diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2016-11-03 14:33:05 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2016-11-03 17:48:31 +0100 |
| commit | f39815aa87272849f8e0c808099c4cee780c2a81 (patch) | |
| tree | d3f59ae226591252e17737e12bae7f90be278b7b | |
| parent | bad0c7caff62aa90225ae8acee43b297bdc28b25 (diff) | |
Static documentation rebuilt by pkgdown::build_site()
Using pkgdown with PR hadley/pkgdown#212
81 files changed, 772 insertions, 542 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index db72a3bd..1a29ec35 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -25,5 +25,4 @@ LazyData: yes Encoding: UTF-8 VignetteBuilder: knitr BugReports: http://github.com/jranke/mkin/issues -URL: http://kinfit.r-forge.r-project.org/mkin_static - http://github.com/jranke/mkin +URL: http://github.com/jranke/mkin @@ -36,8 +36,8 @@ at the package vignettes ## Documentation -The [HTML documentation](http://kinfit.r-forge.r-project.org/mkin_static) is -maintained at the R-Forge project site. +The [HTML documentation](http://jranke.github.io/mkin) is +maintained at the github project site. ## Features diff --git a/_pkgdown.yml b/_pkgdown.yml index cdd8994a..a46bc34f 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -34,6 +34,8 @@ reference: - mccall81_245T - schaefer07_complex_case - synthetic_data_for_UBA_2014 + - mkinds + - print.mkinds - title: Helper functions contents: - mkin_wide_to_long @@ -48,12 +50,15 @@ reference: - title: Analytical solutions desc: Parent only model solutions contents: - - SFO.solution, + - SFO.solution - FOMC.solution - DFOP.solution - SFORB.solution - HS.solution - IORE.solution + - title: Generate synthetic datasets + contents: + - add_err - title: Deprecated functions desc: Functions that have been superseeded contents: diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index df259e21..726c8378 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -16,13 +16,16 @@ </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin"> + <a href="http://github.com/jranke/mkin"> <span class="fa fa-github fa-lg"></span> </a> @@ -38,7 +41,7 @@ <h1>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-10-26</h4> + <h4 class="date">2016-11-03</h4> </div> @@ -105,16 +108,16 @@ <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">fit <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_2006_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</code></pre></div> <p>A plot of the fit including a residual plot for both observed variables is obtained using the <code>plot</code> method for <code>mkinfit</code> objects.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plot</span>(fit, <span class="dt">show_residuals =</span> <span class="ot">TRUE</span>)</code></pre></div> -<p><img src="FOCUS_D_files/figure-html/unnamed-chunk-5-1.png" width="672"></p> +<p><img src="FOCUS_D_files/figure-html/plot-1.png" width="672"></p> <p>Confidence intervals for the parameter estimates are obtained using the <code>mkinparplot</code> function.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/mkinparplot.html">mkinparplot</a></span>(fit)</code></pre></div> -<p><img src="FOCUS_D_files/figure-html/unnamed-chunk-6-1.png" width="672"></p> +<p><img src="FOCUS_D_files/figure-html/plot_2-1.png" width="672"></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"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(fit)</code></pre></div> <pre><code>## mkin version: 0.9.44.9000 -## R version: 3.3.1 -## Date of fit: Wed Oct 26 23:18:10 2016 -## Date of summary: Wed Oct 26 23:18:10 2016 +## R version: 3.3.2 +## Date of fit: Wed Nov 2 16:25:22 2016 +## Date of summary: Wed Nov 2 16:25:22 2016 ## ## Equations: ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent @@ -122,7 +125,7 @@ ## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 0.628 s +## Fitted with method Port using 153 model solutions performed in 0.665 s ## ## Weighting: none ## @@ -243,7 +246,7 @@ <footer><div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/articles/FOCUS_D_cache/html/data_df09328a15a9c09625fe6f7d481671d8.RData b/docs/articles/FOCUS_D_cache/html/data_df09328a15a9c09625fe6f7d481671d8.RData Binary files differnew file mode 100644 index 00000000..969644fa --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/data_df09328a15a9c09625fe6f7d481671d8.RData diff --git a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_97560c30ad0c097f3807f1e18320a130.rdb 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b/docs/articles/FOCUS_L.html index cb3096e0..55caa22e 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -16,13 +16,16 @@ </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin"> + <a href="http://github.com/jranke/mkin"> <span class="fa fa-github fa-lg"></span> </a> @@ -38,7 +41,7 @@ <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-10-26</h4> + <h4 class="date">2016-11-03</h4> </div> @@ -59,16 +62,16 @@ 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">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: 0.9.44.9000 -## R version: 3.3.1 -## Date of fit: Wed Oct 26 23:18:11 2016 -## Date of summary: Wed Oct 26 23:18:11 2016 +## R version: 3.3.2 +## Date of fit: Thu Nov 3 17:47:48 2016 +## Date of summary: Thu Nov 3 17:47:48 2016 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.089 s +## Fitted with method Port using 37 model solutions performed in 0.093 s ## ## Weighting: none ## @@ -152,9 +155,9 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re <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: 0.9.44.9000 -## R version: 3.3.1 -## Date of fit: Wed Oct 26 23:18:12 2016 -## Date of summary: Wed Oct 26 23:18:12 2016 +## R version: 3.3.2 +## Date of fit: Thu Nov 3 17:47:49 2016 +## Date of summary: Thu Nov 3 17:47:49 2016 ## ## ## Warning: Optimisation by method Port did not converge. @@ -166,7 +169,7 @@ 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 188 model solutions performed in 0.434 s +## Fitted with method Port using 188 model solutions performed in 0.447 s ## ## Weighting: none ## @@ -249,16 +252,16 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re <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: 0.9.44.9000 -## R version: 3.3.1 -## Date of fit: Wed Oct 26 23:18:12 2016 -## Date of summary: Wed Oct 26 23:18:12 2016 +## R version: 3.3.2 +## Date of fit: Thu Nov 3 17:47:49 2016 +## Date of summary: Thu Nov 3 17:47:49 2016 ## ## Equations: ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 81 model solutions performed in 0.191 s +## Fitted with method Port using 81 model solutions performed in 0.189 s ## ## Weighting: none ## @@ -319,9 +322,9 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re <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: 0.9.44.9000 -## R version: 3.3.1 -## Date of fit: Wed Oct 26 23:18:13 2016 -## Date of summary: Wed Oct 26 23:18:14 2016 +## R version: 3.3.2 +## Date of fit: Thu Nov 3 17:47:50 2016 +## Date of summary: Thu Nov 3 17:47:50 2016 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -330,7 +333,7 @@ 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 0.803 s +## Fitted with method Port using 336 model solutions performed in 0.836 s ## ## Weighting: none ## @@ -392,8 +395,8 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re <span class="dt">t =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="dv">3</span>, <span class="dv">7</span>, <span class="dv">14</span>, <span class="dv">30</span>, <span class="dv">60</span>, <span class="dv">91</span>, <span class="dv">120</span>), <span class="dt">parent =</span> <span class="kw">c</span>(<span class="fl">97.8</span>, <span class="dv">60</span>, <span class="dv">51</span>, <span class="dv">43</span>, <span class="dv">35</span>, <span class="dv">22</span>, <span class="dv">15</span>, <span class="dv">12</span>)) FOCUS_2006_L3_mkin <-<span class="st"> </span><span class="kw"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_2006_L3)</code></pre></div> -<div id="use-mmkin-to-fit-multiple-models" class="section level2"> -<h2 class="hasAnchor"><html><body><a href="#use-mmkin-to-fit-multiple-models" class="anchor"> </a></body></html>Use mmkin to fit multiple models</h2> +<div id="fit-multiple-models" class="section level2"> +<h2 class="hasAnchor"><html><body><a href="#fit-multiple-models" class="anchor"> </a></body></html>Fit multiple models</h2> <p>As of mkin version 0.9-39 (June 2015), we can fit several models to one or more datasets in one call to the function <code>mmkin</code>. The datasets have to be passed in a list, in this case a named list holding only the L3 dataset prepared above.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Only use one core here, not to offend the CRAN checks</span> mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin.html">mmkin</a></span>(<span class="kw">c</span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>), <span class="dt">cores =</span> <span class="dv">1</span>, @@ -402,15 +405,15 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-12-1.png" width="672"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 21% as well as the plot suggest that the SFO model does not fit very well. The FOMC model performs better, with an error level at which the <span class="math inline">\(\chi^2\)</span> test passes of 7%. Fitting the four parameter DFOP model further reduces the <span class="math inline">\(\chi^2\)</span> error level considerably.