diff options
Diffstat (limited to 'docs')
49 files changed, 175 insertions, 373 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 726c8378..f32d7f82 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -24,13 +24,7 @@ <li> <a href="../news/index.html">News</a> </li> - </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="http://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> - </ul></div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -41,7 +35,7 @@ <h1>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-11-03</h4> + <h4 class="date">2016-11-04</h4> </div> diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 55caa22e..6a9c6ba5 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -24,13 +24,7 @@ <li> <a href="../news/index.html">News</a> </li> - </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="http://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> - </ul></div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -41,7 +35,7 @@ <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-11-03</h4> + <h4 class="date">2016-11-04</h4> </div> @@ -63,15 +57,15 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re <span class="kw">summary</span>(m.L1.SFO)</code></pre></div> <pre><code>## mkin version: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Thu Nov 3 17:47:48 2016 -## Date of summary: Thu Nov 3 17:47:48 2016 +## Date of fit: Fri Nov 4 15:38:03 2016 +## Date of summary: Fri Nov 4 15:38:03 2016 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.093 s +## Fitted with method Port using 37 model solutions performed in 0.089 s ## ## Weighting: none ## @@ -156,8 +150,8 @@ 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">summary</span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> <pre><code>## mkin version: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Thu Nov 3 17:47:49 2016 -## Date of summary: Thu Nov 3 17:47:49 2016 +## Date of fit: Fri Nov 4 15:38:04 2016 +## Date of summary: Fri Nov 4 15:38:04 2016 ## ## ## Warning: Optimisation by method Port did not converge. @@ -169,7 +163,7 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 188 model solutions performed in 0.447 s +## Fitted with method Port using 188 model solutions performed in 0.446 s ## ## Weighting: none ## @@ -253,15 +247,15 @@ FOCUS_2006_L2_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">summary</span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> <pre><code>## mkin version: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Thu Nov 3 17:47:49 2016 -## Date of summary: Thu Nov 3 17:47:49 2016 +## Date of fit: Fri Nov 4 15:38:05 2016 +## Date of summary: Fri Nov 4 15:38:05 2016 ## ## Equations: ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 81 model solutions performed in 0.189 s +## Fitted with method Port using 81 model solutions performed in 0.19 s ## ## Weighting: none ## @@ -323,8 +317,8 @@ FOCUS_2006_L2_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">summary</span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> <pre><code>## mkin version: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Thu Nov 3 17:47:50 2016 -## Date of summary: Thu Nov 3 17:47:50 2016 +## Date of fit: Fri Nov 4 15:38:06 2016 +## Date of summary: Fri Nov 4 15:38:06 2016 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -333,7 +327,7 @@ 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 0.836 s +## Fitted with method Port using 336 model solutions performed in 0.815 s ## ## Weighting: none ## @@ -412,8 +406,8 @@ 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: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Thu Nov 3 17:47:51 2016 -## Date of summary: Thu Nov 3 17:47:52 2016 +## Date of fit: Fri Nov 4 15:38:07 2016 +## Date of summary: Fri Nov 4 15:38:07 2016 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -422,7 +416,7 @@ 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 0.328 s +## Fitted with method Port using 137 model solutions performed in 0.339 s ## ## Weighting: none ## @@ -512,15 +506,15 @@ 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: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Thu Nov 3 17:47:52 2016 -## Date of summary: Thu Nov 3 17:47:52 2016 +## Date of fit: Fri Nov 4 15:38:07 2016 +## Date of summary: Fri Nov 4 15:38:08 2016 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.107 s +## Fitted with method Port using 46 model solutions performed in 0.112 s ## ## Weighting: none ## @@ -572,8 +566,8 @@ 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>## mkin version: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Thu Nov 3 17:47:52 2016 -## Date of summary: Thu Nov 3 17:47:52 2016 +## Date of fit: Fri Nov 4 15:38:08 2016 +## Date of summary: Fri Nov 4 15:38:08 2016 ## ## Equations: ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent