation">(FOCUS Work Group on Degradation Kinetics 2014, 354)</span>.</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">library</span>(mkin, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a>
+<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">LOD =<span class="st"> </span><span class="fl">0.5</span></a>
-<a class="sourceLine" id="cb1-3" data-line-number="3">FOCUS_<span class="dv">2006</span>_Z =<span class="st"> </span><span class="kw">data.frame</span>(</a>
-<a class="sourceLine" id="cb1-4" data-line-number="4"> <span class="dt">t =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="fl">0.04</span>, <span class="fl">0.125</span>, <span class="fl">0.29</span>, <span class="fl">0.54</span>, <span class="dv">1</span>, <span class="dv">2</span>, <span class="dv">3</span>, <span class="dv">4</span>, <span class="dv">7</span>, <span class="dv">10</span>, <span class="dv">14</span>, <span class="dv">21</span>,</a>
+<a class="sourceLine" id="cb1-3" data-line-number="3">FOCUS_<span class="dv">2006</span>_Z =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(</a>
+<a class="sourceLine" id="cb1-4" data-line-number="4"> <span class="dt">t =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="fl">0.04</span>, <span class="fl">0.125</span>, <span class="fl">0.29</span>, <span class="fl">0.54</span>, <span class="dv">1</span>, <span class="dv">2</span>, <span class="dv">3</span>, <span class="dv">4</span>, <span class="dv">7</span>, <span class="dv">10</span>, <span class="dv">14</span>, <span class="dv">21</span>,</a>
<a class="sourceLine" id="cb1-5" data-line-number="5"> <span class="dv">42</span>, <span class="dv">61</span>, <span class="dv">96</span>, <span class="dv">124</span>),</a>
-<a class="sourceLine" id="cb1-6" data-line-number="6"> <span class="dt">Z0 =</span> <span class="kw">c</span>(<span class="dv">100</span>, <span class="fl">81.7</span>, <span class="fl">70.4</span>, <span class="fl">51.1</span>, <span class="fl">41.2</span>, <span class="fl">6.6</span>, <span class="fl">4.6</span>, <span class="fl">3.9</span>, <span class="fl">4.6</span>, <span class="fl">4.3</span>, <span class="fl">6.8</span>,</a>
+<a class="sourceLine" id="cb1-6" data-line-number="6"> <span class="dt">Z0 =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">100</span>, <span class="fl">81.7</span>, <span class="fl">70.4</span>, <span class="fl">51.1</span>, <span class="fl">41.2</span>, <span class="fl">6.6</span>, <span class="fl">4.6</span>, <span class="fl">3.9</span>, <span class="fl">4.6</span>, <span class="fl">4.3</span>, <span class="fl">6.8</span>,</a>
<a class="sourceLine" id="cb1-7" data-line-number="7"> <span class="fl">2.9</span>, <span class="fl">3.5</span>, <span class="fl">5.3</span>, <span class="fl">4.4</span>, <span class="fl">1.2</span>, <span class="fl">0.7</span>),</a>
-<a class="sourceLine" id="cb1-8" data-line-number="8"> <span class="dt">Z1 =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="fl">18.3</span>, <span class="fl">29.6</span>, <span class="fl">46.3</span>, <span class="fl">55.1</span>, <span class="fl">65.7</span>, <span class="fl">39.1</span>, <span class="dv">36</span>, <span class="fl">15.3</span>, <span class="fl">5.6</span>, <span class="fl">1.1</span>,</a>
+<a class="sourceLine" id="cb1-8" data-line-number="8"> <span class="dt">Z1 =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="fl">18.3</span>, <span class="fl">29.6</span>, <span class="fl">46.3</span>, <span class="fl">55.1</span>, <span class="fl">65.7</span>, <span class="fl">39.1</span>, <span class="dv">36</span>, <span class="fl">15.3</span>, <span class="fl">5.6</span>, <span class="fl">1.1</span>,</a>
<a class="sourceLine" id="cb1-9" data-line-number="9"> <span class="fl">1.6</span>, <span class="fl">0.6</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>),</a>
-<a class="sourceLine" id="cb1-10" data-line-number="10"> <span class="dt">Z2 =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="ot">NA</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="fl">2.6</span>, <span class="fl">3.8</span>, <span class="fl">15.3</span>, <span class="fl">37.2</span>, <span class="fl">31.7</span>, <span class="fl">35.6</span>, <span class="fl">14.5</span>,</a>
+<a class="sourceLine" id="cb1-10" data-line-number="10"> <span class="dt">Z2 =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="ot">NA</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="fl">2.6</span>, <span class="fl">3.8</span>, <span class="fl">15.3</span>, <span class="fl">37.2</span>, <span class="fl">31.7</span>, <span class="fl">35.6</span>, <span class="fl">14.5</span>,</a>
<a class="sourceLine" id="cb1-11" data-line-number="11"> <span class="fl">0.8</span>, <span class="fl">2.1</span>, <span class="fl">1.9</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>),</a>
-<a class="sourceLine" id="cb1-12" data-line-number="12"> <span class="dt">Z3 =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="fl">9.2</span>, <span class="fl">13.1</span>, <span class="fl">22.3</span>, <span class="fl">28.4</span>, <span class="fl">32.5</span>,</a>
+<a class="sourceLine" id="cb1-12" data-line-number="12"> <span class="dt">Z3 =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="fl">9.2</span>, <span class="fl">13.1</span>, <span class="fl">22.3</span>, <span class="fl">28.4</span>, <span class="fl">32.5</span>,</a>