</p> </div> -<div id="accessing-elements-of-mmkin-objects" class="section level2"> -<h2 class="hasAnchor"><html><body><a href="#accessing-elements-of-mmkin-objects" class="anchor"> </a></body></html>Accessing elements of mmkin objects</h2> +<div id="accessing-mmkin-objects" class="section level2"> +<h2 class="hasAnchor"><html><body><a href="#accessing-mmkin-objects" class="anchor"> </a></body></html>Accessing mmkin objects</h2> <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: 0.9.44.9000 -## R version: 3.3.1 -## Date of fit: Wed Oct 26 23:18:15 2016 -## Date of summary: Wed Oct 26 23:18:15 2016 +## R version: 3.3.2 +## Date of fit: Thu Nov 3 17:47:51 2016 +## Date of summary: Thu Nov 3 17:47:52 2016 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -419,7 +422,7 @@ 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 0.323 s +## Fitted with method Port using 137 model solutions performed in 0.328 s ## ## Weighting: none ## @@ -508,16 +511,16 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <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: 0.9.44.9000 -## R version: 3.3.1 -## Date of fit: Wed Oct 26 23:18:15 2016 -## Date of summary: Wed Oct 26 23:18:16 2016 +## R version: 3.3.2 +## Date of fit: Thu Nov 3 17:47:52 2016 +## Date of summary: Thu Nov 3 17:47:52 2016 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.108 s +## Fitted with method Port using 46 model solutions performed in 0.107 s ## ## Weighting: none ## @@ -568,16 +571,16 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin ## 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: 0.9.44.9000 -## R version: 3.3.1 -## Date of fit: Wed Oct 26 23:18:16 2016 -## Date of summary: Wed Oct 26 23:18:16 2016 +## R version: 3.3.2 +## Date of fit: Thu Nov 3 17:47:52 2016 +## Date of summary: Thu Nov 3 17:47:52 2016 ## ## Equations: ## d_parent = - (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 0.148 s ## ## Weighting: none ## @@ -647,8 +650,8 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <li><a href="#fomc-fit-for-l2">FOMC fit for L2</a></li> <li><a href="#dfop-fit-for-l2">DFOP fit for L2</a></li> </ul></li> - <li><a href="#laboratory-data-l3">Laboratory Data L3</a><ul class="nav nav-pills nav-stacked"><li><a href="#use-mmkin-to-fit-multiple-models">Use mmkin to fit multiple models</a></li> - <li><a href="#accessing-elements-of-mmkin-objects">Accessing elements of mmkin objects</a></li> + <li><a href="#laboratory-data-l3">Laboratory Data L3</a><ul class="nav nav-pills nav-stacked"><li><a href="#fit-multiple-models">Fit multiple models</a></li> + <li><a href="#accessing-mmkin-objects">Accessing mmkin objects</a></li> </ul></li> <li><a href="#laboratory-data-l4">Laboratory Data L4</a></li> <li><a href="#references">References</a></li> @@ -659,7 +662,7 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <footer><div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/articles/FOCUS_Z.pdf b/docs/articles/FOCUS_Z.pdf Binary files differindex bc37c873..6f71d018 100644 --- a/docs/articles/FOCUS_Z.pdf +++ b/docs/articles/FOCUS_Z.pdf diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index e02b9cf3..5a04168e 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -16,13 +16,16 @@ </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin"> + <a href="http://github.com/jranke/mkin"> <span class="fa fa-github fa-lg"></span> </a> @@ -38,7 +41,7 @@ <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-10-26</h4> + <h4 class="date">2016-11-03</h4> </div> @@ -75,21 +78,21 @@ mb<span class="fl">.1</span> <-<span class="st"> </span><span class="kw">micr <span class="kw">print</span>(mb<span class="fl">.1</span>)</code></pre></div> <pre><code>## Unit: milliseconds ## expr min lq mean median uq -## deSolve, not compiled 6298.7342 6308.6792 6343.9668 6318.6243 6366.5831 -## Eigenvalue based 871.7379 880.7757 903.5267 889.8135 919.4211 -## deSolve, compiled 724.9025 730.6729 732.9837 736.4432 737.0243 +## deSolve, not compiled 6306.4527 6340.7895 6403.5937 6375.1264 6452.1643 +## Eigenvalue based 918.0808 929.7217 948.9742 941.3626 964.4210 +## deSolve, compiled 736.1337 753.6016 773.5605 771.0696 792.2739 ## max neval cld -## 6414.5420 3 c -## 949.0287 3 b -## 737.6054 3 a</code></pre> +## 6529.2022 3 b +## 987.4793 3 a +## 813.4783 3 a</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.1</span>)</code></pre></div> <p><img src="compiled_models_files/figure-html/benchmark_SFO_SFO-1.png" width="672"></p> -<p>We see that using the compiled model is by a factor of 8.6 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:</p> +<p>We see that using the compiled model is by a factor of 8.3 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">rownames</span>(smb<span class="fl">.1</span>) <-<span class="st"> </span>smb<span class="fl">.1</span>$expr smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class="fl">.1</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div> <pre><code>## median -## deSolve, not compiled 8.579920 -## Eigenvalue based 1.208258 +## deSolve, not compiled 8.267900 +## Eigenvalue based 1.220853 ## deSolve, compiled 1.000000</code></pre> </div> <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2"> @@ -111,20 +114,20 @@ smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class=" <span class="kw">print</span>(mb<span class="fl">.2</span>)</code></pre></div> <pre><code>## Unit: seconds ## expr min lq mean median uq -## deSolve, not compiled 13.265212 13.330161 13.412053 13.395109 13.485473 -## deSolve, compiled 1.322466 1.326851 1.364827 1.331236 1.386007 +## deSolve, not compiled 13.604720 13.667244 13.689764 13.729768 13.732286 +## deSolve, compiled 1.305077 1.311124 1.328943 1.317172 1.340876 ## max neval cld -## 13.575837 3 b -## 1.440779 3 a</code></pre> +## 13.734804 3 b +## 1.364579 3 a</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">smb<span class="fl">.2</span>[<span class="st">"median"</span>]/smb<span class="fl">.2</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div> <pre><code>## median ## 1 NA ## 2 NA</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.2</span>)</code></pre></div> <p><img src="compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png" width="672"></p> -<p>Here we get a performance benefit of a factor of 10.1 using the version of the differential equation model compiled from C code!</p> +<p>Here we get a performance benefit of a factor of 10.4 using the version of the differential equation model compiled from C code!</p> <p>This vignette was built with mkin 0.9.44.9000 on</p> -<pre><code>## R version 3.3.1 (2016-06-21) +<pre><code>## R version 3.3.2 (2016-10-31) ## Platform: x86_64-pc-linux-gnu (64-bit) ## Running under: Debian GNU/Linux 8 (jessie)</code></pre> <pre><code>## CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz</code></pre> @@ -144,7 +147,7 @@ smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class=" <footer><div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png Binary files differindex bba259d6..eec55773 100644 --- a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png +++ b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png Binary files differindex 6b732075..b043c13b 100644 --- a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png +++ b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png diff --git a/docs/articles/index.html b/docs/articles/index.html index 9994716d..cd6a7bea 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -49,16 +49,19 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> <li> - <a href="https://github.com/jranke/mkin"> + <a href="http://github.com/jranke/mkin"> <span class="fa fa-github fa-lg"></span> </a> @@ -93,7 +96,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index 74d8ccca..dafaa0e4 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -16,13 +16,16 @@ </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin"> + <a href="http://github.com/jranke/mkin"> <span class="fa fa-github fa-lg"></span> </a> @@ -38,7 +41,7 @@ <h1>mkin - Kinetic evaluation of chemical degradation data</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-10-26</h4> + <h4 class="date">2016-11-03</h4> </div> @@ -67,7 +70,7 @@ d_SFO_SFO_SFO_err <-<span class="st"> </span><span class="kw"><a href="../ref f_SFO_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(m_SFO_SFO_SFO, d_SFO_SFO_SFO_err[[<span class="dv">1</span>]], <span class="dt">quiet =</span> <span class="ot">TRUE</span>) -<span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(f_SFO_SFO_SFO, <span class="dt">lpos =</span> <span class="kw">c</span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>, <span class="st">"bottomright"</span>))</code></pre></div> +<span class="kw">plot_sep</span>(f_SFO_SFO_SFO, <span class="dt">lpos =</span> <span class="kw">c</span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>, <span class="st">"bottomright"</span>))</code></pre></div> <p><img src="mkin_files/figure-html/unnamed-chunk-2-1.png" width="768"></p> </div> <div id="background" class="section level1"> @@ -169,7 +172,7 @@ f_SFO_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../referen <footer><div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/articles/mkin_cache/html/__packages b/docs/articles/mkin_cache/html/__packages index c8b1e877..03ece635 100644 --- a/docs/articles/mkin_cache/html/__packages +++ b/docs/articles/mkin_cache/html/__packages @@ -1,8 +1,13 @@ base +datasets +utils +grDevices +graphics +stats knitr minpack.lm rootSolve +methods inline +parallel mkin -microbenchmark -ggplot2 diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData Binary files differnew file mode 100644 index 00000000..d11ccf31 --- /dev/null +++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb Binary files differnew file mode 100644 index 00000000..5ac4f484 --- /dev/null +++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx Binary files differnew file mode 100644 index 00000000..8983f69e --- /dev/null +++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png Binary files differindex d34e3805..2e7e2244 100644 --- a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png +++ b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png diff --git a/docs/authors.html b/docs/authors.html new file mode 100644 index 00000000..fe3e6114 --- /dev/null +++ b/docs/authors.html @@ -0,0 +1,120 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Authors • mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="pkgdown.css" rel="stylesheet"> +<script src="jquery.sticky-kit.min.js"></script> +<script src="pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container template-authors"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="reference/index.html">Reference</a> +</li> +<li> + <a href="articles/index.html">Articles</a> +</li> +<li> + <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> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="contents col-md-12"> + <div class="page-header"> + <h1>Authors</h1> + </div> + + <ul class="list-unstyled"> + <li> + <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder. + </p> + </li> + <li> + <p><strong>Katrin Lindenberger</strong>. Contributor. + </p> + </li> + <li> + <p><strong>René Lehmann</strong>. Contributor. + </p> + </li> + <li> + <p><strong>Eurofins Regulatory AG</strong>. Copyright holder. + </p> + </li> + </ul> + + </div> + +</div> + + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/index.html b/docs/index.html index 04f10ed8..a3a0e46c 100644 --- a/docs/index.html +++ b/docs/index.html @@ -24,7 +24,13 @@ <li> <a href="news/index.html">News</a> </li> - </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </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></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -54,7 +60,7 @@ <div id="documentation" class="section level2"> <h2 class="hasAnchor"> <a href="#documentation" class="anchor"> </a>Documentation</h2> -<p>The <a href="http://kinfit.r-forge.r-project.org/mkin_static">HTML documentation</a> is maintained at the R-Forge project site.</p> +<p>The <a href="http://jranke.github.io/mkin">HTML documentation</a> is maintained at the github project site.