diff --git a/docs/articles/compiled_models.R b/docs/articles/compiled_models.R index 4f544b0d..5ce343cb 100644 --- a/docs/articles/compiled_models.R +++ b/docs/articles/compiled_models.R @@ -1,3 +1,16 @@ +## ---- include = FALSE---------------------------------------------------- +library(knitr) +opts_chunk$set(tidy = FALSE, cache = FALSE) + +## ----check_gcc----------------------------------------------------------- +Sys.which("gcc") + +## ----create_SFO_SFO------------------------------------------------------ +library("mkin") +SFO_SFO <- mkinmod( + parent = mkinsub("SFO", "m1"), + m1 = mkinsub("SFO")) + ## ----benchmark_SFO_SFO, fig.height = 3----------------------------------- library("microbenchmark") library("ggplot2") diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index 5a04168e..09039f62 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -24,13 +24,7 @@ <li> <a href="../news/index.html">News</a> </li> - </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="http://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> - </ul></div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -41,14 +35,14 @@ <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-11-03</h4> + <h4 class="date">2016-11-04</h4> </div> <div class="contents"> -<div id="benchmark-for-a-model-that-can-also-be-solved-with-eigenvalues" class="section level2"> -<h2 class="hasAnchor"><html><body><a href="#benchmark-for-a-model-that-can-also-be-solved-with-eigenvalues" class="anchor"> </a></body></html>Benchmark for a model that can also be solved with Eigenvalues</h2> +<div id="model-that-can-also-be-solved-with-eigenvalues" class="section level2"> +<h2 class="hasAnchor"><html><body><a href="#model-that-can-also-be-solved-with-eigenvalues" class="anchor"> </a></body></html>Model that can also be solved with Eigenvalues</h2> <p>This evaluation is taken from the example section of mkinfit. When using an mkin version equal to or greater than 0.9-36 and a C compiler (gcc) is available, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod. The <code><a href="../reference/mkinmod.html">mkinmod()</a></code> function checks for presence of the gcc compiler using</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">Sys.which</span>(<span class="st">"gcc"</span>)</code></pre></div> <pre><code>## gcc @@ -78,25 +72,25 @@ mb<span class="fl">.1</span> <-<span class="st"> </span><span class="kw">micr <span class="kw">print</span>(mb<span class="fl">.1</span>)</code></pre></div> <pre><code>## Unit: milliseconds ## expr min lq mean median uq -## deSolve, not compiled 6306.4527 6340.7895 6403.5937 6375.1264 6452.1643 -## Eigenvalue based 918.0808 929.7217 948.9742 941.3626 964.4210 -## deSolve, compiled 736.1337 753.6016 773.5605 771.0696 792.2739 +## deSolve, not compiled 6581.1731 6598.7831 6630.0395 6616.3931 6654.4726 +## Eigenvalue based 880.1617 890.3517 911.2758 900.5416 926.8328 +## deSolve, compiled 739.4343 749.6078 753.6543 759.7813 760.7643 ## max neval cld -## 6529.2022 3 b -## 987.4793 3 a -## 813.4783 3 a</code></pre> +## 6692.5522 3 c +## 953.1240 3 b +## 761.7474 3 a</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.1</span>)</code></pre></div> <p><img src="compiled_models_files/figure-html/benchmark_SFO_SFO-1.png" width="672"></p> -<p>We see that using the compiled model is by a factor of 8.3 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:</p> +<p>We see that using the compiled model is by a factor of 8.7 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 class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">rownames</span>(smb<span class="fl">.1</span>) <-<span class="st"> </span>smb<span class="fl">.1</span>$expr smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class="fl">.1</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div> <pre><code>## median -## deSolve, not compiled 8.267900 -## Eigenvalue based 1.220853 +## deSolve, not compiled 8.708286 +## Eigenvalue based 1.185264 ## deSolve, compiled 1.000000</code></pre> </div> -<div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2"> -<h2 class="hasAnchor"><html><body><a href="#benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="anchor"> </a></body></html>Benchmark for a model that can not be solved with Eigenvalues</h2> +<div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2"> +<h2 class="hasAnchor"><html><body><a href="#model-that-can-not-be-solved-with-eigenvalues" class="anchor"> </a></body></html>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">FOMC_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">"FOMC"</span>, <span class="st">"m1"</span>), @@ -114,18 +108,18 @@ smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class=" <span class="kw">print</span>(mb<span