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diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 6607d614..d6941019 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -62,14 +62,7 @@ <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> +<ul class="nav navbar-nav navbar-right"></ul> </div> <!--/.nav-collapse --> </div> @@ -84,7 +77,7 @@ <h1>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2017-09-14</h4> + <h4 class="date">2017-11-16</h4> </div> 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 c0fab72d..75c4c299 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 47916477..94e7e2b3 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 b89c7b20..7cef7abd 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -62,14 +62,7 @@ <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> +<ul class="nav navbar-nav navbar-right"></ul> </div> <!--/.nav-collapse --> </div> @@ -84,7 +77,7 @@ <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2017-09-14</h4> + <h4 class="date">2017-11-16</h4> </div> @@ -105,17 +98,17 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re <p>Since mkin version 0.9-32 (July 2014), we can use shorthand notation like <code>"SFO"</code> for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.</p> <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: 0.9.46.1 -## R version: 3.4.1 -## Date of fit: Thu Sep 14 12:15:03 2017 -## Date of summary: Thu Sep 14 12:15:03 2017 +<pre><code>## mkin version: 0.9.46.2 +## R version: 3.4.2 +## Date of fit: Thu Nov 16 17:12:46 2017 +## Date of summary: Thu Nov 16 17:12:46 2017 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.255 s +## Fitted with method Port using 37 model solutions performed in 0.253 s ## ## Weighting: none ## @@ -198,10 +191,10 @@ 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"><span class="kw">plot</span>(m.L1.FOMC, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L1 - FOMC"</span>)</code></pre></div> <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: 0.9.46.1 -## R version: 3.4.1 -## Date of fit: Thu Sep 14 12:15:05 2017 -## Date of summary: Thu Sep 14 12:15:05 2017 +<pre><code>## mkin version: 0.9.46.2 +## R version: 3.4.2 +## Date of fit: Thu Nov 16 17:12:47 2017 +## Date of summary: Thu Nov 16 17:12:47 2017 ## ## ## Warning: Optimisation by method Port did not converge. @@ -213,7 +206,7 @@ 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 155 model solutions performed in 0.458 s +## Fitted with method Port using 155 model solutions performed in 0.485 s ## ## Weighting: none ## @@ -298,17 +291,17 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re <span class="dt">main =</span> <span class="st">"FOCUS L2 - FOMC"</span>)</code></pre></div> <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: 0.9.46.1 -## R version: 3.4.1 -## Date of fit: Thu Sep 14 12:15:06 2017 -## Date of summary: Thu Sep 14 12:15:06 2017 +<pre><code>## mkin version: 0.9.46.2 +## R version: 3.4.2 +## Date of fit: Thu Nov 16 17:12:48 2017 +## Date of summary: Thu Nov 16 17:12:48 2017 ## ## 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 0.176 s +## Fitted with method Port using 81 model solutions performed in 0.183 s ## ## Weighting: none ## @@ -369,10 +362,10 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re <span class="dt">main =</span> <span class="st">"FOCUS L2 - DFOP"</span>)</code></pre></div> <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: 0.9.46.1 -## R version: 3.4.1 -## Date of fit: Thu Sep 14 12:15:07 2017 -## Date of summary: Thu Sep 14 12:15:07 2017 +<pre><code>## mkin version: 0.9.46.2 +## R version: 3.4.2 +## Date of fit: Thu Nov 16 17:12:49 2017 +## Date of summary: Thu Nov 16 17:12:49 2017 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -381,7 +374,7 @@ 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 0.821 s +## Fitted with method Port using 336 model solutions performed in 0.84 s ## ## Weighting: none ## @@ -461,10 +454,10 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <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: 0.9.46.1 -## R version: 3.4.1 -## Date of fit: Thu Sep 14 12:15:08 2017 -## Date of summary: Thu Sep 14 12:15:08 2017 +<pre><code>## mkin version: 0.9.46.2 +## R version: 3.4.2 +## Date of fit: Thu Nov 16 17:12:50 2017 +## Date of summary: Thu Nov 16 17:12:50 2017 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -473,7 +466,7 @@ 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 0.302 s +## Fitted with method Port using 137 model solutions performed in 0.309 