<a class="sourceLine" id="cb1-13" data-line-number="13"> <span class="fl">25.2</span>, <span class="fl">17.2</span>, <span class="fl">4.8</span>, <span class="fl">4.5</span>, <span class="fl">2.8</span>, <span class="fl">4.4</span>))</a>
<a class="sourceLine" id="cb1-14" data-line-number="14"></a>
<a class="sourceLine" id="cb1-15" data-line-number="15">FOCUS_<span class="dv">2006</span>_Z_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_<span class="dv">2006</span>_Z)</a></code></pre></div>
@@ -124,7 +125,7 @@
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">m.Z<span class="fl">.2</span>a &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.2</span>a, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb4-2" data-line-number="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.2</span>a)</a></code></pre></div>
<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png" width="700"></p>
-<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">summary</span>(m.Z<span class="fl">.2</span>a, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div>
+<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.2</span>a, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div>
<pre><code>## Estimate se_notrans t value Pr(&gt;t) Lower Upper
## Z0_0 9.7015e+01 3.553140 2.7304e+01 1.6793e-21 NA NA
## k_Z0_sink 1.2790e-11 0.226895 5.6368e-11 5.0000e-01 NA NA
@@ -139,7 +140,7 @@
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1">m.Z<span class="fl">.2</span>a.ff &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.2</span>a.ff, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb9-2" data-line-number="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.2</span>a.ff)</a></code></pre></div>
<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png" width="700"></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">summary</span>(m.Z<span class="fl">.2</span>a.ff, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div>
+<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.2</span>a.ff, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div>
<pre><code>## Estimate se_notrans t value Pr(&gt;t) Lower Upper
## Z0_0 97.01488 3.553145 27.3039 1.6793e-21 NA NA
## k_Z0 2.23601 0.216849 10.3114 3.6623e-11 NA NA
@@ -154,7 +155,7 @@
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" data-line-number="1">m.Z<span class="fl">.3</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.3</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb14-2" data-line-number="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.3</span>)</a></code></pre></div>
<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png" width="700"></p>
-<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="kw">summary</span>(m.Z<span class="fl">.3</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div>
+<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.3</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div>
<pre><code>## Estimate se_notrans t value Pr(&gt;t) Lower Upper
## Z0_0 97.01488 2.681772 36.176 2.3636e-25 91.52152 102.508
## k_Z0 2.23601 0.146861 15.225 2.2464e-15 1.95453 2.558
@@ -186,7 +187,7 @@
## false convergence (8)</code></pre>
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" data-line-number="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.FOCUS)</a></code></pre></div>
<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png" width="700"></p>
-<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1"><span class="kw">summary</span>(m.Z.FOCUS, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div>
+<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z.FOCUS, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div>
<pre><code>## Estimate se_notrans t value Pr(&gt;t) Lower Upper
## Z0_0 96.837112 2.058861 47.0343 5.5877e-44 92.703779 100.970445
## k_Z0 2.215368 0.118098 18.7587 7.6563e-25 1.990525 2.465609
@@ -223,7 +224,7 @@
<div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" data-line-number="1">m.Z.mkin<span class="fl">.1</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.1</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb31-2" data-line-number="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.1</span>)</a></code></pre></div>
<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png" width="700"></p>
-<div class="sourceCode" id="cb32"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb32-1" data-line-number="1"><span class="kw">summary</span>(m.Z.mkin<span class="fl">.1</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>cov.unscaled</a></code></pre></div>
+<div class="sourceCode" id="cb32"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb32-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z.mkin<span class="fl">.1</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>cov.unscaled</a></code></pre></div>
<pre><code>## NULL</code></pre>
<p>Therefore, a further stepwise model building is performed starting from the stage of parent and two metabolites, starting from the assumption that the model fit for the parent compound can be improved by using the SFORB model.</p>
<div class="sourceCode" id="cb34"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb34-1" data-line-number="1">Z.mkin<span class="fl">.3</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
@@ -258,7 +259,7 @@
<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png" width="700"></p>