</p> </div> <div id="features" class="section level2"> <h2 class="hasAnchor"> @@ -102,25 +108,21 @@ </div> <div class="col-md-3" id="sidebar"> - <h2>Links</h2><ul class="list-unstyled"><li>Download from CRAN at <a href="https://cran.r-project.org/package=mkin">https://cran.r-project.org/package=mkin</a></li> -<li>Browse source code at <a href="http://kinfit.r-forge.r-project.org/mkin_static%0A%20%20%20%20%20http://github.com/jranke/mkin">http://kinfit.r-forge.r-project.org/mkin_static - http://github.com/jranke/mkin</a></li> -<li>Report a bug at <a href="http://github.com/jranke/mkin/issues">http://github.com/jranke/mkin/issues</a></li> -</ul><h2>Authors</h2><ul class="list-unstyled"><li>Johannes Ranke<br><small class="roles">Author, maintainer, copyright holder</small></li> -<li>Katrin Lindenberger<br><small class="roles">Contributor</small></li> -<li>René Lehmann<br><small class="roles">Contributor</small></li> -<li>Eurofins Regulatory AG<br><small class="roles">Copyright holder</small></li> + <h2>Links</h2><ul class="list-unstyled"><li>Download from CRAN at <br><a href="https://cran.r-project.org/package=mkin">https://​cran.r-project.org/​package=mkin</a></li> +<li>Browse source code at <br><a href="http://github.com/jranke/mkin">http://​github.com/​jranke/​mkin</a></li> +<li>Report a bug at <br><a href="http://github.com/jranke/mkin/issues">http://​github.com/​jranke/​mkin/​issues</a></li> </ul><h2>License</h2> <p>GPL</p> - - <html><body><h2>Dev status</h2><ul class="list-unstyled"><li><a href="http://cran.r-project.org/package=mkin"> +<h2>Developers</h2><ul class="list-unstyled"><li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> </li> +<li><a href="authors.html">All authors...</a></li> +</ul><html><body><h2>Dev status</h2><ul class="list-unstyled"><li><a href="http://cran.r-project.org/package=mkin"> <img src="http://www.r-pkg.org/badges/version/mkin"></a></li> </ul></body></html></div> </div> <footer><div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/news/index.html b/docs/news/index.html index b30b400f..94d5d197 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -49,16 +49,19 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> <li> - <a href="https://github.com/jranke/mkin"> + <a href="http://github.com/jranke/mkin"> <span class="fa fa-github fa-lg"></span> </a> @@ -161,7 +164,7 @@ <h2 class="hasAnchor"> <a href="#bug-fixes-2" class="anchor"> </a>Bug fixes</h2> <ul><li> -<code><a href="../reference/summary.mkinfit.html">print.summary.mkinfit()</a></code>: Avoid an error that occurred when printing summaries generated with mkin versions before 0.9-36</li> +<code>print.summary.mkinfit()</code>: Avoid an error that occurred when printing summaries generated with mkin versions before 0.9-36</li> </ul></div> </div> <div id="mkin-0-9-40-2015-07-21" class="section level1"> @@ -218,7 +221,7 @@ <div id="major-changes-3" class="section level2"> <h2 class="hasAnchor"> <a href="#major-changes-3" class="anchor"> </a>Major changes</h2> -<ul><li><p><code><a href="../reference/summary.mkinfit.html">summary.mkinfit()</a></code>: A one-sided t-test for significant difference of untransformed parameters from zero is now always shown, based on the assumption of normal distribution for estimators of all untransformed parameters. Use with caution, as this assumption is unrealistic e.g. for rate constants in these nonlinear kinetic models.</p></li> +<ul><li><p><code>summary.mkinfit()</code>: A one-sided t-test for significant difference of untransformed parameters from zero is now always shown, based on the assumption of normal distribution for estimators of all untransformed parameters. Use with caution, as this assumption is unrealistic e.g. for rate constants in these nonlinear kinetic models.</p></li> <li><p>If a compiler (gcc) is installed, use a version of the differential equation model compiled from C code, which is a huge performance boost for models where only the deSolve method works.</p></li> <li><p><code><a href="../reference/mkinmod.html">mkinmod()</a></code>: Create a list component $cf (of class CFuncList) in the list returned by mkinmod, if a version can be compiled from autogenerated C code (see above).</p></li> <li><p><code><a href="../reference/mkinfit.html">mkinfit()</a></code>: Set the default <code>solution_type</code> to <code>deSolve</code> when a compiled version of the model is present, except when an analytical solution is possible.</p></li> @@ -241,7 +244,7 @@ <h2 class="hasAnchor"> <a href="#bug-fixes-6" class="anchor"> </a>Bug fixes</h2> <ul><li><p><code><a href="../reference/mkinparplot.html">mkinparplot()</a></code>: Avoid warnings that occurred when not all confidence intervals were available in the summary of the fit</p></li> -<li><p><code><a href="../reference/summary.mkinfit.html">print.summary.mkinfit()</a></code>: Fix printing the summary for the case that the number of iterations is not available</p></li> +<li><p><code>print.summary.mkinfit()</code>: Fix printing the summary for the case that the number of iterations is not available</p></li> <li><p>NAMESPACE: export S3 methods plot.mkinfit, summary.mkinfit and print.summary.mkinfit to satisfy R CMD check on R-devel</p></li> <li><p><code><a href="../reference/mkinparplot.html">mkinparplot()</a></code>: Avoid warning in R CMD check about undeclared global variable <code>Lower</code></p></li> </ul></div> @@ -286,14 +289,14 @@ <ul><li><p><code><a href="../reference/mkinfit.html">mkinfit()</a></code>: The internally fitted parameter for <code>g</code> was named <code>g_ilr</code> even when <code>transform_fractions=FALSE</code></p></li> <li><p><code><a href="../reference/mkinfit.html">mkinfit()</a></code>: The initial value (state.ini) for the parent compound was not set when the parent was not the (only) variable with the highest value in the observed data.</p></li> <li><p><code><a href="../reference/mkinerrmin.html">mkinerrmin()</a></code>: When checking for degrees of freedom for metabolites, check if their time zero value is fixed instead of checking if the observed value is zero. This ensures correct calculation of degrees of freedom also in cases where the metabolite residue at time zero is greater zero.</p></li> -<li><p><code><a href="../reference/plot.mkinfit.html">plot.mkinfit()</a></code>: Avoid a warning message about only using the first component of ylim that occurred when ylim was specified explicitly</p></li> +<li><p><code>plot.mkinfit()</code>: Avoid a warning message about only using the first component of ylim that occurred when ylim was specified explicitly</p></li> </ul></div> <div id="minor-changes-7" class="section level2"> <h2 class="hasAnchor"> <a href="#minor-changes-7" class="anchor"> </a>Minor changes</h2> <ul><li><p>The formatting of differential equations in the summary was improved by wrapping overly long lines</p></li> <li><p>The FOCUS_Z vignette was rebuilt with the above improvement and using a width of 70 to avoid output outside of the grey area</p></li> -<li><p><code><a href="../reference/summary.mkinfit.html">print.summary.mkinfit()</a></code>: Avoid a warning that occurred when gmkin showed summaries ofinitial fits without iterations</p></li> +<li><p><code>print.summary.mkinfit()</code>: Avoid a warning that occurred when gmkin showed summaries ofinitial fits without iterations</p></li> <li><p><code><a href="../reference/mkinfit.html">mkinfit()</a></code>: Avoid a warning that occurred when summarising a fit that was performed with maxitmodFit = 0 as done in gmkin for configuring new fits.</p></li> </ul></div> </div> @@ -454,7 +457,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/pkgdown.css b/docs/pkgdown.css index ec6cc73b..fd7b0ba4 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -30,6 +30,10 @@ footer p { margin-bottom: 0; } +img.icon { + float: right; +} + /* Section anchors ---------------------------------*/ .hasAnchor { @@ -63,11 +67,6 @@ a.anchor { #sidebar { margin-top: 30px; - word-wrap: break-word; - - hyphens: auto; - -ms-hyphens: auto; - -webkit-hyphens: auto; } #sidebar h2 { font-size: 1.5em; @@ -92,6 +91,10 @@ code a { color: #375f84; } +.warning { color: red; } +.message { font-weight: bolder; } +.error { color: red; font-weight: bolder; } + .fl,.number {color:rgb(21,20,181);} .fu,.functioncall {color:#264D66 ;} .ch,.st,.string {color:#375D81 ;} diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 3b8e0e03..e05cdc29 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -113,10 +118,7 @@ <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>DFOP.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>5</span>, <span class='fl'>0.5</span>, <span class='fl'>0.3</span>), <span class='fl'>0</span>, <span class='fl'>4</span>, <span class='kw'>ylim</span><span class='kw'>=</span><span class='fu'>c</span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><img src='DFOP.solution-2.png' alt='' width='540' height='400' /></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -136,7 +138,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 4ea16d10..fe39ce6e 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -60,7 +60,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -102,10 +107,7 @@ <p>An object of class <code><a href='mmkin.html'>mmkin</a></code>.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='co'># Only use one core, to pass R CMD check --as-cran</span> <span class='no'>fits</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'>c</span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>), <span class='fu'>list</span>(<span class='kw'>B</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='kw'>C</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>), <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) @@ -113,14 +115,12 @@ #> model B C #> FOMC List,42 List,42 #> attr(,"class") -#> [1] "mmkin" -#> </div><div class='input'> <span class='no'>fits</span>[, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset +#> [1] "mmkin"</div><div class='input'> <span class='no'>fits</span>[, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset #> model B #> SFO List,42 #> FOMC List,42 #> attr(,"class") -#> [1] "mmkin" -#> </div><div class='input'> <span class='no'>fits</span>[, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]$<span class='no'>FOMC</span></div><div class='output co'>#> $par +#> [1] "mmkin"</div><div class='input'> <span class='no'>fits</span>[, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]$<span class='no'>FOMC</span></div><div class='output co'>#> $par #> parent_0 log_alpha log_beta #> 99.666193 2.549849 5.050586 #> @@ -193,7 +193,7 @@ #> #> $time #> user system elapsed -#> 0.26 0.00 0.26 +#> 0.256 0.000 0.256 #> #> $mkinmod #> <mkinmod> model generated with @@ -379,7 +379,7 @@ #> } #> return(mC) #> } -#> <environment: 0x5421f48> +#> <environment: 0x5b47f50> #> #> $cost_notrans #> function (P) @@ -401,7 +401,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x5421f48> +#> <environment: 0x5b47f50> #> #> $hessian_notrans #> parent_0 alpha beta @@ -467,16 +467,14 @@ #> 99.66619 #> #> $date -#> [1] "Wed Oct 26 23:50:33 2016" +#> [1] "Thu Nov 3 17:46:18 2016" #> #> attr(,"class") -#> [1] "mkinfit" "modFit" -#> </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset +#> [1] "mkinfit" "modFit" </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset #> model B #> SFO List,42 #> attr(,"class") -#> [1] "mmkin" -#> </div><div class='input'> <span class='no'>fits</span><span class='kw'>[[</span><span class='st'>"SFO"</span>, <span class='st'>"B"</span>]] <span class='co'># This is equivalent to</span></div><div class='output co'>#> $par +#> [1] "mmkin"</div><div class='input'> <span class='no'>fits</span><span class='kw'>[[</span><span class='st'>"SFO"</span>, <span class='st'>"B"</span>]] <span class='co'># This is equivalent to</span></div><div class='output co'>#> $par #> parent_0 log_k_parent_sink #> 99.174072 -2.549028 #> @@ -735,7 +733,7 @@ #> } #> return(mC) #> } -#> <environment: 0x2b30d68> +#> <environment: 0x46881c0> #> #> $cost_notrans #> function (P) @@ -757,7 +755,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x2b30d68> +#> <environment: 0x46881c0> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -820,11 +818,10 @@ #> 99.17407 #> #> $date -#> [1] "Wed Oct 26 23:50:32 2016" +#> [1] "Thu Nov 3 17:46:18 2016" #> #> attr(,"class") -#> [1] "mkinfit" "modFit" -#> </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]</div><div class='output co'>#> [[1]] +#> [1] "mkinfit" "modFit" </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]</div><div class='output co'>#> [[1]] #> $par #> parent_0 log_k_parent_sink #> 99.174072 -2.549028 @@ -1084,7 +1081,7 @@ #> } #> return(mC) #> } -#> <environment: 0x2b30d68> +#> <environment: 0x46881c0> #> #> $cost_notrans #> function (P) @@ -1106,7 +1103,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x2b30d68> +#> <environment: 0x46881c0> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -1169,11 +1166,10 @@ #> 99.17407 #> #> $date -#> [1] "Wed Oct 26 23:50:32 2016" +#> [1] "Thu Nov 3 17:46:18 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" -#> #> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -1195,7 +1191,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html index 6f071674..9f098ff3 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -110,10 +115,7 @@ in this fit.</p> <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>FOCUS_2006_DFOP_ref_A_to_B</span>)</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -132,7 +134,7 @@ in this fit.</p> <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html index d721b2d9..e45463ba 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -109,10 +114,7 @@ in this fit.</p> <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>FOCUS_2006_FOMC_ref_A_to_F</span>)</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -131,7 +133,7 @@ in this fit.</p> <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html index 11fcea7c..247c3e00 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -110,10 +115,7 @@ in this fit.</p> <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>FOCUS_2006_HS_ref_A_to_F</span>)</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -132,7 +134,7 @@ in this fit.</p> <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html index 17c34f0f..006a3876 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -108,10 +113,7 @@ in this fit.</p> <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>FOCUS_2006_SFO_ref_A_to_F</span>)</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -130,7 +132,7 @@ in this fit.</p> <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index c5bdae8b..c2501a7f 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -101,10 +106,7 @@ <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>FOCUS_2006_C</span></div><div class='output co'>#> name time value #> 1 parent 0 85.1 #> 2 parent 1 57.9 @@ -114,8 +116,7 @@ #> 6 parent 28 6.6 #> 7 parent 63 4.0 #> 8 parent 91 3.9 -#> 9 parent 119 0.6 -#> </div></pre> +#> 9 parent 119 0.6</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -133,7 +134,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index a2e84ce0..1fbf7741 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -60,7 +60,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -125,10 +130,7 @@ Technology</em> <b>24</b>, 1032-1038</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>FOMC.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>10</span>, <span class='fl'>2</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><img src='FOMC.solution-2.png' alt='' width='540' height='400' /></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -150,7 +152,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index e41b7b6a..2cecda28 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -60,7 +60,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -111,10 +116,7 @@ <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>HS.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>2</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span><span class='kw'>=</span><span class='fu'>c</span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><img src='HS.solution-2.png' alt='' width='540' height='400' /></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -134,7 +136,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index c39e7818..68b7be44 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -60,7 +60,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -112,10 +117,7 @@ Media</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>IORE.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.2</span>, <span class='fl'>1.3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><img src='IORE.solution-2.png' alt='' width='540' height='400' /><div class='input'> <span class='no'>fit.fomc</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='no'>fit.iore</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"IORE"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) @@ -125,13 +127,11 @@ <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fu'>paste</span>(<span class='st'>"model par"</span>, <span class='fl'>1</span>:<span class='fl'>3</span>)))</div><div class='output co'>#> coef.fit.fomc. coef.fit.iore. coef.fit.iore.deS. #> model par 1 85.87489063 85.874891 85.874890 #> model par 2 0.05192238 -4.826631 -4.826631 -#> model par 3 0.65096665 1.949403 1.949403 -#> </div><div class='input'> <span class='fu'>print</span>(<span class='fu'>rbind</span>(<span class='kw'>fomc</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.fomc</span>)$<span class='no'>distimes</span>, <span class='kw'>iore</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>, +#> model par 3 0.65096665 1.949403 1.949403</div><div class='input'> <span class='fu'>print</span>(<span class='fu'>rbind</span>(<span class='kw'>fomc</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.fomc</span>)$<span class='no'>distimes</span>, <span class='kw'>iore</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>, <span class='kw'>iore.deS</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>))</div><div class='output co'>#> DT50 DT90 DT50back #> fomc 1.785233 15.1479 4.559973 #> iore 1.785233 15.1479 4.559973 -#> iore.deS 1.785233 15.1479 4.559973 -#> </div></pre> +#> iore.deS 1.785233 15.1479 4.559973</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -152,7 +152,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 3ce813bf..51c35eee 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -60,7 +60,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -104,10 +109,7 @@ <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='co'>## Not run: plot(function(x) SFO.solution(x, 100, 3), 0, 2)</span></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -127,7 +129,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 942fa576..2f7dcb5d 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -60,7 +60,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -113,10 +118,7 @@ <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='co'>## Not run: plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)</span></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -136,7 +138,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 2500e092..82a0b039 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -135,13 +140,10 @@ http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># The kinetic model</span> <span class='no'>m_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='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='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> + <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='co'># Generate a prediction for a specific set of parameters</span> <span class='no'>sampling_times</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span>) @@ -200,7 +202,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 73d7e746..6ff7ac36 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -96,7 +101,7 @@ with the advantage that the SFORB model can also be used for metabolites.</p> <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> - <p>The function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> + <p>The function is used internally by <code>summary.mkinfit</code>.</p> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> @@ -123,7 +128,7 @@ with the advantage that the SFORB model can also be used for metabolites.</p> <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 62a9163f..a4b661e2 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -60,7 +60,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -94,14 +99,8 @@ <p>The geometric mean.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> - <pre class="examples"><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>3</span>, <span class='fl'>9</span>))</div><div class='output co'>#> [1] 3 -#> </div><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>3</span>, <span class='fl'>NA</span>))</div><div class='output co'>#> [1] NA -#> </div><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>3</span>, <span class='fl'>NA</span>), <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> [1] 1.732051 -#> </div></pre> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>3</span>, <span class='fl'>9</span>))</div><div class='output co'>#> [1] 3</div><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>3</span>, <span class='fl'>NA</span>))</div><div class='output co'>#> [1] NA</div><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>3</span>, <span class='fl'>NA</span>), <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> [1] 1.732051</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -118,7 +117,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 82accca4..d2551059 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -107,31 +112,17 @@ <p>Another implementation can be found in R package <code>robCompositions</code>.