class="fl">.2</span>)</code></pre></div> <pre><code>## Unit: seconds ## expr min lq mean median uq -## deSolve, not compiled 13.604720 13.667244 13.689764 13.729768 13.732286 -## deSolve, compiled 1.305077 1.311124 1.328943 1.317172 1.340876 +## deSolve, not compiled 13.756286 13.813205 13.874083 13.870125 13.932982 +## deSolve, compiled 1.323196 1.372916 1.391915 1.422635 1.426274 ## max neval cld -## 13.734804 3 b -## 1.364579 3 a</code></pre> +## 13.995838 3 b +## 1.429913 3 a</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">smb<span class="fl">.2</span>[<span class="st">"median"</span>]/smb<span class="fl">.2</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div> <pre><code>## median ## 1 NA ## 2 NA</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.2</span>)</code></pre></div> <p><img src="compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png" width="672"></p> -<p>Here we get a performance benefit of a factor of 10.4 using the version of the differential equation model compiled from C code!</p> +<p>Here we get a performance benefit of a factor of 9.7 using the version of the differential equation model compiled from C code!</p> <p>This vignette was built with mkin 0.9.44.9000 on</p> <pre><code>## R version 3.3.2 (2016-10-31) ## Platform: x86_64-pc-linux-gnu (64-bit) @@ -138,8 +132,8 @@ smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class=" <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div id="tocnav"> <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"><li><a href="#benchmark-for-a-model-that-can-also-be-solved-with-eigenvalues">Benchmark for a model that can also be solved with Eigenvalues</a></li> - <li><a href="#benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues">Benchmark for a model that can not be solved with Eigenvalues</a></li> + <ul class="nav nav-pills nav-stacked"><li><a href="#model-that-can-also-be-solved-with-eigenvalues">Model that can also be solved with Eigenvalues</a></li> + <li><a href="#model-that-can-not-be-solved-with-eigenvalues">Model that can not be solved with Eigenvalues</a></li> </ul></div> </div> diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png Binary files differindex eec55773..51846e6c 100644 --- a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png +++ b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png Binary files differindex b043c13b..f6e4cb08 100644 --- a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png +++ b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png diff --git a/docs/articles/index.html b/docs/articles/index.html index cd6a7bea..9f7cdd74 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -60,12 +60,7 @@ </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 --> diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index dafaa0e4..5f6ae46c 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -24,13 +24,7 @@ <li> <a href="../news/index.html">News</a> </li> - </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="http://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> - </ul></div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -41,7 +35,7 @@ <h1>mkin - Kinetic evaluation of chemical degradation data</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-11-03</h4> + <h4 class="date">2016-11-04</h4> </div> @@ -70,7 +64,7 @@ d_SFO_SFO_SFO_err <-<span class="st"> </span><span class="kw"><a href="../ref f_SFO_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(m_SFO_SFO_SFO, d_SFO_SFO_SFO_err[[<span class="dv">1</span>]], <span class="dt">quiet =</span> <span class="ot">TRUE</span>) -<span class="kw">plot_sep</span>(f_SFO_SFO_SFO, <span class="dt">lpos =</span> <span class="kw">c</span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>, <span class="st">"bottomright"</span>))</code></pre></div> +<span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(f_SFO_SFO_SFO, <span class="dt">lpos =</span> <span class="kw">c</span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>, <span class="st">"bottomright"</span>))</code></pre></div> <p><img src="mkin_files/figure-html/unnamed-chunk-2-1.png" width="768"></p> </div> <div id="background" class="section level1"> diff --git a/docs/authors.html b/docs/authors.html index fe3e6114..1490de9b 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -60,12 +60,7 @@ </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 --> diff --git a/docs/index.html b/docs/index.html index a3a0e46c..c7d07e39 100644 --- a/docs/index.html +++ b/docs/index.html @@ -24,13 +24,7 @@ <li> <a href="news/index.html">News</a> </li> - </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="http://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> - </ul></div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -109,7 +103,6 @@ <div class="col-md-3" id="sidebar"> <h2>Links</h2><ul