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- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
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- <h1>Example evaluation of FOCUS Example Dataset D</h1>
+ <h1 data-toc-skip>Example evaluation of FOCUS Example Dataset D</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-11-01</h4>
-
+ <h4 class="date">2020-05-07</h4>
+ <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/FOCUS_D.Rmd"><code>vignettes/FOCUS_D.Rmd</code></a></small>
<div class="hidden name"><code>FOCUS_D.Rmd</code></div>
</div>
@@ -100,8 +107,8 @@
<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" title="1"><span class="kw"><a href="https://rdrr.io/r/base/library.html">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://rdrr.io/r/base/print.html">print</a></span>(FOCUS_<span class="dv">2006</span>_D)</a></code></pre></div>
+<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">mkin</span>, <span class="kw">quietly</span> <span class="kw">=</span> <span class="fl">TRUE</span>)
+<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">FOCUS_2006_D</span>)</pre></body></html></div>
<pre><code>## name time value
## 1 parent 0 99.46
## 2 parent 0 102.04
@@ -149,29 +156,29 @@
## 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>$diffs</code> of the <code>mkinmod</code> object. If a C compiler (gcc) is installed and functional, the differential equation model will be compiled from auto-generated C code.</p>
-<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>), <span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div>
+<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">SFO_SFO</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>), <span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</pre></body></html></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
-<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(SFO_SFO<span class="op">$</span>diffs)</a></code></pre></div>
+<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">SFO_SFO</span>$<span class="no">diffs</span>)</pre></body></html></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" title="1">fit &lt;-<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>
-<pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
-## value of zero were removed from the data</code></pre>
+<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="no">fit</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOCUS_2006_D</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div>
+<pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with value
+## of zero were removed from the data</code></pre>
<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="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" 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://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>))</a></code></pre></div>
+<div class="sourceCode" id="cb9"><html><body><pre class="r"><span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">fit</span>, <span class="kw">lpos</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>))</pre></body></html></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="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1"><span class="kw"><a href="../reference/mkinparplot.html">mkinparplot</a></span>(fit)</a></code></pre></div>
+<div class="sourceCode" id="cb10"><html><body><pre class="r"><span class="fu"><a href="../reference/mkinparplot.html">mkinparplot</a></span>(<span class="no">fit</span>)</pre></body></html></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="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(fit)</a></code></pre></div>
-<pre><code>## mkin version used for fitting: 0.9.49.6
-## R version used for fitting: 3.6.1
-## Date of fit: Fri Nov 1 10:10:44 2019
-## Date of summary: Fri Nov 1 10:10:44 2019
+<div class="sourceCode" id="cb11"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">fit</span>)</pre></body></html></div>
+<pre><code>## mkin version used for fitting: 0.9.49.11
+## R version used for fitting: 4.0.0
+## Date of fit: Thu May 7 08:59:27 2020
+## Date of summary: Thu May 7 08:59:27 2020
##
## Equations:
## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -179,7 +186,7 @@
##
## Model predictions using solution type deSolve
##
-## Fitted using 389 model solutions performed in 1.015 s
+## Fitted using 389 model solutions performed in 1.031 s
##
## Error model: Constant variance
##
@@ -212,18 +219,18 @@
## sigma 3.126 0.35850 2.396 3.855
##
## Parameter correlation:
-## parent_0 log_k_parent_sink log_k_parent_m1
-## parent_0 1.000e+00 6.067e-01 -6.372e-02
-## log_k_parent_sink 6.067e-01 1.000e+00 -8.550e-02
-## log_k_parent_m1 -6.372e-02 -8.550e-02 1.000e+00
-## log_k_m1_sink -1.688e-01 -6.252e-01 4.731e-01
-## sigma 1.164e-09 -8.908e-10 1.652e-08
-## log_k_m1_sink sigma
-## parent_0 -1.688e-01 1.164e-09
-## log_k_parent_sink -6.252e-01 -8.908e-10
-## log_k_parent_m1 4.731e-01 1.652e-08
-## log_k_m1_sink 1.000e+00 -1.340e-10
-## sigma -1.340e-10 1.000e+00
+## parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+## parent_0 1.000e+00 6.067e-01 -6.372e-02 -1.688e-01
+## log_k_parent_sink 6.067e-01 1.000e+00 -8.550e-02 -6.252e-01
+## log_k_parent_m1 -6.372e-02 -8.550e-02 1.000e+00 4.731e-01
+## log_k_m1_sink -1.688e-01 -6.252e-01 4.731e-01 1.000e+00
+## sigma 5.287e-10 3.306e-09 4.421e-08 -3.319e-10
+## sigma
+## parent_0 5.287e-10
+## log_k_parent_sink 3.306e-09
+## log_k_parent_m1 4.421e-08
+## log_k_m1_sink -3.319e-10
+## sigma 1.000e+00
##
## Backtransformed parameters:
## Confidence intervals for internally transformed parameters are asymmetric.
@@ -295,7 +302,7 @@
## 120 m1 33.31 28.78984 4.520e+00</code></pre>
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- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
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index 6f4fa093..a7944b84 100644
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+ <li>
+ <a href="http://github.com/jranke/mkin/">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
@@ -132,16 +141,24 @@
<h3>All vignettes</h3>
<p class="section-desc"></p>
- <ul>
- <li><a href="FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a></li>
- <li><a href="FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></li>
- <li><a href="mkin.html">Introduction to mkin</a></li>
- <li><a href="twa.html">Calculation of time weighted average concentrations with mkin</a></li>
- <li><a href="web_only/FOCUS_Z.html">Example evaluation of FOCUS dataset Z</a></li>
- <li><a href="web_only/NAFTA_examples.html">Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</a></li>
- <li><a href="web_only/benchmarks.html">Benchmark timings for mkin on various systems</a></li>
- <li><a href="web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></li>
- </ul>
+ <dl>
+ <dt><a href="FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a></dt>
+ <dd></dt>
+ <dt><a href="FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></dt>
+ <dd></dt>
+ <dt><a href="mkin.html">Introduction to mkin</a></dt>
+ <dd></dt>
+ <dt><a href="twa.html">Calculation of time weighted average concentrations with mkin</a></dt>
+ <dd></dt>
+ <dt><a href="web_only/FOCUS_Z.html">Example evaluation of FOCUS dataset Z</a></dt>
+ <dd></dt>
+ <dt><a href="web_only/NAFTA_examples.html">Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</a></dt>
+ <dd></dt>
+ <dt><a href="web_only/benchmarks.html">Benchmark timings for mkin on various systems</a></dt>
+ <dd></dt>
+ <dt><a href="web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></dt>
+ <dd></dt>
+ </dl>
</div>
</div>
</div>
@@ -153,7 +170,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
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