s ## ## Weighting: none ## @@ -562,10 +555,10 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-15-1.png" width="672"></p> <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: 0.9.46.1 -## R version: 3.4.1 -## Date of fit: Thu Sep 14 12:15:08 2017 -## Date of summary: Thu Sep 14 12:15:09 2017 +<pre><code>## mkin version: 0.9.46.2 +## R version: 3.4.2 +## Date of fit: Thu Nov 16 17:12:50 2017 +## Date of summary: Thu Nov 16 17:12:51 2017 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent @@ -622,17 +615,17 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin ## DT50 DT90 ## 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: 0.9.46.1 -## R version: 3.4.1 -## Date of fit: Thu Sep 14 12:15:08 2017 -## Date of summary: Thu Sep 14 12:15:09 2017 +<pre><code>## mkin version: 0.9.46.2 +## R version: 3.4.2 +## Date of fit: Thu Nov 16 17:12:51 2017 +## Date of summary: Thu Nov 16 17:12:51 2017 ## ## Equations: ## d_parent/dt = - (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 0.136 s ## ## Weighting: none ## diff --git a/docs/articles/FOCUS_Z.R b/docs/articles/FOCUS_Z.R index 5c70b57e..a77441cf 100644 --- a/docs/articles/FOCUS_Z.R +++ b/docs/articles/FOCUS_Z.R @@ -1,10 +1,9 @@ -## ----include=FALSE-------------------------------------------------- +## ---- include = FALSE---------------------------------------------------- require(knitr) -opts_chunk$set(engine='R', tidy = FALSE, cache = TRUE) -options(width=70) +opts_chunk$set(engine='R', tidy = FALSE) -## ----FOCUS_2006_Z_data, echo=TRUE, eval=TRUE------------------------ -require(mkin) +## ---- echo = TRUE, fig = TRUE, fig.width = 8, fig.height = 7------------- +library(mkin, quiet = TRUE) LOD = 0.5 FOCUS_2006_Z = data.frame( t = c(0, 0.04, 0.125, 0.29, 0.54, 1, 2, 3, 4, 7, 10, 14, 21, @@ -20,14 +19,14 @@ FOCUS_2006_Z = data.frame( FOCUS_2006_Z_mkin <- mkin_wide_to_long(FOCUS_2006_Z) -## ----FOCUS_2006_Z_fits_1, echo=TRUE, fig.height=6------------------- +## ----FOCUS_2006_Z_fits_1, echo=TRUE, fig.height=6------------------------ Z.2a <- mkinmod(Z0 = mkinsub("SFO", "Z1"), Z1 = mkinsub("SFO")) m.Z.2a <- mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE) plot_sep(m.Z.2a) summary(m.Z.2a, data = FALSE)$bpar -## ----FOCUS_2006_Z_fits_2, echo=TRUE, fig.height=6------------------- +## ----FOCUS_2006_Z_fits_2, echo=TRUE, fig.height=6------------------------ Z.2a.ff <- mkinmod(Z0 = mkinsub("SFO", "Z1"), Z1 = mkinsub("SFO"), use_of_ff = "max") @@ -36,21 +35,21 @@ m.Z.2a.ff <- mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE) plot_sep(m.Z.2a.ff) summary(m.Z.2a.ff, data = FALSE)$bpar -## ----FOCUS_2006_Z_fits_3, echo=TRUE, fig.height=6------------------- +## ----FOCUS_2006_Z_fits_3, echo=TRUE, fig.height=6------------------------ Z.3 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE), Z1 = mkinsub("SFO"), use_of_ff = "max") m.Z.3 <- mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE) plot_sep(m.Z.3) summary(m.Z.3, data = FALSE)$bpar -## ----FOCUS_2006_Z_fits_5, echo=TRUE, fig.height=7------------------- +## ----FOCUS_2006_Z_fits_5, echo=TRUE, fig.height=7------------------------ Z.5 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE), Z1 = mkinsub("SFO", "Z2", sink = FALSE), Z2 = mkinsub("SFO"), use_of_ff = "max") m.Z.5 <- mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE) plot_sep(m.Z.5) -## ----FOCUS_2006_Z_fits_6, echo=TRUE, fig.height=8------------------- +## ----FOCUS_2006_Z_fits_6, echo=TRUE, fig.height=8------------------------ Z.FOCUS <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE), Z1 = mkinsub("SFO", "Z2", sink = FALSE), Z2 = mkinsub("SFO", "Z3"), @@ -63,7 +62,7 @@ plot_sep(m.Z.FOCUS) summary(m.Z.FOCUS, data = FALSE)$bpar endpoints(m.Z.FOCUS) -## ----FOCUS_2006_Z_fits_7, echo=TRUE, fig.height=8------------------- +## ----FOCUS_2006_Z_fits_7, echo=TRUE, fig.height=8------------------------ Z.mkin.1 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE), Z1 = mkinsub("SFO", "Z2", sink = FALSE), Z2 = mkinsub("SFO", "Z3"), @@ -72,14 +71,14 @@ m.Z.mkin.1 <- mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE) plot_sep(m.Z.mkin.1) summary(m.Z.mkin.1, data = FALSE)$cov.unscaled -## ----FOCUS_2006_Z_fits_9, echo=TRUE, fig.height=8------------------- +## ----FOCUS_2006_Z_fits_9, echo=TRUE, fig.height=8------------------------ Z.mkin.3 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE), Z1 = mkinsub("SFO", "Z2", sink = FALSE), Z2 = mkinsub("SFO")) m.Z.mkin.3 <- mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE) plot_sep(m.Z.mkin.3) -## ----FOCUS_2006_Z_fits_10, echo=TRUE, fig.height=8------------------ +## ----FOCUS_2006_Z_fits_10, echo=TRUE, fig.height=8----------------------- Z.mkin.4 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE), Z1 = mkinsub("SFO", "Z2", sink = FALSE), Z2 = mkinsub("SFO", "Z3"), @@ -89,7 +88,7 @@ m.Z.mkin.4 <- mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, quiet = TRUE) plot_sep(m.Z.mkin.4) -## ----FOCUS_2006_Z_fits_11, echo=TRUE, fig.height=8------------------ +## ----FOCUS_2006_Z_fits_11, echo=TRUE, fig.height=8----------------------- Z.mkin.5 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE), Z1 = mkinsub("SFO", "Z2", sink = FALSE), Z2 = mkinsub("SFO", "Z3"), @@ -99,7 +98,7 @@ m.Z.mkin.5 <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, quiet = TRUE) plot_sep(m.Z.mkin.5) -## ----FOCUS_2006_Z_fits_11a, echo=TRUE------------------------------- +## ----FOCUS_2006_Z_fits_11a, echo=TRUE------------------------------------ m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = c(m.Z.mkin.5$bparms.ode[1:7], k_Z3_bound_free = 0), @@ -107,9 +106,9 @@ m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, quiet = TRUE) plot_sep(m.Z.mkin.5a) -## ----FOCUS_2006_Z_fits_11b, echo=TRUE------------------------------- +## ----FOCUS_2006_Z_fits_11b, echo=TRUE------------------------------------ mkinparplot(m.Z.mkin.5a) -## ----FOCUS_2006_Z_fits_11b_endpoints, echo=TRUE--------------------- +## ----FOCUS_2006_Z_fits_11b_endpoints, echo=TRUE-------------------------- endpoints(m.Z.mkin.5a) diff --git a/docs/articles/FOCUS_Z.html b/docs/articles/FOCUS_Z.html index c3bb5180..d16299ca 100644 --- a/docs/articles/FOCUS_Z.html +++ b/docs/articles/FOCUS_Z.html @@ -62,14 +62,7 @@ <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> +<ul class="nav navbar-nav navbar-right"></ul> </div> <!--/.nav-collapse --> </div> @@ -84,13 +77,13 @@ <h1>Example evaluation of FOCUS dataset Z</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2017-09-14</h4> + <h4 class="date">2017-11-16</h4> </div> <div class="contents"> -<p><a href="http://www.jrwb.de">Wissenschaftlicher Berater, Kronacher Str. 8, 79639 Grenzach-Wyhlen, Germany</a><br><a href="http://chem.uft.uni-bremen.de/ranke">Privatdozent at the University of Bremen</a></p> +<p><a href="http://www.jrwb.de">Wissenschaftlicher Berater, Kronacher Str. 12, 79639 Grenzach-Wyhlen, Germany</a><br><a href="http://chem.uft.uni-bremen.de/ranke">Privatdozent at the University of Bremen</a></p> <div id="the-data" class="section level1"> <h1 class="hasAnchor"> <a href="#the-data" class="anchor"></a>The data</h1> diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index af47841b..68aa1bac 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -62,14 +62,7 @@ <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> +<ul class="nav navbar-nav navbar-right"></ul> </div> <!--/.nav-collapse --> </div> @@ -84,7 +77,7 @@ <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2017-09-14</h4> + <h4 class="date">2017-11-16</h4> </div> @@ -98,13 +91,8 @@ <pre><code>## gcc ## "/usr/bin/gcc"</code></pre> <p>First, we build a simple degradation model for a parent compound with one metabolite.</p> -<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(<span class="st">"mkin"</span>)</code></pre></div> -<pre><code>## Lade nötiges Paket: minpack.lm</code></pre> -<pre><code>## Lade nötiges Paket: rootSolve</code></pre> -<pre><code>## Lade nötiges Paket: inline</code></pre> -<pre><code>## Lade nötiges Paket: methods</code></pre> -<pre><code>## Lade nötiges Paket: parallel</code></pre> -<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>( +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(<span class="st">"mkin"</span>) +SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>( <span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>), <span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> @@ -127,9 +115,9 @@ }</code></pre></div> <pre><code>## Lade nötiges Paket: rbenchmark</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 3 deSolve, compiled 3 2.038 1.000 2.036 0 -## 1 deSolve, not compiled 3 14.822 7.273 14.824 0 -## 2 Eigenvalue based 3 2.543 1.248 2.544 0 +## 3 deSolve, compiled 3 2.029 1.000 2.028 0 +## 1 deSolve, not compiled 3 14.237 7.017 14.236 0 +## 2 Eigenvalue based 3 2.700 1.331 2.700 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 @@ -158,14 +146,14 @@ }</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 3.488 1.000 3.488 0 -## 1 deSolve, not compiled 3 30.604 8.774 30.600 0 +## 2 deSolve, compiled 3 3.495 1.000 3.496 0 +## 1 deSolve, not compiled 3 29.264 8.373 29.260 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> -<p>Here we get a performance benefit of a factor of 9 using the version of the differential equation model compiled from C code!