class="list-unstyled"><li>Download from CRAN at <br><a href="https://cran.r-project.org/package=mkin">https://​cran.r-project.org/​package=mkin</a></li> -<li>Browse source code at <br><a href="http://github.com/jranke/mkin">http://​github.com/​jranke/​mkin</a></li> <li>Report a bug at <br><a href="http://github.com/jranke/mkin/issues">http://​github.com/​jranke/​mkin/​issues</a></li> </ul><h2>License</h2> <p>GPL</p> diff --git a/docs/news/index.html b/docs/news/index.html index 94d5d197..7c9b63f7 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -60,12 +60,7 @@ </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 --> @@ -164,7 +159,7 @@ <h2 class="hasAnchor"> <a href="#bug-fixes-2" class="anchor"> </a>Bug fixes</h2> <ul><li> -<code>print.summary.mkinfit()</code>: Avoid an error that occurred when printing summaries generated with mkin versions before 0.9-36</li> +<code><a href="../reference/summary.mkinfit.html">print.summary.mkinfit()</a></code>: Avoid an error that occurred when printing summaries generated with mkin versions before 0.9-36</li> </ul></div> </div> <div id="mkin-0-9-40-2015-07-21" class="section level1"> @@ -221,7 +216,7 @@ <div id="major-changes-3" class="section level2"> <h2 class="hasAnchor"> <a href="#major-changes-3" class="anchor"> </a>Major changes</h2> -<ul><li><p><code>summary.mkinfit()</code>: A one-sided t-test for significant difference of untransformed parameters from zero is now always shown, based on the assumption of normal distribution for estimators of all untransformed parameters. Use with caution, as this assumption is unrealistic e.g. for rate constants in these nonlinear kinetic models.</p></li> +<ul><li><p><code><a href="../reference/summary.mkinfit.html">summary.mkinfit()</a></code>: A one-sided t-test for significant difference of untransformed parameters from zero is now always shown, based on the assumption of normal distribution for estimators of all untransformed parameters. Use with caution, as this assumption is unrealistic e.g. for rate constants in these nonlinear kinetic models.</p></li> <li><p>If a compiler (gcc) is installed, use a version of the differential equation model compiled from C code, which is a huge performance boost for models where only the deSolve method works.</p></li> <li><p><code><a href="../reference/mkinmod.html">mkinmod()</a></code>: Create a list component $cf (of class CFuncList) in the list returned by mkinmod, if a version can be compiled from autogenerated C code (see above).</p></li> <li><p><code><a href="../reference/mkinfit.html">mkinfit()</a></code>: Set the default <code>solution_type</code> to <code>deSolve</code> when a compiled version of the model is present, except when an analytical solution is possible.</p></li> @@ -244,7 +239,7 @@ <h2 class="hasAnchor"> <a href="#bug-fixes-6" class="anchor"> </a>Bug fixes</h2> <ul><li><p><code><a href="../reference/mkinparplot.html">mkinparplot()</a></code>: Avoid warnings that occurred when not all confidence intervals were available in the summary of the fit</p></li> -<li><p><code>print.summary.mkinfit()</code>: Fix printing the summary for the case that the number of iterations is not available</p></li> +<li><p><code><a href="../reference/summary.mkinfit.html">print.summary.mkinfit()</a></code>: Fix printing the summary for the case that the number of iterations is not available</p></li> <li><p>NAMESPACE: export S3 methods plot.mkinfit, summary.mkinfit and print.summary.mkinfit to satisfy R CMD check on R-devel</p></li> <li><p><code><a href="../reference/mkinparplot.html">mkinparplot()</a></code>: Avoid warning in R CMD check about undeclared global variable <code>Lower</code></p></li> </ul></div> @@ -289,14 +284,14 @@ <ul><li><p><code><a href="../reference/mkinfit.html">mkinfit()</a></code>: The internally fitted parameter for <code>g</code> was named <code>g_ilr</code> even when <code>transform_fractions=FALSE</code></p></li> <li><p><code><a href="../reference/mkinfit.html">mkinfit()</a></code>: The initial value (state.ini) for the parent compound was not set when the parent was not the (only) variable with the highest value in the observed data.</p></li> <li><p><code><a href="../reference/mkinerrmin.html">mkinerrmin()</a></code>: When checking for degrees of freedom for metabolites, check if their time zero value is fixed instead of checking if the observed value is zero. This ensures correct calculation of degrees of freedom also in cases where the metabolite residue at time zero is greater zero.