diff options
94 files changed, 111 insertions, 409 deletions
diff --git a/.Rbuildignore b/.Rbuildignore index 359e5879..5125a068 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -6,7 +6,6 @@ ^README.html$ ^mkin.Rcheck ^inst/web/* -^docs/* ^vignettes/.build.timestamp$ ^vignettes/*_cache$ ^vignettes/*cache$ @@ -24,5 +23,6 @@ ^vignettes/figure ^vignettes/FOCUS_Z.tex$ ^vignettes/mkin.tex$ -^_pkgdown.yml$ ^mkin_.*\.tar\.gz +^docs$ +^_pkgdown\.yml$ @@ -1,6 +1,8 @@ docs/articles/*_cache/ +docs/articles/*.R install.log mkin*.tar.gz +mkin.tar mkin.Rcheck test.R vignettes/.build.timestamp diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index af04f755..d85246f8 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -9,10 +9,7 @@ <!-- 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"> <!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Example evaluation of FOCUS Example Dataset D"> -<meta property="og:description" content=""> -<meta name="twitter:card" content="summary"> -<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/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]--> @@ -80,7 +77,7 @@ <h1>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-01</h4> + <h4 class="date">2018-03-09</h4> </div> @@ -155,8 +152,8 @@ <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(fit)</code></pre></div> <pre><code>## mkin version: 0.9.46.3 ## R version: 3.4.3 -## Date of fit: Thu Mar 1 14:17:55 2018 -## Date of summary: Thu Mar 1 14:17:55 2018 +## Date of fit: Fri Mar 9 23:09:48 2018 +## Date of summary: Fri Mar 9 23:09:48 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -164,7 +161,7 @@ ## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 0.993 s +## Fitted with method Port using 153 model solutions performed in 0.99 s ## ## Weighting: none ## diff --git a/docs/articles/FOCUS_D_files/figure-html/plot-1.png b/docs/articles/FOCUS_D_files/figure-html/plot-1.png Binary files differindex b4fa2ff4..c0fab72d 100644 --- a/docs/articles/FOCUS_D_files/figure-html/plot-1.png +++ b/docs/articles/FOCUS_D_files/figure-html/plot-1.png diff --git a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png Binary files differindex ba06ce31..47916477 100644 --- a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png +++ b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 5de06ad5..196a0c4f 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -9,10 +9,7 @@ <!-- 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"> <!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Example evaluation of FOCUS Laboratory Data L1 to L3"> -<meta property="og:description" content=""> -<meta name="twitter:card" content="summary"> -<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/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]--> @@ -80,7 +77,7 @@ <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-01</h4> + <h4 class="date">2018-03-09</h4> </div> @@ -103,15 +100,15 @@ FOCUS_<span class="dv">2006</span>_L1_mkin <-<span class="st"> </span><span c <span class="kw">summary</span>(m.L1.SFO)</code></pre></div> <pre><code>## mkin version: 0.9.46.3 ## R version: 3.4.3 -## Date of fit: Thu Mar 1 14:31:57 2018 -## Date of summary: Thu Mar 1 14:31:57 2018 +## Date of fit: Fri Mar 9 23:09:50 2018 +## Date of summary: Fri Mar 9 23:09:50 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.24 s +## Fitted with method Port using 37 model solutions performed in 0.264 s ## ## Weighting: none ## @@ -194,15 +191,15 @@ FOCUS_<span class="dv">2006</span>_L1_mkin <-<span class="st"> </span><span c <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: 0.9.46.3 ## R version: 3.4.3 -## Date of fit: Thu Mar 1 14:31:59 2018 -## Date of summary: Thu Mar 1 14:32:00 2018 +## Date of fit: Fri Mar 9 23:09:52 2018 +## Date of summary: Fri Mar 9 23:09:52 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 611 model solutions performed in 1.375 s +## Fitted with method Port using 611 model solutions performed in 1.451 s ## ## Weighting: none ## @@ -289,15 +286,15 @@ FOCUS_<span class="dv">2006</span>_L2_mkin <-<span class="st"> </span><span c <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: 0.9.46.3 ## R version: 3.4.3 -## Date of fit: Thu Mar 1 14:32:00 2018 -## Date of summary: Thu Mar 1 14:32:00 2018 +## Date of fit: Fri Mar 9 23:09:53 2018 +## Date of summary: Fri Mar 9 23:09:53 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 81 model solutions performed in 0.158 s +## Fitted with method Port using 81 model solutions performed in 0.175 s ## ## Weighting: none ## @@ -360,8 +357,8 @@ FOCUS_<span class="dv">2006</span>_L2_mkin <-<span class="st"> </span><span c <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: 0.9.46.3 ## R version: 3.4.3 -## Date of fit: Thu Mar 1 14:32:01 2018 -## Date of summary: Thu Mar 1 14:32:01 2018 +## Date of fit: Fri Mar 9 23:09:54 2018 +## Date of summary: Fri Mar 9 23:09:54 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -370,7 +367,7 @@ FOCUS_<span class="dv">2006</span>_L2_mkin <-<span class="st"> </span><span c ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.708 s +## Fitted with method Port using 336 model solutions performed in 0.739 s ## ## Weighting: none ## @@ -452,8 +449,8 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <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: 0.9.46.3 ## R version: 3.4.3 -## Date of fit: Thu Mar 1 14:32:02 2018 -## Date of summary: Thu Mar 1 14:32:02 2018 +## Date of fit: Fri Mar 9 23:09:55 2018 +## Date of summary: Fri Mar 9 23:09:55 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -462,7 +459,7 @@ 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 0.287 s +## Fitted with method Port using 137 model solutions performed in 0.293 s ## ## Weighting: none ## @@ -553,15 +550,15 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <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: 0.9.46.3 ## R version: 3.4.3 -## Date of fit: Thu Mar 1 14:32:03 2018 -## Date of summary: Thu Mar 1 14:32:03 2018 +## Date of fit: Fri Mar 9 23:09:55 2018 +## Date of summary: Fri Mar 9 23:09:56 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.089 s +## Fitted with method Port using 46 model solutions performed in 0.09 s ## ## Weighting: none ## @@ -613,8 +610,8 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <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>## 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src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/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]--> @@ -80,7 +77,7 @@ <h1>Example evaluation of FOCUS dataset Z</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-01</h4> + <h4 class="date">2018-03-09</h4> </div> diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png Binary files differindex b66289d9..cb32b3c6 100644 --- a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png +++ 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src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Performance benefit by using compiled model definitions in mkin"> -<meta property="og:description" content=""> -<meta name="twitter:card" content="summary"> -<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/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]--> @@ -80,7 +77,7 @@ <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-01</h4> + <h4 class="date">2018-03-09</h4> </div> @@ -101,7 +98,7 @@ SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mki <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <p>We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the benchmark package.