</p> -<p>This vignette was built with mkin 0.9.46.1 on</p> -<pre><code>## R version 3.4.1 (2017-06-30) +<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 0.9.46.2 on</p> +<pre><code>## R version 3.4.2 (2017-09-28) ## 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> diff --git a/docs/articles/index.html b/docs/articles/index.html index d02bfe80..0a355e17 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -86,12 +86,7 @@ </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 --> @@ -101,7 +96,7 @@ </header> <div class="page-header"> - <h1>Articles <small>version 0.9.46.1</small></h1> + <h1>Articles <small>version 0.9.46.3</small></h1> </div> <div class="row"> diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index 92bd2bb4..14349e53 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -62,14 +62,7 @@ <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> +<ul class="nav navbar-nav navbar-right"></ul> </div> <!--/.nav-collapse --> </div> @@ -84,13 +77,13 @@ <h1>Introduction to mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2017-09-14</h4> + <h4 class="date">2017-11-16</h4> </div> <div class="contents"> -<p><a href="http://www.jrwb.de">Wissenschaftlicher Berater, Kronacher Str. 8, 79639 Grenzach-Wyhlen, Germany</a><br><a href="http://chem.uft.uni-bremen.de/ranke">Privatdozent at the University of Bremen</a></p> +<p><a href="http://www.jrwb.de">Wissenschaftlicher Berater, Kronacher Str. 12, 79639 Grenzach-Wyhlen, Germany</a><br><a href="http://chem.uft.uni-bremen.de/ranke">Privatdozent at the University of Bremen</a></p> <div id="abstract" class="section level1"> <h1 class="hasAnchor"> <a href="#abstract" class="anchor"></a>Abstract</h1> @@ -147,7 +140,7 @@ f_SFO_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../referen <p>Soon after the publication of <code>mkin</code>, two derived tools were published, namely KinGUII (available from Bayer Crop Science) and CAKE (commissioned to Tessella by Syngenta), which added a graphical user interface (GUI), and added fitting by iteratively reweighted least squares (IRLS) and characterisation of likely parameter distributions by Markov Chain Monte Carlo (MCMC) sampling.</p> <p>CAKE focuses on a smooth use experience, sacrificing some flexibility in the model definition, originally allowing only two primary metabolites in parallel. The current version 3.2 of CAKE release in March 2016 uses a basic scheme for up to six metabolites in a flexible arrangement, but does not support back-reactions (non-instantaneous equilibria) or biphasic kinetics for metabolites.</p> <p>KinGUI offers an even more flexible widget for specifying complex kinetic models. Back-reactions (non-instanteneous equilibria) were supported early on, but until 2014, only simple first-order models could be specified for transformation products. Starting with KinGUII version 2.1, biphasic modelling of metabolites was also available in KinGUII.</p> -<p>A further graphical user interface (GUI) that has recently been brought to a decent degree of maturity is the browser based GUI named <code>gmkin</code>. Please see its <a href="http://kinfit.r-forge.r-project.org/gmkin_static">documentation page</a> and <a href="http://kinfit.r-forge.r-project.org/gmkin_static/vignettes/gmkin_manual.html">manual</a> for further information.</p> +<p>A further graphical user interface (GUI) that has recently been brought to a decent degree of maturity is the browser based GUI named <code>gmkin</code>. Please see its <a href="https://pkgdown.jrwb.de/gmkin">documentation page</a> and <a href="https://pkgdown.jrwb.de/gmkin/articles/gmkin_manual.html">manual</a> for further information.</p> </div> <div id="recent-developments" class="section level2"> <h2 class="hasAnchor"> diff --git a/docs/articles/twa.html b/docs/articles/twa.html index 3a1d5731..0a4df0ff 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -62,14 +62,7 @@ <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> +<ul class="nav navbar-nav navbar-right"></ul> </div> <!--/.nav-collapse --> </div> @@ -84,7 +77,7 @@ <h1>Calculation of time weighted average concentrations with mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2017-09-14</h4> + <h4 class="date">2017-11-16</h4> </div> |