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># Order matters</span> -<span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>0.1</span>, <span class='fl'>1</span>, <span class='fl'>10</span>))</div><div class='output co'>#> [1] -1.628174 -2.820079 -#> </div><div class='input'><span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>10</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>))</div><div class='output co'>#> [1] 1.628174 2.820079 -#> </div><div class='input'><span class='co'># Equal entries give ilr transformations with zeros as elements</span> -<span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>3</span>, <span class='fl'>3</span>, <span class='fl'>3</span>))</div><div class='output co'>#> [1] 0 0 -#> </div><div class='input'><span class='co'># Almost equal entries give small numbers</span> -<span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>0.3</span>, <span class='fl'>0.4</span>, <span class='fl'>0.3</span>))</div><div class='output co'>#> [1] -0.2034219 0.1174457 -#> </div><div class='input'><span class='co'># Only the ratio between the numbers counts, not their sum</span> -<span class='fu'>invilr</span>(<span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>0.7</span>, <span class='fl'>0.29</span>, <span class='fl'>0.01</span>)))</div><div class='output co'>#> [1] 0.70 0.29 0.01 -#> </div><div class='input'><span class='fu'>invilr</span>(<span class='fu'>ilr</span>(<span class='fl'>2.1</span> * <span class='fu'>c</span>(<span class='fl'>0.7</span>, <span class='fl'>0.29</span>, <span class='fl'>0.01</span>)))</div><div class='output co'>#> [1] 0.70 0.29 0.01 -#> </div><div class='input'><span class='co'># Inverse transformation of larger numbers gives unequal elements</span> -<span class='fu'>invilr</span>(-<span class='fl'>10</span>)</div><div class='output co'>#> [1] 7.213536e-07 9.999993e-01 -#> </div><div class='input'><span class='fu'>invilr</span>(<span class='fu'>c</span>(-<span class='fl'>10</span>, <span class='fl'>0</span>))</div><div class='output co'>#> [1] 7.207415e-07 9.991507e-01 8.486044e-04 -#> </div><div class='input'><span class='co'># The sum of the elements of the inverse ilr is 1</span> -<span class='fu'>sum</span>(<span class='fu'>invilr</span>(<span class='fu'>c</span>(-<span class='fl'>10</span>, <span class='fl'>0</span>)))</div><div class='output co'>#> [1] 1 -#> </div><div class='input'><span class='co'># This is why we do not need all elements of the inverse transformation to go back:</span> +<span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>0.1</span>, <span class='fl'>1</span>, <span class='fl'>10</span>))</div><div class='output co'>#> [1] -1.628174 -2.820079</div><div class='input'><span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>10</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>))</div><div class='output co'>#> [1] 1.628174 2.820079</div><div class='input'><span class='co'># Equal entries give ilr transformations with zeros as elements</span> +<span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>3</span>, <span class='fl'>3</span>, <span class='fl'>3</span>))</div><div class='output co'>#> [1] 0 0</div><div class='input'><span class='co'># Almost equal entries give small numbers</span> +<span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>0.3</span>, <span class='fl'>0.4</span>, <span class='fl'>0.3</span>))</div><div class='output co'>#> [1] -0.2034219 0.1174457</div><div class='input'><span class='co'># Only the ratio between the numbers counts, not their sum</span> +<span class='fu'>invilr</span>(<span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>0.7</span>, <span class='fl'>0.29</span>, <span class='fl'>0.01</span>)))</div><div class='output co'>#> [1] 0.70 0.29 0.01</div><div class='input'><span class='fu'>invilr</span>(<span class='fu'>ilr</span>(<span class='fl'>2.1</span> * <span class='fu'>c</span>(<span class='fl'>0.7</span>, <span class='fl'>0.29</span>, <span class='fl'>0.01</span>)))</div><div class='output co'>#> [1] 0.70 0.29 0.01</div><div class='input'><span class='co'># Inverse transformation of larger numbers gives unequal elements</span> +<span class='fu'>invilr</span>(-<span class='fl'>10</span>)</div><div class='output co'>#> [1] 7.213536e-07 9.999993e-01</div><div class='input'><span class='fu'>invilr</span>(<span class='fu'>c</span>(-<span class='fl'>10</span>, <span class='fl'>0</span>))</div><div class='output co'>#> [1] 7.207415e-07 9.991507e-01 8.486044e-04</div><div class='input'><span class='co'># The sum of the elements of the inverse ilr is 1</span> +<span class='fu'>sum</span>(<span class='fu'>invilr</span>(<span class='fu'>c</span>(-<span class='fl'>10</span>, <span class='fl'>0</span>)))</div><div class='output co'>#> [1] 1</div><div class='input'><span class='co'># This is why we do not need all elements of the inverse transformation to go back:</span> <span class='no'>a</span> <span class='kw'><-</span> <span class='fu'>c</span>(<span class='fl'>0.1</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span>) <span class='no'>b</span> <span class='kw'><-</span> <span class='fu'>invilr</span>(<span class='no'>a</span>) -<span class='fu'>length</span>(<span class='no'>b</span>) <span class='co'># Four elements</span></div><div class='output co'>#> [1] 4 -#> </div><div class='input'><span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='fl'>1</span> - <span class='fu'>sum</span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>]))) <span class='co'># Gives c(0.1, 0.3, 0.5)</span></div><div class='output co'>#> [1] 0.1 0.3 0.5 -#> </div></pre> +<span class='fu'>length</span>(<span class='no'>b</span>) <span class='co'># Four elements</span></div><div class='output co'>#> [1] 4</div><div class='input'><span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='fl'>1</span> - <span class='fu'>sum</span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>]))) <span class='co'># Gives c(0.1, 0.3, 0.5)</span></div><div class='output co'>#> [1] 0.1 0.3 0.5</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -156,7 +147,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/index.html b/docs/reference/index.html index 6fcf39c8..23eb608b 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -60,7 +60,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -80,175 +85,180 @@ <h2 id="section-main-functions" class="hasAnchor"><a href="#section-main-functions" class="anchor"></a>Main functions</h2> <p class="section-desc"><p>Essential functionality</p></p> - <p><a href="mkinfit.html"> -</a></p> + + <p><a href="mkinfit.html">Fit a kinetic model to data with one or more state variables</a></p> <ul> <li><code><a href="mkinfit.html">mkinfit</a></code></li> </ul> - <p><a href="mkinmod.html"> -</a></p> + + <p><a href="mkinmod.html">Function to set up a kinetic model with one or more state variables</a></p> <ul> <li><code><a href="mkinmod.html">mkinmod</a></code></li> </ul> - <p><a href="mmkin.html"> -</a></p> + + <p><a href="mmkin.html">Fit one or more kinetic models with one or more state variables to one or more datasets</a></p> <ul> <li><code><a href="mmkin.html">mmkin</a></code></li> </ul> <h2 id="section-show-results" class="hasAnchor"><a href="#section-show-results" class="anchor"></a>Show results</h2> <p class="section-desc"><p>Functions working with mkinfit objects</p></p> - <p><a href="endpoints.html"> -</a></p> + + <p><a href="endpoints.html">Function to calculate endpoints for further use from kinetic models fitted with mkinfit</a></p> <ul> <li><code><a href="endpoints.html">endpoints</a></code></li> </ul> - <p><a href="mkinerrmin.html"> -</a></p> + + <p><a href="mkinerrmin.html">Calculate the minimum error to assume in order to pass the variance test</a></p> <ul> <li><code><a href="mkinerrmin.html">mkinerrmin</a></code></li> </ul> - <p><a href="mkinparplot.html"> -</a></p> + + <p><a href="mkinparplot.html">Function to plot the confidence intervals obtained using + mkinfit</a></p> <ul> <li><code><a href="mkinparplot.html">mkinparplot</a></code></li> </ul> - <p><a href="mkinresplot.html"> -</a></p> + + <p><a href="mkinresplot.html">Function to plot residuals stored in an mkin object</a></p> <ul> <li><code><a href="mkinresplot.html">mkinresplot</a></code></li> </ul> - <p><a href="plot.mkinfit.html"> -</a></p> - <ul> - <li><code><a href="plot.mkinfit.html">plot.mkinfit</a></code></li><li><code><a href="plot.mkinfit.html">plot_sep</a></code></li> - </ul> - <p><a href="summary.mkinfit.html"> -</a></p> - <ul> - <li><code><a href="summary.mkinfit.html">summary.mkinfit</a></code></li><li><code><a href="summary.mkinfit.html">print.summary.mkinfit</a></code></li> - </ul> <h2 id="section-work-with-mmkin-objects" class="hasAnchor"><a href="#section-work-with-mmkin-objects" class="anchor"></a>Work with mmkin objects</h2> <p class="section-desc"><p>Functions working with aggregated results</p></p> + <p><a href="Extract.mmkin.html">Subsetting method for mmkin objects</a></p> <ul> <li><code><a href="Extract.mmkin.html">[.mmkin</a></code></li> </ul> - <p><a href="plot.mmkin.html"> -</a></p> + + <p><a href="plot.mmkin.html">Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object</a></p> <ul> <li><code><a href="plot.mmkin.html">plot.mmkin</a></code></li> </ul> <h2 id="section-datasets-and-known-results" class="hasAnchor"><a href="#section-datasets-and-known-results" class="anchor"></a>Datasets and known results</h2> <p class="section-desc"></p> - <p><a href="FOCUS_2006_DFOP_ref_A_to_B.html"> -</a></p> + + <p><a href="FOCUS_2006_DFOP_ref_A_to_B.html">Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</a></p> <ul> <li><code><a href="FOCUS_2006_DFOP_ref_A_to_B.html">FOCUS_2006_DFOP_ref_A_to_B</a></code></li> </ul> - <p><a href="FOCUS_2006_FOMC_ref_A_to_F.html"> -</a></p> + + <p><a href="FOCUS_2006_FOMC_ref_A_to_F.html">Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)</a></p> <ul> <li><code><a href="FOCUS_2006_FOMC_ref_A_to_F.html">FOCUS_2006_FOMC_ref_A_to_F</a></code></li> </ul> - <p><a href="FOCUS_2006_HS_ref_A_to_F.html"> -</a></p> + + <p><a href="FOCUS_2006_HS_ref_A_to_F.html">Results of fitting the HS model to Datasets A to F of FOCUS (2006)</a></p> <ul> <li><code><a href="FOCUS_2006_HS_ref_A_to_F.html">FOCUS_2006_HS_ref_A_to_F</a></code></li> </ul> - <p><a href="FOCUS_2006_SFO_ref_A_to_F.html"> -</a></p> + + <p><a href="FOCUS_2006_SFO_ref_A_to_F.html">Results of fitting the SFO model to Datasets A to F of FOCUS (2006)</a></p> <ul> <li><code><a href="FOCUS_2006_SFO_ref_A_to_F.html">FOCUS_2006_SFO_ref_A_to_F</a></code></li> </ul> - <p><a href="mccall81_245T.html"> -</a></p> + + <p><a href="mccall81_245T.html">Datasets on aerobic soil metabolism of 2,4,5-T in six soils</a></p> <ul> <li><code><a href="mccall81_245T.html">mccall81_245T</a></code></li> </ul> - <p><a href="schaefer07_complex_case.html"> -</a></p> + + <p><a href="mkinds.html">A dataset class for mkin</a></p> <ul> - <li><code><a href="schaefer07_complex_case.html">schaefer07_complex_case</a></code></li><li><code><a href="schaefer07_complex_case.html">schaefer07_complex_results</a></code></li> + <li><code><a href="mkinds.html">mkinds</a></code></li> </ul> - <p><a href="synthetic_data_for_UBA.html"> -</a></p> + + <p><a