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="cf">if</span> (<span class="kw">require</span>(rbenchmark)) { - b<span class="fl">.1</span> <-<span class="st"> </span><span class="kw">benchmark</span>( + b<span class="fl">.1</span> <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></span>( <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">solution_type =</span> <span class="st">"deSolve"</span>, <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>), @@ -117,10 +114,15 @@ SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mki <span class="kw">print</span>(<span class="st">"R package benchmark is not available"</span>) }</code></pre></div> <pre><code>## Lade nötiges Paket: rbenchmark</code></pre> -<pre><code>## Warning in library(package, lib.loc = lib.loc, character.only = TRUE, -## logical.return = TRUE, : es gibt kein Paket namens 'rbenchmark'</code></pre> -<pre><code>## [1] "R package benchmark is not available"</code></pre> -<p>We see that using the compiled model is by a factor of around NA 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> +<pre><code>## test replications elapsed relative user.self sys.self +## 3 deSolve, compiled 3 2.044 1.000 2.042 0 +## 1 deSolve, not compiled 3 14.198 6.946 14.185 0 +## 2 Eigenvalue based 3 2.751 1.346 2.747 0 +## user.child sys.child +## 3 0 0 +## 1 0 0 +## 2 0 0</code></pre> +<p>We see that using the compiled model is by a factor of around 7 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> <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2"> <h2 class="hasAnchor"> @@ -131,7 +133,7 @@ SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mki <span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>), <span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>( <span class="st">"SFO"</span>)) - b<span class="fl">.2</span> <-<span class="st"> </span><span class="kw">benchmark</span>( + b<span class="fl">.2</span> <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></span>( <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>), <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>), @@ -142,11 +144,14 @@ SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mki factor_FOMC_SFO <-<span class="st"> </span><span class="ot">NA</span> <span class="kw">print</span>(<span class="st">"R package benchmark is not available"</span>) }</code></pre></div> -<pre><code>## Lade nötiges Paket: rbenchmark</code></pre> -<pre><code>## Warning in library(package, lib.loc = lib.loc, character.only = TRUE, -## logical.return = TRUE, : es gibt kein Paket namens 'rbenchmark'</code></pre> -<pre><code>## [1] "R package benchmark is not available"</code></pre> -<p>Here we get a performance benefit of a factor of NA using the version of the differential equation model compiled from C code!</p> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> +<pre><code>## test replications elapsed relative user.self sys.self +## 2 deSolve, compiled 3 3.695 1.000 3.692 0 +## 1 deSolve, not compiled 3 31.143 8.428 31.114 0 +## user.child sys.child +## 2 0 0 +## 1 0 0</code></pre> +<p>Here we get a performance benefit of a factor of 8 using the version of the differential equation model compiled from C code!</p> <p>This vignette was built with mkin 0.9.46.3 on</p> <pre><code>## R version 3.4.3 (2017-11-30) ## Platform: x86_64-pc-linux-gnu (64-bit) diff --git a/docs/articles/index.html b/docs/articles/index.html index 2b16580a..c0c5864b 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -27,7 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Articles" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index a91da0a4..f668b500 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -9,10 +9,7 @@ <!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" 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src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Introduction to mkin"> -<meta property="og:description" content=""> -<meta name="twitter:card" content="summary"> -<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/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]--> @@ -80,7 +77,7 @@ <h1>Introduction to mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-01</h4> + <h4 class="date">2018-03-09</h4> </div> 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 5a3e3b6c..fafe8afd 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/articles/twa.html b/docs/articles/twa.html index 400b1383..e5b68cfe 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -9,10 +9,7 @@ <!-- 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" 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src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/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]--> @@ -80,7 +77,7 @@ <h1>Calculation of time weighted average concentrations with mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-01</h4> + <h4 class="date">2018-03-09</h4> </div> diff --git a/docs/authors.html b/docs/authors.html index 7abb53de..af022eab 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -27,7 +27,6 @@ <script src="pkgdown.js"></script> -<meta property="og:title" content="Authors" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -107,19 +106,19 @@ <ul class="list-unstyled"> <li> - <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder. <a href='https://orcid.org/0000-0003-4371-6538' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid'></a> - </p> + <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder. + <br /><small>0000-0003-4371-6538</small></p> </li> <li> - <p><strong>Katrin Lindenberger</strong>. Contributor. + <p><strong>Katrin Lindenberger</strong>. Contributor. </p> </li> <li> - <p><strong>René Lehmann</strong>. Contributor. + <p><strong>René Lehmann</strong>. Contributor. </p> </li> <li> - <p><strong>Eurofins Regulatory AG</strong>. Copyright holder. + <p><strong>Eurofins Regulatory AG</strong>. Copyright holder. </p> </li> </ul> diff --git a/docs/index.html b/docs/index.html index c20d124b..88fd4f6d 100644 --- a/docs/index.html +++ b/docs/index.html @@ -9,17 +9,7 @@ <!-- 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"> <!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"> -<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><meta property="og:title" content="Kinetic Evaluation of Chemical Degradation Data"> -<meta property="og:description" content="Calculation routines based on the FOCUS Kinetics Report (2006, - 2014). Includes a function for conveniently defining differential equation - models, model solution based on eigenvalues if possible or using numerical - solvers and a choice of the optimisation methods made available by the 'FME' - package. If a C compiler (on windows: 'Rtools') is installed, differential - equation models are solved using compiled C functions. Please note that no - warranty is implied for correctness of results or fitness for a particular - purpose."