<p>The summary view of the backtransformed parameters shows that we get no confidence intervals due to overparameterisation. As the optimized is excessively small, it seems reasonable to fix it to zero.</p>
<div class="sourceCode" id="cb43"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb43-1" data-line-number="1">m.Z.mkin<span class="fl">.5</span>a &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a>
-<a class="sourceLine" id="cb43-2" data-line-number="2"> <span class="dt">parms.ini =</span> <span class="kw">c</span>(m.Z.mkin<span class="fl">.5</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">7</span>],</a>
+<a class="sourceLine" id="cb43-2" data-line-number="2"> <span class="dt">parms.ini =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(m.Z.mkin<span class="fl">.5</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">7</span>],</a>
<a class="sourceLine" id="cb43-3" data-line-number="3"> <span class="dt">k_Z3_bound_free =</span> <span class="dv">0</span>),</a>
<a class="sourceLine" id="cb43-4" data-line-number="4"> <span class="dt">fixed_parms =</span> <span class="st">"k_Z3_bound_free"</span>,</a>
<a class="sourceLine" id="cb43-5" data-line-number="5"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a>
@@ -320,9 +321,8 @@
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- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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@@ -1,18 +1,18 @@
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+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.47.6</span>
</span>
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@@ -84,7 +85,7 @@
<h1>Performance benefit by using compiled model definitions in mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-11-26</h4>
+ <h4 class="date">2019-01-31</h4>
<div class="hidden name"><code>compiled_models.Rmd</code></div>
@@ -97,18 +98,18 @@
<h2 class="hasAnchor">
<a href="#model-that-can-also-be-solved-with-eigenvalues" class="anchor"></a>Model that can also be solved with Eigenvalues</h2>
<p>This evaluation is taken from the example section of mkinfit. When using an mkin version equal to or greater than 0.9-36 and a C compiler (gcc) is available, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod. The <code><a href="../../reference/mkinmod.html">mkinmod()</a></code> function checks for presence of the gcc compiler using</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">Sys.which</span>(<span class="st">"gcc"</span>)</a></code></pre></div>
+<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/Sys.which">Sys.which</a></span>(<span class="st">"gcc"</span>)</a></code></pre></div>
<pre><code>## gcc
## "/usr/bin/gcc"</code></pre>
<p>First, we build a simple degradation model for a parent compound with one metabolite.</p>
-<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw">library</span>(<span class="st">"mkin"</span>, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a>
+<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(<span class="st">"mkin"</span>, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb3-2" data-line-number="2">SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a>
<a class="sourceLine" id="cb3-3" data-line-number="3"> <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>),</a>
<a class="sourceLine" id="cb3-4" data-line-number="4"> <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>
<p>We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the benchmark package.</p>
-<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="cf">if</span> (<span class="kw">require</span>(rbenchmark)) {</a>
-<a class="sourceLine" id="cb5-2" data-line-number="2"> b<span class="fl">.1</span> &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></span>(</a>
+<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="cf">if</span> (<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">require</a></span>(rbenchmark)) {</a>
+<a class="sourceLine" id="cb5-2" data-line-number="2"> b<span class="fl">.1</span> &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></span>(</a>
<a class="sourceLine" id="cb5-3" data-line-number="3"> <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D,</a>
<a class="sourceLine" id="cb5-4" data-line-number="4"> <span class="dt">solution_type =</span> <span class="st">"deSolve"</span>,</a>
<a class="sourceLine" id="cb5-5" data-line-number="5"> <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a>
@@ -117,17 +118,17 @@
<a class="sourceLine" id="cb5-8" data-line-number="8"> <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D,</a>
<a class="sourceLine" id="cb5-9" data-line-number="9"> <span class="dt">solution_type =</span> <span class="st">"deSolve"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a>
<a class="sourceLine" id="cb5-10" data-line-number="10"> <span class="dt">replications =</span> <span class="dv">3</span>)</a>
-<a class="sourceLine" id="cb5-11" data-line-number="11"> <span class="kw">print</span>(b<span class="fl">.1</span>)</a>
-<a class="sourceLine" id="cb5-12" data-line-number="12"> factor_SFO_SFO &lt;-<span class="st"> </span><span class="kw">round</span>(b<span class="fl">.1</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>])</a>
+<a class="sourceLine" id="cb5-11" data-line-number="11"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(b<span class="fl">.1</span>)</a>