href="print.mkinds.html">Print mkinds objects</a></p> + <ul> + <li><code><a href="print.mkinds.html">print.mkinds</a></code></li> + </ul> + + <p><a href="synthetic_data_for_UBA.html">Synthetic datasets for one parent compound with two metabolites</a></p> <ul> <li><code><a href="synthetic_data_for_UBA.html">synthetic_data_for_UBA_2014</a></code></li> </ul> <h2 id="section-helper-functions" class="hasAnchor"><a href="#section-helper-functions" class="anchor"></a>Helper functions</h2> <p class="section-desc"></p> - <p><a href="geometric_mean.html"> Calculate the geometric mean </a></p> + + <p><a href="geometric_mean.html">Calculate the geometric mean</a></p> <ul> <li><code><a href="geometric_mean.html">geometric_mean</a></code></li> </ul> - <p><a href="ilr.html"> -</a></p> + + <p><a href="mkin_long_to_wide.html">Convert a dataframe from long to wide format</a></p> <ul> - <li><code><a href="ilr.html">ilr</a></code></li><li><code><a href="ilr.html">invilr</a></code></li> + <li><code><a href="mkin_long_to_wide.html">mkin_long_to_wide</a></code></li> </ul> - <p><a href="mkin_long_to_wide.html"> -</a></p> + + <p><a href="mkin_wide_to_long.html">Convert a dataframe with observations over time into long format</a></p> <ul> - <li><code><a href="mkin_long_to_wide.html">mkin_long_to_wide</a></code></li> + <li><code><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></code></li> </ul> - <p><a href="mkinpredict.html"> -</a></p> + + <p><a href="mkinpredict.html">Produce predictions from a kinetic model using specific parameters</a></p> <ul> <li><code><a href="mkinpredict.html">mkinpredict</a></code></li> </ul> - <p><a href="mkinsub.html"> -</a></p> + + <p><a href="mkinsub.html">Function to set up a kinetic submodel for one state variable</a></p> <ul> <li><code><a href="mkinsub.html">mkinsub</a></code></li> </ul> - <p><a href="mkin_wide_to_long.html"> -</a></p> - <ul> - <li><code><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></code></li> - </ul> - <p><a href="print.mkinmod.html"> -</a></p> + + <p><a href="print.mkinmod.html">Print mkinmod objects</a></p> <ul> <li><code><a href="print.mkinmod.html">print.mkinmod</a></code></li> </ul> - <p><a href="transform_odeparms.html"> -</a></p> - <ul> - <li><code><a href="transform_odeparms.html">transform_odeparms</a></code></li><li><code><a href="transform_odeparms.html">backtransform_odeparms</a></code></li> - </ul> <h2 id="section-analytical-solutions" class="hasAnchor"><a href="#section-analytical-solutions" class="anchor"></a>Analytical solutions</h2> <p class="section-desc"><p>Parent only model solutions</p></p> - <p><a href="DFOP.solution.html"> -</a></p> + + <p><a href="DFOP.solution.html">Double First-Order in Parallel kinetics</a></p> <ul> <li><code><a href="DFOP.solution.html">DFOP.solution</a></code></li> </ul> - <p><a href="FOMC.solution.html"> First-Order Multi-Compartment kinetics </a></p> + + <p><a href="FOMC.solution.html">First-Order Multi-Compartment kinetics</a></p> <ul> <li><code><a href="FOMC.solution.html">FOMC.solution</a></code></li> </ul> - <p><a href="HS.solution.html"> Hockey-Stick kinetics </a></p> + + <p><a href="HS.solution.html">Hockey-Stick kinetics</a></p> <ul> <li><code><a href="HS.solution.html">HS.solution</a></code></li> </ul> - <p><a href="IORE.solution.html"> Indeterminate order rate equation kinetics </a></p> + + <p><a href="IORE.solution.html">Indeterminate order rate equation kinetics</a></p> <ul> <li><code><a href="IORE.solution.html">IORE.solution</a></code></li> </ul> - <p><a href="SFORB.solution.html"> Single First-Order Reversible Binding kinetics </a></p> + + <p><a href="SFO.solution.html">Single First-Order kinetics</a></p> + <ul> + <li><code><a href="SFO.solution.html">SFO.solution</a></code></li> + </ul> + + <p><a href="SFORB.solution.html">Single First-Order Reversible Binding kinetics</a></p> <ul> <li><code><a href="SFORB.solution.html">SFORB.solution</a></code></li> </ul> + <h2 id="section-generate-synthetic-datasets" class="hasAnchor"><a href="#section-generate-synthetic-datasets" class="anchor"></a>Generate synthetic datasets</h2> + <p class="section-desc"></p> + + + <p><a href="add_err.html">Add normally distributed errors to simulated kinetic degradation data</a></p> + <ul> + <li><code><a href="add_err.html">add_err</a></code></li> + </ul> <h2 id="section-deprecated-functions" class="hasAnchor"><a href="#section-deprecated-functions" class="anchor"></a>Deprecated functions</h2> <p class="section-desc"><p>Functions that have been superseeded</p></p> - <p><a href="mkinplot.html"> -</a></p> + + <p><a href="mkinplot.html">Plot the observed data and the fitted model of an mkinfit object</a></p> <ul> <li><code><a href="mkinplot.html">mkinplot</a></code></li> </ul> @@ -265,6 +275,7 @@ <li><a href="#section-datasets-and-known-results">Datasets and known results</a></li> <li><a href="#section-helper-functions">Helper functions</a></li> <li><a href="#section-analytical-solutions">Analytical solutions</a></li> + <li><a href="#section-generate-synthetic-datasets">Generate synthetic datasets</a></li> <li><a href="#section-deprecated-functions">Deprecated functions</a></li> </ul> </div> @@ -272,7 +283,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 74b9c088..8309a23e 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -105,13 +110,10 @@ <a href = 'http://dx.doi.org/10.1021/jf00103a026'>http://dx.doi.org/10.1021/jf00103a026</a></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"phenol"</span>), <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"anisole"</span>), - <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> <span class='co'>## Not run: ------------------------------------</span> + <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='co'>## Not run: ------------------------------------</span> <span class='co'># fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"))</span> <span class='co'># summary(fit.1, data = FALSE)</span> <span class='co'># </span> @@ -121,9 +123,9 @@ <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 -#> R version: 3.3.1 -#> Date of fit: Wed Oct 26 23:50:40 2016 -#> Date of summary: Wed Oct 26 23:50:40 2016 +#> R version: 3.3.2 +#> Date of fit: Thu Nov 3 17:46:24 2016 +#> Date of summary: Thu Nov 3 17:46:24 2016 #> #> Equations: #> d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -133,7 +135,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.43 s +#> Fitted with method Port using 246 model solutions performed in 1.662 s #> #> Weighting: none #> @@ -213,8 +215,7 @@ #> DT50 DT90 #> T245 15.982 53.091 #> phenol 1.711 5.685 -#> anisole 103.784 344.763 -#> </div></pre> +#> anisole 103.784 344.763</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -232,7 +233,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index cc50bf7d..0385ccbb 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -108,10 +113,7 @@ <p>Dataframe in wide format.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='fu'>mkin_long_to_wide</span>(<span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#> time parent m1 #> 1 0 99.46 0.00 #> 2 0 102.04 0.00 @@ -134,8 +136,7 @@ #> 19 100 NA 31.04 #> 20 100 NA 33.13 #> 21 120 NA 25.15 -#> 22 120 NA 33.31 -#> </div></pre> +#> 22 120 NA 33.31</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -156,7 +157,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index bce6d6a4..965262ce 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -102,10 +107,7 @@ <p>Dataframe in long format as needed for <code>modCost</code>.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>wide</span> <span class='kw'><-</span> <span class='fu'>data.frame</span>(<span class='kw'>t</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>2</span>,<span class='fl'>3</span>), <span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>4</span>,<span class='fl'>7</span>), <span class='kw'>y</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>3</span>,<span class='fl'>4</span>,<span class='fl'>5</span>)) <span class='fu'>mkin_wide_to_long</span>(<span class='no'>wide</span>)</div><div class='output co'>#> name time value #> 1 x 1 1 @@ -113,8 +115,7 @@ #> 3 x 3 7 #> 4 y 1 3 #> 5 y 2 4 -#> 6 y 3 5 -#> </div></pre> +#> 6 y 3 5</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -135,7 +136,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index e5d99fd5..522aab33 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -60,7 +60,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -100,10 +105,7 @@ in order to be compatible with mkinfit</dd> </dl></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>mds</span> <span class='kw'><-</span> <span class='no'>mkinds</span>$<span class='fu'>new</span>(<span class='st'>"FOCUS A"</span>, <span class='no'>FOCUS_2006_A</span>)</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -122,7 +124,7 @@ in order to be compatible with mkinfit</dd> <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 5b437b08..4e1be39c 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -105,7 +110,7 @@ as defined in the FOCUS kinetics report from 2006.</p> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - <p>This function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> + <p>This function is used internally by <code>summary.mkinfit</code>.</p> <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> @@ -116,24 +121,19 @@ as defined in the FOCUS kinetics report from 2006.</p> <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>SFO_SFO</span> <span class='kw'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), - <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> + <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='no'>fit_FOCUS_D</span> <span class='kw'>=</span> <span class='fu'><a href='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>) <span class='fu'>round</span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_D</span>), <span class='fl'>4</span>)</div><div class='output co'>#> err.min n.optim df #> All data 0.0640 4 15 #> parent 0.0646 2 7 -#> m1 0.0469 2 8 -#> </div><div class='input'><span class='no'>fit_FOCUS_E</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_E</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +#> m1 0.0469 2 8</div><div class='input'><span class='no'>fit_FOCUS_E</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_E</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>round</span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_E</span>), <span class='fl'>4</span>)</div><div class='output co'>#> err.min n.optim df #> All data 0.1544 4 13 #> parent 0.1659 2 7 -#> m1 0.1095 2 6 -#> </div></pre> +#> m1 0.1095 2 6</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -154,7 +154,7 @@ as defined in the FOCUS kinetics report from 2006.