> -<meta name="twitter:card" content="summary"> -<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/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]--> @@ -102,7 +92,7 @@ <div id="usage" class="section level2"> <h2 class="hasAnchor"> <a href="#usage" class="anchor"></a>Usage</h2> -<p>For a start, have a look a the code examples provided for <a href="http://kinfit.r-forge.r-project.org/mkin_static/reference/plot.mkinfit.html"><code>plot.mkinfit</code></a> and <a href="http://kinfit.r-forge.r-project.org/mkin_static/reference/plot.mmkin.html"><code>plot.mmkin</code></a>, and at the package vignettes <a href="http://kinfit.r-forge.r-project.org/mkin_static/articles/FOCUS_L.html"><code>FOCUS L</code></a> and <a href="http://kinfit.r-forge.r-project.org/mkin_static/articles/FOCUS_D.html"><code>FOCUS D</code></a>.</p> +<p>For a start, have a look a the code examples provided for <a href="https://pkgdown.jrwb.de/mkin/reference/plot.mkinfit.html"><code>plot.mkinfit</code></a> and <a href="https://pkgdown.jrwb.de/mkin/reference/plot.mmkin.html"><code>plot.mmkin</code></a>, and at the package vignettes <a href="https://pkgdown.jrwb.de/mkin/articles/FOCUS_L.html"><code>FOCUS L</code></a> and <a href="https://pkgdown.jrwb.de/mkin/articles/FOCUS_D.html"><code>FOCUS D</code></a>.</p> </div> <div id="documentation" class="section level2"> <h2 class="hasAnchor"> @@ -113,17 +103,17 @@ <h2 class="hasAnchor"> <a href="#features" class="anchor"></a>Features</h2> <ul> -<li>Highly flexible model specification using <a href="http://kinfit.r-forge.r-project.org/mkin_static/reference/mkinmod.html"><code>mkinmod</code></a>, including equilibrium reactions and using the single first-order reversible binding (SFORB) model, which will automatically create two latent state variables for the observed variable.</li> -<li>As of version 0.9-39, fitting of several models to several datasets, optionally in parallel, is supported, see for example <a href="http://kinfit.r-forge.r-project.org/mkin_static/reference/plot.mmkin.html"><code>plot.mmkin</code></a>.</li> -<li>Model solution (forward modelling) in the function <a href="http://kinfit.r-forge.r-project.org/mkin_static/reference/mkinpredict.html"><code>mkinpredict</code></a> is performed either using the analytical solution for the case of parent only degradation, an eigenvalue based solution if only simple first-order (SFO) or SFORB kinetics are used in the model, or using a numeric solver from the <code>deSolve</code> package (default is <code>lsoda</code>).</li> -<li>If a C compiler is installed, the kinetic models are compiled from automatically generated C code, see <a href="http://kinfit.r-forge.r-project.org/mkin_static/articles/compiled_models.html">vignette <code>compiled_models</code></a>. The autogeneration of C code was inspired by the <a href="https://github.com/karlines/ccSolve"><code>ccSolve</code></a> package. Thanks to Karline Soetaert for her work on that.</li> -<li>By default, kinetic rate constants and kinetic formation fractions are transformed internally using <a href="http://kinfit.r-forge.r-project.org/mkin_static/reference/transform_odeparms.html"><code>transform_odeparms</code></a> so their estimators can more reasonably be expected to follow a normal distribution. This has the side effect that no constraints are needed in the optimisation. Thanks to René Lehmann for the nice cooperation on this, especially the isometric logration transformation that is now used for the formation fractions.</li> +<li>Highly flexible model specification using <a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html"><code>mkinmod</code></a>, including equilibrium reactions and using the single first-order reversible binding (SFORB) model, which will automatically create two latent state variables for the observed variable.</li> +<li>As of version 0.9-39, fitting of several models to several datasets, optionally in parallel, is supported, see for example <a href="https://pkgdown.jrwb.de/mkin/reference/plot.mmkin.html"><code>plot.mmkin</code></a>.</li> +<li>Model solution (forward modelling) in the function <a href="https://pkgdown.jrwb.de/mkin/reference/mkinpredict.html"><code>mkinpredict</code></a> is performed either using the analytical solution for the case of parent only degradation, an eigenvalue based solution if only simple first-order (SFO) or SFORB kinetics are used in the model, or using a numeric solver from the <code>deSolve</code> package (default is <code>lsoda</code>).</li> +<li>If a C compiler is installed, the kinetic models are compiled from automatically generated C code, see <a href="https://pkgdown.jrwb.de/mkin/articles/compiled_models.html">vignette <code>compiled_models</code></a>. The autogeneration of C code was inspired by the <a href="https://github.com/karlines/ccSolve"><code>ccSolve</code></a> package. Thanks to Karline Soetaert for her work on that.</li> +<li>By default, kinetic rate constants and kinetic formation fractions are transformed internally using <a href="https://pkgdown.jrwb.de/mkin/reference/transform_odeparms.html"><code>transform_odeparms</code></a> so their estimators can more reasonably be expected to follow a normal distribution. This has the side effect that no constraints are needed in the optimisation. Thanks to René Lehmann for the nice cooperation on this, especially the isometric logration transformation that is now used for the formation fractions.</li> <li>A side effect of this is that when parameter estimates are backtransformed to match the model definition, confidence intervals calculated from standard errors are also backtransformed to the correct scale, and will not include meaningless values like negative rate constants or formation fractions adding up to more than 1, which can not occur in a single experiment with a single defined radiolabel position.</li> <li>The usual one-sided t-test for significant difference from zero is nevertheless shown based on estimators for the untransformed parameters.</li> <li>Summary and plotting functions. The <code>summary</code> of an <code>mkinfit</code> object is in fact a full report that should give enough information to be able to approximately reproduce the fit with other tools.</li> <li>The chi-squared error level as defined in the FOCUS kinetics guidance (see below) is calculated for each observed variable.</li> <li>Iteratively reweighted least squares fitting is implemented in a similar way as in KinGUII and CAKE (see below). Simply add the argument <code>reweight.method = "obs"</code> to your call to <code>mkinfit</code> and a separate variance componenent for each of the observed variables will be optimised in a second stage after the primary optimisation algorithm has converged.