+<a class="sourceLine" id="cb5-12" data-line-number="12"> factor_SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/Round">round</a></span>(b<span class="fl">.1</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>])</a>
<a class="sourceLine" id="cb5-13" data-line-number="13">} <span class="cf">else</span> {</a>
<a class="sourceLine" id="cb5-14" data-line-number="14"> factor_SFO_SFO &lt;-<span class="st"> </span><span class="ot">NA</span></a>
-<a class="sourceLine" id="cb5-15" data-line-number="15"> <span class="kw">print</span>(<span class="st">"R package benchmark is not available"</span>)</a>
+<a class="sourceLine" id="cb5-15" data-line-number="15"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(<span class="st">"R package benchmark is not available"</span>)</a>
<a class="sourceLine" id="cb5-16" data-line-number="16">}</a></code></pre></div>
<pre><code>## Lade nötiges Paket: rbenchmark</code></pre>
<pre><code>## test replications elapsed relative user.self sys.self
-## 3 deSolve, compiled 3 2.344 1.000 2.343 0.000
-## 1 deSolve, not compiled 3 18.171 7.752 18.152 0.008
-## 2 Eigenvalue based 3 2.887 1.232 2.885 0.000
+## 3 deSolve, compiled 3 2.319 1.000 2.317 0.000
+## 1 deSolve, not compiled 3 17.483 7.539 17.473 0.000
+## 2 Eigenvalue based 3 2.857 1.232 2.852 0.003
## user.child sys.child
## 3 0 0
## 1 0 0
@@ -138,32 +139,32 @@
<h2 class="hasAnchor">
<a href="#model-that-can-not-be-solved-with-eigenvalues" class="anchor"></a>Model that can not be solved with Eigenvalues</h2>
<p>This evaluation is also taken from the example section of mkinfit.</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="cf">if</span> (<span class="kw">require</span>(rbenchmark)) {</a>
+<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="cf">if</span> (<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">require</a></span>(rbenchmark)) {</a>
<a class="sourceLine" id="cb8-2" data-line-number="2"> FOMC_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a>
<a class="sourceLine" id="cb8-3" data-line-number="3"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),</a>
<a class="sourceLine" id="cb8-4" data-line-number="4"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>( <span class="st">"SFO"</span>))</a>
<a class="sourceLine" id="cb8-5" data-line-number="5"></a>
-<a class="sourceLine" id="cb8-6" data-line-number="6"> b<span class="fl">.2</span> &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></span>(</a>
+<a class="sourceLine" id="cb8-6" data-line-number="6"> b<span class="fl">.2</span> &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></span>(</a>
<a class="sourceLine" id="cb8-7" data-line-number="7"> <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D,</a>
<a class="sourceLine" id="cb8-8" data-line-number="8"> <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a>
<a class="sourceLine" id="cb8-9" data-line-number="9"> <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a>
<a class="sourceLine" id="cb8-10" data-line-number="10"> <span class="dt">replications =</span> <span class="dv">3</span>)</a>
-<a class="sourceLine" id="cb8-11" data-line-number="11"> <span class="kw">print</span>(b<span class="fl">.2</span>)</a>
-<a class="sourceLine" id="cb8-12" data-line-number="12"> factor_FOMC_SFO &lt;-<span class="st"> </span><span class="kw">round</span>(b<span class="fl">.2</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>])</a>
+<a class="sourceLine" id="cb8-11" data-line-number="11"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(b<span class="fl">.2</span>)</a>
+<a class="sourceLine" id="cb8-12" data-line-number="12"> factor_FOMC_SFO &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/Round">round</a></span>(b<span class="fl">.2</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>])</a>
<a class="sourceLine" id="cb8-13" data-line-number="13">} <span class="cf">else</span> {</a>
<a class="sourceLine" id="cb8-14" data-line-number="14"> factor_FOMC_SFO &lt;-<span class="st"> </span><span class="ot">NA</span></a>
-<a class="sourceLine" id="cb8-15" data-line-number="15"> <span class="kw">print</span>(<span class="st">"R package benchmark is not available"</span>)</a>
+<a class="sourceLine" id="cb8-15" data-line-number="15"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(<span class="st">"R package benchmark is not available"</span>)</a>
<a class="sourceLine" id="cb8-16" data-line-number="16">}</a></code></pre></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
<pre><code>## test replications elapsed relative user.self sys.self
-## 2 deSolve, compiled 3 4.173 1.000 4.169 0.000
-## 1 deSolve, not compiled 3 38.623 9.255 38.592 0.008
+## 2 deSolve, compiled 3 4.102 1.000 4.100 0
+## 1 deSolve, not compiled 3 37.059 9.034 37.041 0
## user.child sys.child
## 2 0 0
## 1 0 0</code></pre>
<p>Here we get a performance benefit of a factor of 9 using the version of the differential equation model compiled from C code!</p>
-<p>This vignette was built with mkin 0.9.47.6 on</p>
-<pre><code>## R version 3.5.1 (2018-07-02)
+<p>This vignette was built with mkin 0.9.47.5 on</p>
+<pre><code>## R version 3.5.2 (2018-12-20)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 9 (stretch)</code></pre>
<pre><code>## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</code></pre>
@@ -189,9 +190,8 @@
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- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
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