</p> <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 6bfb9352..867fb9ff 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -251,7 +256,7 @@ to do transformations. If TRUE, the g parameter of the DFOP and HS models are also transformed, as they can also be seen as compositional data. The transformation used for these transformations is the - <code><a href='ilr.html'>ilr</a></code> transformation. + <code>ilr</code> transformation. </dd> <dt>plot</dt> <dd> @@ -327,11 +332,11 @@ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>A list with "mkinfit" and "modFit" in the class attribute. - A summary can be obtained by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> + A summary can be obtained by <code>summary.mkinfit</code>.</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <p>Plotting methods <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and + <p>Plotting methods <code>plot.mkinfit</code> and <code><a href='mkinparplot.html'>mkinparplot</a></code>.</p> <p>Fitting of several models to several datasets in a single call to <code><a href='mmkin.html'>mmkin</a></code>.</p> @@ -351,23 +356,20 @@ internal rate transformation.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># Use shorthand notation for parent only degradation</span> <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 -#> R version: 3.3.1 -#> Date of fit: Wed Oct 26 23:50:42 2016 -#> Date of summary: Wed Oct 26 23:50:42 2016 +#> R version: 3.3.2 +#> Date of fit: Thu Nov 3 17:46:27 2016 +#> Date of summary: Thu Nov 3 17:46:27 2016 #> #> Equations: #> d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.168 s +#> Fitted with method Port using 64 model solutions performed in 0.147 s #> #> Weighting: none #> @@ -428,19 +430,16 @@ #> 28 parent 6.6 4.754 1.8460 #> 63 parent 4.0 2.102 1.8977 #> 91 parent 3.9 1.441 2.4590 -#> 119 parent 0.6 1.092 -0.4919 -#> </div><div class='input'> +#> 119 parent 0.6 1.092 -0.4919</div><div class='input'> <span class='co'># One parent compound, one metabolite, both single first order.</span> <span class='co'># Use mkinsub for convenience in model formulation. Pathway to sink included per default.</span> <span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='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='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#> user system elapsed -#> 1.272 1.204 0.943 -#> </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink -#> 99.59848 -3.03822 -2.98030 -5.24750 -#> </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff +#> 1.204 1.244 0.932 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -451,7 +450,6 @@ #> DT50 DT90 #> parent 7.022929 23.32967 #> m1 131.760712 437.69961 -#> #> </div><div class='input'><span class='co'>## Not run: ------------------------------------</span> <span class='co'># # deSolve is slower when no C compiler (gcc) was available during model generation</span> <span class='co'># print(system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D, </span> @@ -535,7 +533,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 40381656..bdfd0e09 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -153,17 +158,14 @@ Media</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span> <span class='no'>SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)) <span class='co'># One parent compound, one metabolite, both single first order</span> <span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='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='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='co'>## Not run: ------------------------------------</span> <span class='co'># # The above model used to be specified like this, before the advent of mkinsub()</span> <span class='co'># SFO_SFO <- mkinmod(</span> @@ -210,7 +212,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index dff30930..f8151c16 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -97,14 +102,11 @@ <p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>model</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"phenol"</span>), <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>), <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"anisole"</span>)), - <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>mkinparplot</span>(<span class='no'>fit</span>)</div><img src='mkinparplot-4.png' alt='' width='540' height='400' /></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -126,7 +128,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index d3f0c1f6..9ed92dd0 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -78,7 +83,7 @@ </div> - <p>Deprecated function. It now only calls the plot method <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p> + <p>Deprecated function. It now only calls the plot method <code>plot.mkinfit</code>.</p> <pre><span class='fu'>mkinplot</span>(<span class='no'>fit</span>, <span class='no'>...</span>)</pre> @@ -91,7 +96,7 @@ </dd> <dt>&#8230;</dt> <dd> - further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>. + further arguments passed to <code>plot.mkinfit</code>. </dd> </dl> @@ -118,7 +123,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 31556527..57bb747c 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -154,10 +159,7 @@ <p>A matrix in the same format as the output of <code>ode</code>.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='no'>SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)) <span class='co'># Compare solution types</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, @@ -182,8 +184,7 @@ #> 18 17 0.6096747 #> 19 18 0.4516581 #> 20 19 0.3345965 -#> 21 20 0.2478752 -#> </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, +#> 21 20 0.2478752</div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)</div><div class='output co'>#> time degradinol #> 1 0 100.0000000 #> 2 1 74.0818221 @@ -205,8 +206,7 @@ #> 18 17 0.6096747 #> 19 18 0.4516581 #> 20 19 0.3345965 -#> 21 20 0.2478752 -#> </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, +#> 21 20 0.2478752</div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> time degradinol #> 1 0 100.0000000 #> 2 1 74.0818221 @@ -228,8 +228,7 @@ #> 18 17 0.6096747 #> 19 18 0.4516581 #> 20 19 0.3345965 -#> 21 20 0.2478752 -#> </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, +#> 21 20 0.2478752</div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)</div><div class='output co'>#> time degradinol #> 1 0 100.0000000 #> 2 1 74.0818221 @@ -251,57 +250,44 @@ #> 18 17 0.6096747 #> 19 18 0.4516581 #> 20 19 0.3345965 -#> 21 20 0.2478752 -#> </div><div class='input'> +#> 21 20 0.2478752</div><div class='input'> <span class='co'># Compare integration methods to analytical solution</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#> time degradinol -#> 21 20 0.2478752 -#> </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, +#> 21 20 0.2478752</div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#> time degradinol -#> 21 20 0.2478752 -#> </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, +#> 21 20 0.2478752</div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"ode45"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#> time degradinol -#> 21 20 0.2478752 -#> </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, +#> 21 20 0.2478752</div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"rk4"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#> time degradinol -#> 21 20 0.2480043 -#> </div><div class='input'> <span class='co'># rk4 is not as precise here</span> +#> 21 20 0.2480043</div><div class='input'> <span class='co'># rk4 is not as precise here</span> <span class='co'># The number of output times used to make a lot of difference until the</span> <span class='co'># default for atol was adjusted</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>))[<span class='fl'>201</span>,]</div><div class='output co'>#> time degradinol -#> 201 20 0.2478752 -#> </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), +#> 201 20 0.2478752</div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.01</span>))[<span class='fl'>2001</span>,]</div><div class='output co'>#> time degradinol -#> 2001 20 0.2478752 -#> </div><div class='input'> +#> 2001 20 0.2478752</div><div class='input'> <span class='co'># Check compiled model versions - they are faster than the eigenvalue based solutions!</span> <span class='no'>SFO_SFO</span> <span class='kw'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> <span class='fu'>system.time</span>( + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 -#> 201 20 4.978707 27.46227 -#> </div><div class='output co'>#> user system elapsed -#> 0.028 0.004 0.004 -#> </div><div class='input'> <span class='fu'>system.time</span>( +#> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed +#> 0.004 0.024 0.004 </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 -#> 201 20 4.978707 27.46227 -#> </div><div class='output co'>#> user system elapsed -#> 0.016 0.004 0.002 -#> </div><div class='input'> <span class='fu'>system.time</span>( +#> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed +#> 0.004 0.016 0.003 </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 -#> 201 20 4.978707 27.46227 -#> </div><div class='output co'>#> user system elapsed -#> 0.052 0.000 0.052 -#> </div></pre> +#> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed +#> 0.036 0.000 0.033 </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -322,7 +308,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index d8c84191..53c4f62f 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -80,7 +85,7 @@ <p>This function plots the residuals for the specified subset of the observed variables from an mkinfit object. A combined plot of the fitted - model and the residuals can be obtained using <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> + model and the residuals can be obtained using <code>plot.mkinfit</code> using the argument <code>show_residuals = TRUE</code>.</p> @@ -142,11 +147,8 @@ mkinfit object.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> - <pre class="examples"><div class='input'><span class='no'>model</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='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='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='no'>model</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='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='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>mkinresplot</span>(<span class='no'>fit</span>, <span class='st'>"m1"</span>)</div><img src='mkinresplot-4.png' alt='' width='540' height='400' /></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -170,7 +172,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index 89387468..86374e4b 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -115,22 +120,19 @@ <p>A list for use with <code><a href='mkinmod.html'>mkinmod</a></code>.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># One parent compound, one metabolite, both single first order.</span> <span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='co'># The same model using mkinsub</span> <span class='no'>SFO_SFO.