</li> -<li>Iterative reweighting is also possible using the two-component error model for analytical data of <a href="http://kinfit.r-forge.r-project.org/mkin_static/reference/sigma_rl.html">Rocke and Lorenzato</a> using the argument <code>reweight.method = "tc"</code>.</li> +<li>Iterative reweighting is also possible using the two-component error model for analytical data of <a href="https://pkgdown.jrwb.de/mkin/reference/sigma_rl.html">Rocke and Lorenzato</a> using the argument <code>reweight.method = "tc"</code>.</li> <li>When a metabolite decline phase is not described well by SFO kinetics, SFORB kinetics can be used for the metabolite.</li> </ul> </div> @@ -169,7 +159,8 @@ <p>GPL</p> <h2>Developers</h2> <ul class="list-unstyled"> -<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> <a href="https://orcid.org/0000-0003-4371-6538" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid"></a> </li> +<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> <br><small>(0000-0003-4371-6538)</small> +</li> <li><a href="authors.html">All authors...</a></li> </ul> <h2>Dev status</h2> diff --git a/docs/news/index.html b/docs/news/index.html index dfb70875..39b21d12 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -27,7 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="All news" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/pkgdown.css b/docs/pkgdown.css index 181fe639..59b659f2 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -100,11 +100,6 @@ a.anchor { margin-bottom: 0.5em; } -.orcid { - height: 16px; - vertical-align: middle; -} - /* Reference index & topics ----------------------------------------------- */ .ref-index th {font-weight: normal;} @@ -142,12 +137,6 @@ pre, code { color: #333; } -pre code { - overflow: auto; - word-wrap: normal; - white-space: pre; -} - pre .img { margin: 5px 0; } @@ -162,10 +151,6 @@ code a, pre a { color: #375f84; } -a.sourceLine:hover { - text-decoration: none; -} - .fl {color: #1514b5;} .fu {color: #000000;} /* function */ .ch,.st {color: #036a07;} /* string */ diff --git a/docs/reference/DFOP.solution-1.png b/docs/reference/DFOP.solution-1.png Binary files differindex 1549a73b..e9268f94 100644 --- a/docs/reference/DFOP.solution-1.png +++ b/docs/reference/DFOP.solution-1.png diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index ff1ad823..f89a66e2 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -27,11 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Double First-Order in Parallel kinetics — DFOP.solution" /> - -<meta property="og:description" content="Function describing decline from a defined starting value using the sum - of two exponential decline functions." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 11738484..3b96f9ae 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -27,10 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Subsetting method for mmkin objects — [.mmkin" /> - -<meta property="og:description" content="Subsetting method for mmkin objects." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -263,7 +259,7 @@ #> #> $time #> user system elapsed -#> 0.058 0.000 0.057 +#> 0.06 0.00 0.06 #> #> $mkinmod #> <mkinmod> model generated with @@ -452,8 +448,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555ad80908> -#> <environment: 0x55555b1b4b90> +#> <bytecode: 0x5555599fd348> +#> <environment: 0x555557684190> #> #> $cost_notrans #> function (P) @@ -475,8 +471,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555b174428> -#> <environment: 0x55555b1b4b90> +#> <bytecode: 0x555559feb960> +#> <environment: 0x555557684190> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -543,7 +539,7 @@ #> 99.17407 #> #> $date -#> [1] "Thu Mar 1 14:26:09 2018" +#> [1] "Fri Mar 9 23:08:11 2018" #> #> $version #> [1] "0.9.47.1" 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 5fb3ccfe..de986f3f 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -27,14 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B" /> - -<meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values -generated with different software packages. Taken directly from FOCUS (2006). -The results from fitting the data with the Topfit software was removed, as -the initial concentration of the parent compound was fixed to a value of 100 -in this fit." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> 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 c1665dee..4bc0fd4b 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -27,14 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F" /> - -<meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values -generated with different software packages. Taken directly from FOCUS (2006). -The results from fitting the data with the Topfit software was removed, as -the initial concentration of the parent compound was fixed to a value of 100 -in this fit." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> 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 db3d228d..bf0331cc 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -27,14 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F" /> - -<meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values -generated with different software packages. Taken directly from FOCUS (2006). -The results from fitting the data with the Topfit software was removed, as -the initial concentration of the parent compound was fixed to a value of 100 -in this fit." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> 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 cc4fcb1d..6f05cbb9 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -27,14 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F" /> - -<meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values -generated with different software packages. Taken directly from FOCUS (2006). -The results from fitting the data with the Topfit software was removed, as -the initial concentration of the parent compound was fixed to a value of 100 -in this fit." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 4548c983..9ea69f23 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -27,10 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets" /> - -<meta property="og:description" content="Data taken from FOCUS (2006), p. 258." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/FOMC.solution-1.png b/docs/reference/FOMC.solution-1.png Binary files differindex 58178df5..f10cff4e 100644 --- a/docs/reference/FOMC.solution-1.png +++ b/docs/reference/FOMC.solution-1.png diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 810b0eba..b5b4c87c 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -27,14 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="First-Order Multi-Compartment kinetics — FOMC.solution" /> - -<meta property="og:description" content="Function describing exponential decline from a defined starting value, with - a decreasing rate constant. -The form given here differs slightly from the original reference by Gustafson - and Holden (1990). The parameter beta corresponds to 1/beta in the - original equation." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/HS.solution-1.png b/docs/reference/HS.solution-1.png Binary files differindex e259134e..5e04d343 100644 --- a/docs/reference/HS.solution-1.png +++ b/docs/reference/HS.solution-1.png diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 79358efb..0dc432ef 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -27,11 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Hockey-Stick kinetics — HS.solution" /> - -<meta property="og:description" content="Function describing two exponential decline functions with a break point - between them." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/IORE.solution-1.png b/docs/reference/IORE.solution-1.png Binary files differindex 674c25d3..e421d562 100644 --- a/docs/reference/IORE.solution-1.png +++ b/docs/reference/IORE.solution-1.png diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index f705ab2f..b055534a 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -27,11 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Indeterminate order rate equation kinetics — IORE.solution" /> - -<meta property="og:description" content="Function describing exponential decline from a defined starting value, with - a concentration dependent rate constant." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index a7934a35..eda43e4d 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -27,10 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Single First-Order kinetics — SFO.solution" /> - -<meta property="og:description" content="Function describing exponential decline from a defined starting value." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index aaae7cdd..2b6b2bc6 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -27,14 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Single First-Order Reversible Binding kinetics — SFORB.solution" /> - -<meta property="og:description" content="Function describing the solution of the differential equations describing - the kinetic model with first-order terms for a two-way transfer from a free - to a bound fraction, and a first-order degradation term for the free - fraction. The initial condition is a defined amount in the free fraction and - no substance in the bound fraction." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png Binary files differindex 4f9b1534..fecfc52d 100644 --- a/docs/reference/add_err-1.png +++ b/docs/reference/add_err-1.png diff --git a/docs/reference/add_err-2.png b/docs/reference/add_err-2.png Binary files differindex 8fcf4625..907001ed 100644 --- a/docs/reference/add_err-2.png +++ b/docs/reference/add_err-2.png diff --git a/docs/reference/add_err-3.png b/docs/reference/add_err-3.png Binary files differindex e44839a6..3786d934 100644 --- a/docs/reference/add_err-3.png +++ b/docs/reference/add_err-3.png diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 42bec993..407e1a3e 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -27,12 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Add normally distributed errors to simulated kinetic degradation data — add_err" /> - -<meta property="og:description" content="Normally distributed errors are added to data predicted for a specific - degradation model using mkinpredict. The variance of the error - may depend on the predicted value and is specified as a standard deviation." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index c45a0b7c..4ab395cb 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -27,13 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Function to calculate endpoints for further use from kinetic models fitted with mkinfit — endpoints" /> - -<meta property="og:description" content="This function calculates DT50 and DT90 values as well as formation fractions from kinetic models -fitted with mkinfit. If the SFORB model was specified for one of the parents or metabolites, -the Eigenvalues are returned. These are equivalent to the rate constantes of the DFOP model, but -with the advantage that the SFORB model can also be used for metabolites." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 2d46b4de..7e27c1dc 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -27,10 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Calculate the geometric mean — geometric_mean" /> - -<meta property="og:description" content="Function calculating the geometric mean of numeric vectors" /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 2c51001f..7ed15db5 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -27,10 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Function to perform isometric log-ratio transformation — ilr" /> - -<meta property="og:description" content="This implementation is a special case of the class of isometric log-ratio transformations." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/index.html b/docs/reference/index.html index 218194ad..84bc1dfc 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -27,7 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Function reference" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 5d6baf6a..9e1e3974 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -27,14 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit — max_twa_parent" /> - -<meta property="og:description" content="This function calculates maximum moving window time weighted average concentrations -(TWAs) for kinetic models fitted with mkinfit. Currently, only -calculations for the parent are implemented for the SFO, FOMC and DFOP models, -using the analytical formulas given in the PEC soil section of the FOCUS -guidance." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index ec7f8ccd..30aa894e 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -27,12 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T" /> - -<meta property="og:description" content="Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding - 2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether - extracts." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -151,8 +145,8 @@ <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 used for fitting: 0.9.47.1 #> R version used for fitting: 3.4.3 -#> Date of fit: Thu Mar 1 14:26:15 2018 -#> Date of summary: Thu Mar 1 14:26:15 2018 +#> Date of fit: Fri Mar 9 23:08:18 2018 +#> Date of summary: Fri Mar 9 23:08:18 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index a5432dac..dc781aaf 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -27,12 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Convert a dataframe from long to wide format — mkin_long_to_wide" /> - -<meta property="og:description" content="This function takes a dataframe in the long form as required by modCost - and converts it into a dataframe with one independent variable and several - dependent variables as columns." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 6798efa6..2a8d20a3 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -27,11 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Convert a dataframe with observations over time into long format — mkin_wide_to_long" /> - -<meta property="og:description" content="This function simply takes a dataframe with one independent variable and several - dependent variable and converts it into the long form as required by modCost." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index ab06e903..fd707cfd 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -27,10 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="A dataset class for mkin — mkinds" /> - -<meta property="og:description" content="A dataset class for mkin" /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 496cce15..045e5805 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -27,11 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Calculate the minimum error to assume in order to pass the variance test — mkinerrmin" /> - -<meta property="og:description" content="This function finds the smallest relative error still resulting in passing the -chi-squared test as defined in the FOCUS kinetics report from 2006." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 4fb5ef9a..10052053 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -27,20 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Fit a kinetic model to data with one or more state variables — mkinfit" /> - -<meta property="og:description" content="This function uses the Flexible Modelling Environment package - FME to create a function calculating the model cost, i.e. the - deviation between the kinetic model and the observed data. This model cost is - then minimised using the Port algorithm nlminb, - using the specified initial or fixed parameters and starting values. - Per default, parameters in the kinetic models are internally transformed in order - to better satisfy the assumption of a normal distribution of their estimators. - In each step of the optimsation, the kinetic model is solved using the - function mkinpredict. The variance of the residuals for each - observed variable can optionally be iteratively reweighted until convergence - using the argument reweight.method = "obs"." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -414,15 +400,15 @@ <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 used for fitting: 0.9.47.1 #> R version used for fitting: 3.4.3 -#> Date of fit: Thu Mar 1 14:26:18 2018 -#> Date of summary: Thu Mar 1 14:26:18 2018 +#> Date of fit: Fri Mar 9 23:08:20 2018 +#> Date of summary: Fri Mar 9 23:08:20 2018 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.135 s +#> Fitted with method Port using 64 model solutions performed in 0.148 s #> #> Weighting: none #> @@ -491,7 +477,7 @@ <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 -#> 0.84 0.00 0.84 </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 +#> 0.839 0.000 0.840 </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 diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index c1287905..032fcbb6 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -27,15 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Function to set up a kinetic model with one or more state variables — mkinmod" /> - -<meta property="og:description" content="The function usually takes several expressions, each assigning a compound name to - a list, specifying the kinetic model type and reaction or transfer to other - observed compartments. Instead of specifying several expressions, a list - of lists can be given in the speclist argument. -For the definition of model types and their parameters, the equations given - in the FOCUS and NAFTA guidance documents are used." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png Binary files differindex 42811535..1e7603d7 100644 --- a/docs/reference/mkinparplot-1.png +++ b/docs/reference/mkinparplot-1.png diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 30954168..e416d67c 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -27,11 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Function to plot the confidence intervals obtained using mkinfit — mkinparplot" /> - -<meta property="og:description" content="This function plots the confidence intervals for the parameters - fitted using mkinfit." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 5df3f872..e1ee1607 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -27,10 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Plot the observed data and the fitted model of an mkinfit object — mkinplot" /> - -<meta property="og:description" content="Deprecated function. It now only calls the plot method plot.mkinfit." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index df6316e1..7354c496 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -27,12 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Produce predictions from a kinetic model using specific parameters — mkinpredict" /> - -<meta property="og:description" content="This function produces a time series for all the observed variables in a - kinetic model as specified by mkinmod, using a specific set of - kinetic parameters and initial values for the state variables." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -311,7 +305,7 @@ <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 -#> 0.002 0.000 0.001 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.002 0.000 0.002 </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 diff --git a/docs/reference/mkinresplot-1.png b/docs/reference/mkinresplot-1.png Binary files differindex 8636baf2..5b201616 100644 --- a/docs/reference/mkinresplot-1.png +++ b/docs/reference/mkinresplot-1.png diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index 036917f1..b4b6b116 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -27,13 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Function to plot residuals stored in an mkin object — mkinresplot" /> - -<meta property="og:description" content="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 plot.mkinfit - using the argument show_residuals = TRUE." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index 7724220f..b4915112 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -27,11 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Function to set up a kinetic submodel for one state variable — mkinsub" /> - -<meta property="og:description" content="This is a convenience function to set up the lists used as arguments for - mkinmod." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index e97e3f81..78033dd2 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -27,11 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Fit one or more kinetic models with one or more state variables to one or more datasets — mmkin" /> - -<meta property="og:description" content="This function calls mkinfit on all combinations of models and datasets - specified in its first two arguments." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/plot.mkinfit-1.png b/docs/reference/plot.mkinfit-1.png Binary files differindex 2bb8f5dd..0d54d2fe 100644 --- a/docs/reference/plot.mkinfit-1.png +++ b/docs/reference/plot.mkinfit-1.png diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png Binary files differindex 22a3f8b0..377d63b6 100644 --- a/docs/reference/plot.mkinfit-2.png +++ b/docs/reference/plot.mkinfit-2.png diff --git a/docs/reference/plot.mkinfit-3.png b/docs/reference/plot.mkinfit-3.png Binary files differindex 93e859c7..b23ddfe7 100644 --- a/docs/reference/plot.mkinfit-3.png +++ b/docs/reference/plot.mkinfit-3.png diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png Binary files differindex 27edd6f3..0dd9f4d6 100644 --- a/docs/reference/plot.mkinfit-4.png +++ b/docs/reference/plot.mkinfit-4.png diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 4bdad93f..b6dd1525 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -27,15 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit" /> - -<meta property="og:description" content="Solves the differential equations with the optimised and fixed parameters - from a previous successful call to mkinfit and plots - the observed data together with the solution of the fitted model. -If the current plot device is a tikz device, - then latex is being used for the formatting of the chi2 error level, - if show_errmin = TRUE." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/plot.mmkin-1.png b/docs/reference/plot.mmkin-1.png Binary files differindex 2554b68b..c2c25e90 100644 --- a/docs/reference/plot.mmkin-1.png +++ b/docs/reference/plot.mmkin-1.png diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png Binary files differindex 9a66294f..b40ae0d5 100644 --- a/docs/reference/plot.mmkin-2.png +++ b/docs/reference/plot.mmkin-2.png diff --git a/docs/reference/plot.mmkin-3.png b/docs/reference/plot.mmkin-3.png Binary files differindex b0f7fa21..dfbe014f 100644 --- a/docs/reference/plot.mmkin-3.png +++ b/docs/reference/plot.mmkin-3.png diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 11da6685..8b80273c 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -27,14 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object — plot.mmkin" /> - -<meta property="og:description" content="When x is a row selected from an mmkin object ([.mmkin), the same model - fitted for at least one dataset is shown. When it is a column, the fit of at least one model - to the same dataset is shown. -If the current plot device is a tikz device, - then latex is being used for the formatting of the chi2 error level." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index 8e0d18b2..02882776 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -27,10 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Print mkinds objects — print.mkinds" /> - -<meta property="og:description" content="Print mkinds objects." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index db15cc60..cd6678a6 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -27,10 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Print mkinmod objects — print.mkinmod" /> - -<meta property="og:description" content="Print mkinmod objects in a way that the user finds his way to get to its components." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 6c53f805..04c72edd 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -27,12 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case" /> - -<meta property="og:description" content="This dataset was used for a comparison of KinGUI and ModelMaker to check the - software quality of KinGUI in the original publication (Schäfer et al., 2007). - The results from the fitting are also included." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/sigma_rl.html b/docs/reference/sigma_rl.html index 868c0d4f..4b287e55 100644 --- a/docs/reference/sigma_rl.html +++ b/docs/reference/sigma_rl.html @@ -27,12 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Two component error model of Rocke and Lorenzato — sigma_rl" /> - -<meta property="og:description" content="Function describing the standard deviation of the measurement error - in dependence of the measured value \(y\): -$$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$" /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 977ff8d8..f34736b3 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -27,13 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Summary method for class "mkinfit" — summary.mkinfit" /> - -<meta property="og:description" content="Lists model equations, the summary as returned by summary.modFit, - the chi2 error levels calculated according to FOCUS guidance (2006) as far - as defined therein, and optionally the data, consisting of observed, predicted - and residual values." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -191,15 +184,15 @@ <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'><a href='mkinsub.html'>mkinsub</a></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 used for fitting: 0.9.47.1 #> R version used for fitting: 3.4.3 -#> Date of fit: Thu Mar 1 14:26:27 2018 -#> Date of summary: Thu Mar 1 14:26:27 2018 +#> Date of fit: Fri Mar 9 23:08:29 2018 +#> Date of summary: Fri Mar 9 23:08:29 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.076 s +#> Fitted with method Port using 35 model solutions performed in 0.075 s #> #> Weighting: none #> diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index 192e8dc2..396a6e2b 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -27,22 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014" /> - -<meta property="og:description" content="The 12 datasets were generated using four different models and three different - variance components. The four models are either the SFO or the DFOP model with either - two sequential or two parallel metabolites. -Variance component 'a' is based on a normal distribution with standard deviation of 3, - Variance component 'b' is also based on a normal distribution, but with a standard deviation of 7. - Variance component 'c' is based on the error model from Rocke and Lorenzato (1995), with the - minimum standard deviation (for small y values) of 0.5, and a proportionality constant of 0.07 - for the increase of the standard deviation with y. -Initial concentrations for metabolites and all values where adding the variance component resulted - in a value below the assumed limit of detection of 0.1 were set to NA. -As an example, the first dataset has the title SFO_lin_a and is based on the SFO model - with two sequential metabolites (linear pathway), with added variance component 'a'. -Compare also the code in the example section to see the degradation models." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index c4292d9c..13e072c6 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -27,11 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014" /> - -<meta property="og:description" content="The datasets were used for the comparative validation of several kinetic evaluation - software packages (Ranke, 2014)." