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diff --git a/docs/dev/articles/FOCUS_D.html b/docs/dev/articles/FOCUS_D.html index a7617d55..4a9406de 100644 --- a/docs/dev/articles/FOCUS_D.html +++ b/docs/dev/articles/FOCUS_D.html @@ -34,14 +34,14 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../reference/index.html">Functions and data</a> + <a href="../reference/index.html">Reference</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> @@ -53,6 +53,9 @@ <li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> + <li class="divider"> + </li> +<li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> <li> <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> </li> @@ -60,22 +63,31 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li class="divider"> </li> +<li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> <li> - <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> - <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> </li> <li> - <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li class="divider"> + </li> +<li class="dropdown-header">Performance</li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> @@ -83,6 +95,15 @@ <li> <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> + <li class="divider"> + </li> +<li class="dropdown-header">Miscellaneous</li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> </ul> </li> <li> @@ -106,13 +127,16 @@ - </header><script src="FOCUS_D_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> - <h1 data-toc-skip>Example evaluation of FOCUS Example Dataset D</h1> - <h4 data-toc-skip class="author">Johannes Ranke</h4> + <h1 data-toc-skip>Example evaluation of FOCUS Example Dataset +D</h1> + <h4 data-toc-skip class="author">Johannes +Ranke</h4> - <h4 data-toc-skip class="date">Last change 31 January 2019 (rebuilt 2022-11-24)</h4> + <h4 data-toc-skip class="date">Last change 31 January 2019 +(rebuilt 2023-04-16)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/FOCUS_D.rmd" class="external-link"><code>vignettes/FOCUS_D.rmd</code></a></small> <div class="hidden name"><code>FOCUS_D.rmd</code></div> @@ -121,7 +145,12 @@ -<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> +<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="downlit sourceCode r"> <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span><span class="op">)</span></span></code></pre></div> @@ -170,8 +199,14 @@ <span><span class="co">## 42 m1 100 33.13</span></span> <span><span class="co">## 43 m1 120 25.15</span></span> <span><span class="co">## 44 m1 120 33.31</span></span></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>$diffs</code> of the <code>mkinmod</code> object. If a C compiler (gcc) is installed and functional, the differential equation model will be compiled from auto-generated C code.</p> +<p>Next we specify the degradation model: The parent compound degrades +with simple first-order kinetics (SFO) to one metabolite named m1, which +also degrades with SFO kinetics.</p> +<p>The call to mkinmod returns a degradation model. The differential +equations represented in R code can be found in the character vector +<code>$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="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> @@ -181,26 +216,32 @@ <span><span class="co">## "d_parent = - k_parent * parent" </span></span> <span><span class="co">## m1 </span></span> <span><span class="co">## "d_m1 = + f_parent_to_m1 * k_parent * parent - k_m1 * m1"</span></span></code></pre> -<p>We do the fitting without progress report (<code>quiet = TRUE</code>).</p> +<p>We do the fitting without progress report +(<code>quiet = TRUE</code>).</p> <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with value</span></span> -<span><span class="co">## of zero were removed from the data</span></span></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> +<pre><code><span><span class="co">## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with</span></span> +<span><span class="co">## value of zero were removed from the data</span></span></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="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></span></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> +<p>Confidence intervals for the parameter estimates are obtained using +the <code>mkinparplot</code> function.</p> <div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="../reference/mkinparplot.html">mkinparplot</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></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> +<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="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.2.2 </span></span> -<span><span class="co">## R version used for fitting: 4.2.2 </span></span> -<span><span class="co">## Date of fit: Thu Nov 24 08:12:04 2022 </span></span> -<span><span class="co">## Date of summary: Thu Nov 24 08:12:05 2022 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.3 </span></span> +<span><span class="co">## R version used for fitting: 4.2.3 </span></span> +<span><span class="co">## Date of fit: Sun Apr 16 08:35:12 2023 </span></span> +<span><span class="co">## Date of summary: Sun Apr 16 08:35:12 2023 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - k_parent * parent</span></span> @@ -208,7 +249,7 @@ <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 401 model solutions performed in 0.152 s</span></span> +<span><span class="co">## Fitted using 401 model solutions performed in 0.05 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -341,7 +382,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> </footer> |