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='co'># Now supplying full names</span> <span class='no'>SFO_SFO.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Test compound"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div></pre> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -151,7 +153,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index a6e74b8a..21461986 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -124,10 +129,7 @@ <p><code><a href='[.mmkin.html'>[.mmkin</a></code> for subsetting, <code><a href='plot.mmkin.html'>plot.mmkin</a></code> for plotting.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'>## Not run: ------------------------------------</span> <span class='co'># m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),</span> <span class='co'># M1 = mkinsub("SFO", "M2"),</span> @@ -182,7 +184,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 4eb7369a..61a597e7 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -199,14 +204,11 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … <p>The function is called for its side effect.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># One parent compound, one metabolite, both single first order, path from</span> <span class='co'># parent to sink included, use Levenberg-Marquardt for speed</span> <span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, <span class='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Parent"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</span> ))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='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>, <span class='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>) + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</span> ))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='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>, <span class='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>) <span class='fu'>plot</span>(<span class='no'>fit</span>)</div><img src='plot.mkinfit-4.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='plot.mkinfit-6.png' alt='' width='540' height='400' /><div class='input'> <span class='co'># Show the observed variables separately</span> <span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><img src='plot.mkinfit-8.png' alt='' width='540' height='400' /><div class='input'> @@ -235,7 +237,7 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index e0a20f3d..b107ca70 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -119,7 +124,7 @@ </dd> <dt>&#8230;</dt> <dd> - Further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and <code><a href='mkinresplot.html'>mkinresplot</a></code>. + Further arguments passed to <code>plot.mkinfit</code> and <code><a href='mkinresplot.html'>mkinresplot</a></code>. </dd> </dl> @@ -128,10 +133,7 @@ <p>The function is called for its side effect.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='co'># Only use one core not to offend CRAN checks, use Levenberg-Marquardt for speed</span> <span class='no'>fits</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'>c</span>(<span class='st'>"FOMC"</span>, <span class='st'>"HS"</span>), <span class='fu'>list</span>(<span class='st'>"FOCUS B"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='st'>"FOCUS C"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>), <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>) @@ -160,7 +162,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index a586a103..9bd088b1 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -109,7 +114,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index 73bfd60e..11b96036 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -109,7 +114,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 4714747a..526dde10 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -106,17 +111,14 @@ Symposium Pesticide Chemistry, Piacenza, 2007, p. 916-923.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>data</span> <span class='kw'><-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span>(<span class='no'>schaefer07_complex_case</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>) <span class='no'>model</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"A1"</span>, <span class='st'>"B1"</span>, <span class='st'>"C1"</span>), <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>), <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A2"</span>), <span class='kw'>B1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>C1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), - <span class='kw'>A2</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='co'>## Not run: mkinfit(model, data, plot=TRUE)</span></div></pre> + <span class='kw'>A2</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'>## Not run: mkinfit(model, data, plot=TRUE)</span></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -134,7 +136,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index b88a5469..46d078bf 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -136,21 +141,18 @@ <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version: 0.9.44.9000 -#> R version: 3.3.1 -#> Date of fit: Wed Oct 26 23:50:50 2016 -#> Date of summary: Wed Oct 26 23:50:50 2016 +#> R version: 3.3.2 +#> Date of fit: Thu Nov 3 17:46:35 2016 +#> Date of summary: Thu Nov 3 17:46:35 2016 #> #> Equations: #> d_parent = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.083 s +#> Fitted with method Port using 35 model solutions performed in 0.08 s #> #> Weighting: none #> @@ -209,8 +211,7 @@ #> 30 parent 29.71 35.738 -6.0283 #> 62 parent 5.98 10.862 -4.8818 #> 90 parent 1.54 3.831 -2.2911 -#> 118 parent 0.39 1.351 -0.9613 -#> </div></pre> +#> 118 parent 0.39 1.351 -0.9613</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -233,7 +234,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index 45d5f53a..a46a5781 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -117,10 +122,7 @@ measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'>## Not run: ------------------------------------</span> <span class='co'># m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),</span> <span class='co'># M1 = list(type = "SFO", to = "M2"),</span> @@ -160,7 +162,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index ab5ce062..ccd56ca4 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -61,7 +61,12 @@ </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> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -83,7 +88,7 @@ constants and other paramters that can only take on positive values, a simple log transformation is used. For compositional parameters, such as the formations fractions that should always sum up to 1 and can not be - negative, the <code><a href='ilr.html'>ilr</a></code> transformation is used.</p> + negative, the <code>ilr</code> transformation is used.</p> <p>The transformation of sets of formation fractions is fragile, as it supposes the same ordering of the components in forward and backward transformation. @@ -109,7 +114,7 @@ <dd> The kinetic model of class <code><a href='mkinmod.html'>mkinmod</a></code>, containing the names of the model variables that are needed for grouping the formation fractions - before <code><a href='ilr.html'>ilr</a></code> transformation, the parameter names and + before <code>ilr</code> transformation, the parameter names and the information if the pathway to sink is included in the model. </dd> <dt>transform_rates</dt> @@ -128,7 +133,7 @@ assumption of normal distribution of the estimator. The default (TRUE) is to do transformations. The g parameter of the DFOP and HS models are also transformed, as they can also be seen as compositional data. The - transformation used for these transformations is the <code><a href='ilr.html'>ilr</a></code> + transformation used for these transformations is the <code>ilr</code> transformation. </dd> </dl> @@ -139,18 +144,15 @@ as the original parameters.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='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>) <span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#> mkin version: 0.9.44.9000 -#> R version: 3.3.1 -#> Date of fit: Wed Oct 26 23:50:51 2016 -#> Date of summary: Wed Oct 26 23:50:51 2016 +#> R version: 3.3.2 +#> Date of fit: Thu Nov 3 17:46:36 2016 +#> Date of summary: Thu Nov 3 17:46:36 2016 #> #> Equations: #> d_parent = - k_parent_sink * parent - k_parent_m1 * parent @@ -158,7 +160,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.629 s +#> Fitted with method Port using 153 model solutions performed in 0.657 s #> #> Weighting: none #> @@ -221,8 +223,7 @@ #> Estimated disappearance times: #> DT50 DT90 #> parent 7.023 23.33 -#> m1 131.761 437.70 -#> </div><div class='input'> +#> m1 131.761 437.70</div><div class='input'> <span class='co'>## Not run: ------------------------------------</span> <span class='co'># fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE)</span> <span class='co'># summary(fit.2, data=FALSE) </span> @@ -233,10 +234,8 @@ <span class='no'>transformed</span> <span class='kw'><-</span> <span class='no'>fit</span>$<span class='no'>start_transformed</span>$<span class='no'>value</span> <span class='fu'>names</span>(<span class='no'>transformed</span>) <span class='kw'><-</span> <span class='fu'>rownames</span>(<span class='no'>fit</span>$<span class='no'>start_transformed</span>) <span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink -#> 100.750000 -2.302585 -2.301586 -2.300587 -#> </div><div class='input'><span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#> parent_0 k_parent_sink k_parent_m1 k_m1_sink -#> 100.7500 0.1000 0.1001 0.1002 -#> </div><div class='input'> +#> 100.750000 -2.302585 -2.301586 -2.300587 </div><div class='input'><span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#> parent_0 k_parent_sink k_parent_m1 k_m1_sink +#> 100.7500 0.1000 0.1001 0.1002 </div><div class='input'> <span class='co'>## Not run: ------------------------------------</span> <span class='co'># # The case of formation fractions</span> <span class='co'># SFO_SFO.ff <- mkinmod(</span> @@ -280,7 +279,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> @@ -0,0 +1,33 @@ +library(pkgdown) + +debug(pkgdown:::as_pkgdown) +debug(pkgdown:::topic_index) +debug(pkgdown:::package_rd) # creates rd object (list of Rd file representations) + + +undebug(pkgdown:::rd_file) # creates rd file representations + +build_reference_index(".") + +extract_tag(rd[[1]], "tag_title") # gives "\n" +extract_tag(rd[[4]], "tag_title") # gives the title + +library(magrittr) +library(stringr) +extract_tag_local <- function(x, tag) { + x %>% + purrr::keep(inherits, tag) %>% + unlist %>% + paste(collapse = "") %>% + str_trim +} + +extract_tag_local(rd[[1]], "tag_title") +extract_tag_local(rd[[4]], "tag_title") + + +titles <- purrr::map_chr(rd, extract_tag, "tag_title") + +titles <- purrr::map_chr(rd, extract_tag_local, "tag_title") + +rd[[2]] |