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 630a5103..266db603 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -27,18 +27,6 @@ <script src="../pkgdown.js"></script> -<meta property="og:title" content="Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms" /> - -<meta property="og:description" content="The transformations are intended to map parameters that should only take - on restricted values to the full scale of real numbers. For kinetic rate - 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 ilr transformation is used. -The transformation of sets of formation fractions is fragile, as it supposes - the same ordering of the components in forward and backward transformation. - This is no problem for the internal use in mkinfit." /> -<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -185,8 +173,8 @@ The transformation of sets of formation fractions is fragile, as it supposes <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 used for fitting: 0.9.47.1 #> R version used for fitting: 3.4.3 -#> Date of fit: Thu Mar 1 14:26:28 2018 -#> Date of summary: Thu Mar 1 14:26:28 2018 +#> Date of fit: Fri Mar 9 23:08:30 2018 +#> Date of summary: Fri Mar 9 23:08:30 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -194,7 +182,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.571 s +#> Fitted with method Port using 153 model solutions performed in 0.657 s #> #> Weighting: none #> diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html index 8aaa70d6..d8c5b19b 100644 --- a/vignettes/compiled_models.html +++ b/vignettes/compiled_models.html @@ -12,7 +12,7 @@ <meta name="author" content="Johannes Ranke" /> -<meta name="date" content="2018-01-14" /> +<meta name="date" content="2018-03-09" /> <title>Performance benefit by using compiled model definitions in mkin</title> @@ -70,7 +70,7 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf <h1 class="title toc-ignore">Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author"><em>Johannes Ranke</em></h4> -<h4 class="date"><em>2018-01-14</em></h4> +<h4 class="date"><em>2018-03-09</em></h4> @@ -87,27 +87,27 @@ SFO_SFO <-<span class="st"> </span><span class="kw">mkinmod</span>( <span class="dt">m1 =</span> <span class="kw">mkinsub</span>(<span class="st">"SFO"</span>))</code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <p>We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the benchmark package.</p> -<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">if (<span class="kw">require</span>(rbenchmark)) { +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="cf">if</span> (<span class="kw">require</span>(rbenchmark)) { b<span class="fl">.1</span> <-<span class="st"> </span><span class="kw">benchmark</span>( - <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw">mkinfit</span>(SFO_SFO, FOCUS_2006_D, + <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw">mkinfit</span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">solution_type =</span> <span class="st">"deSolve"</span>, <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>), - <span class="st">"Eigenvalue based"</span> =<span class="st"> </span><span class="kw">mkinfit</span>(SFO_SFO, FOCUS_2006_D, + <span class="st">"Eigenvalue based"</span> =<span class="st"> </span><span class="kw">mkinfit</span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">solution_type =</span> <span class="st">"eigen"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>), - <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw">mkinfit</span>(SFO_SFO, FOCUS_2006_D, + <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw">mkinfit</span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">solution_type =</span> <span class="st">"deSolve"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>), <span class="dt">replications =</span> <span class="dv">3</span>) <span class="kw">print</span>(b<span class="fl">.1</span>) factor_SFO_SFO <-<span class="st"> </span><span class="kw">round</span>(b<span class="fl">.1</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>]) -} else { +} <span class="cf">else</span> { factor_SFO_SFO <-<span class="st"> </span><span class="ot">NA</span> <span class="kw">print</span>(<span class="st">"R package benchmark is not available"</span>) }</code></pre></div> <pre><code>## Loading required package: rbenchmark</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 3 deSolve, compiled 3 2.005 1.000 2.000 0.004 -## 1 deSolve, not compiled 3 14.202 7.083 14.196 0.000 -## 2 Eigenvalue based 3 2.427 1.210 2.428 0.000 +## 3 deSolve, compiled 3 1.980 1.000 1.979 0 +## 1 deSolve, not compiled 3 13.926 7.033 13.914 0 +## 2 Eigenvalue based 3 2.362 1.193 2.360 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 @@ -117,35 +117,35 @@ SFO_SFO <-<span class="st"> </span><span class="kw">mkinmod</span>( <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2"> <h2>Model that can not be solved with Eigenvalues</h2> <p>This evaluation is also taken from the example section of mkinfit.</p> -<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">if (<span class="kw">require</span>(rbenchmark)) { +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="cf">if</span> (<span class="kw">require</span>(rbenchmark)) { FOMC_SFO <-<span class="st"> </span><span class="kw">mkinmod</span>( <span class="dt">parent =</span> <span class="kw">mkinsub</span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>), <span class="dt">m1 =</span> <span class="kw">mkinsub</span>( <span class="st">"SFO"</span>)) b<span class="fl">.2</span> <-<span class="st"> </span><span class="kw">benchmark</span>( - <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw">mkinfit</span>(FOMC_SFO, FOCUS_2006_D, + <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw">mkinfit</span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>), - <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw">mkinfit</span>(FOMC_SFO, FOCUS_2006_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>), + <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw">mkinfit</span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>), <span class="dt">replications =</span> <span class="dv">3</span>) <span class="kw">print</span>(b<span class="fl">.2</span>) factor_FOMC_SFO <-<span class="st"> </span><span class="kw">round</span>(b<span class="fl">.2</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>]) -} else { +} <span class="cf">else</span> { factor_FOMC_SFO <-<span class="st"> </span><span class="ot">NA</span> <span class="kw">print</span>(<span class="st">"R package benchmark is not available"</span>) }</code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 2 deSolve, compiled 3 3.489 1.000 3.488 0 -## 1 deSolve, not compiled 3 28.906 8.285 28.904 0 +## 2 deSolve, compiled 3 3.437 1.000 3.433 0 +## 1 deSolve, not compiled 3 30.406 8.847 30.380 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> -<p>Here we get a performance benefit of a factor of 8 using the version of the differential equation model compiled from C code!</p> -<p>This vignette was built with mkin 0.9.47.1 on</p> +<p>Here we get a performance benefit of a factor of 9 using the version of the differential equation model compiled from C code!</p> +<p>This vignette was built with mkin 0.9.46.3 on</p> <pre><code>## R version 3.4.3 (2017-11-30) ## Platform: x86_64-pc-linux-gnu (64-bit) ## Running under: Debian GNU/Linux 9 (stretch)</code></pre> -<pre><code>## CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz</code></pre> +<pre><code>## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</code></pre> </div> |