</p></li> -<li><p><code>plot.mkinfit()</code>: Avoid a warning message about only using the first component of ylim that occurred when ylim was specified explicitly</p></li> +<li><p><code><a href="../reference/plot.mkinfit.html">plot.mkinfit()</a></code>: Avoid a warning message about only using the first component of ylim that occurred when ylim was specified explicitly</p></li> </ul></div> <div id="minor-changes-7" class="section level2"> <h2 class="hasAnchor"> <a href="#minor-changes-7" class="anchor"> </a>Minor changes</h2> <ul><li><p>The formatting of differential equations in the summary was improved by wrapping overly long lines</p></li> <li><p>The FOCUS_Z vignette was rebuilt with the above improvement and using a width of 70 to avoid output outside of the grey area</p></li> -<li><p><code>print.summary.mkinfit()</code>: Avoid a warning that occurred when gmkin showed summaries ofinitial fits without iterations</p></li> +<li><p><code><a href="../reference/summary.mkinfit.html">print.summary.mkinfit()</a></code>: Avoid a warning that occurred when gmkin showed summaries ofinitial fits without iterations</p></li> <li><p><code><a href="../reference/mkinfit.html">mkinfit()</a></code>: Avoid a warning that occurred when summarising a fit that was performed with maxitmodFit = 0 as done in gmkin for configuring new fits.</p></li> </ul></div> </div> diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index e05cdc29..7d036804 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index fe39ce6e..cfe6329b 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -60,12 +60,7 @@ </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 --> @@ -193,7 +188,7 @@ #> #> $time #> user system elapsed -#> 0.256 0.000 0.256 +#> 0.316 0.000 0.317 #> #> $mkinmod #> <mkinmod> model generated with @@ -379,7 +374,7 @@ #> } #> return(mC) #> } -#> <environment: 0x5b47f50> +#> <environment: 0x5d4a3b0> #> #> $cost_notrans #> function (P) @@ -401,7 +396,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x5b47f50> +#> <environment: 0x5d4a3b0> #> #> $hessian_notrans #> parent_0 alpha beta @@ -467,7 +462,7 @@ #> 99.66619 #> #> $date -#> [1] "Thu Nov 3 17:46:18 2016" +#> [1] "Fri Nov 4 15:36:31 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset @@ -546,7 +541,7 @@ #> #> $time #> user system elapsed -#> 0.068 0.000 0.070 +#> 0.076 0.000 0.077 #> #> $mkinmod #> <mkinmod> model generated with @@ -733,7 +728,7 @@ #> } #> return(mC) #> } -#> <environment: 0x46881c0> +#> <environment: 0x5d98970> #> #> $cost_notrans #> function (P) @@ -755,7 +750,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x46881c0> +#> <environment: 0x5d98970> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -818,7 +813,7 @@ #> 99.17407 #> #> $date -#> [1] "Thu Nov 3 17:46:18 2016" +#> [1] "Fri Nov 4 15:36:30 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]</div><div class='output co'>#> [[1]] @@ -894,7 +889,7 @@ #> #> $time #> user system elapsed -#> 0.068 0.000 0.070 +#> 0.076 0.000 0.077 #> #> $mkinmod #> <mkinmod> model generated with @@ -1081,7 +1076,7 @@ #> } #> return(mC) #> } -#> <environment: 0x46881c0> +#> <environment: 0x5d98970> #> #> $cost_notrans #> function (P) @@ -1103,7 +1098,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x46881c0> +#> <environment: 0x5d98970> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -1166,7 +1161,7 @@ #> 99.17407 #> #> $date -#> [1] "Thu Nov 3 17:46:18 2016" +#> [1] "Fri Nov 4 15:36:30 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" 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 9f098ff3..97af2f9c 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -61,12 +61,7 @@ </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 --> 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 e45463ba..1487e2c9 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -61,12 +61,7 @@ </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 --> 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 247c3e00..4571c175 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -61,12 +61,7 @@ </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 --> 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 006a3876..7003fa0e 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index c2501a7f..83edd323 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 1fbf7741..83bca886 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -60,12 +60,7 @@ </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 --> diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 2cecda28..13db29aa 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -60,12 +60,7 @@ </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 --> diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 68b7be44..56c2b48e 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -60,12 +60,7 @@ </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 --> diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 51c35eee..8ff5b5ba 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -60,12 +60,7 @@ </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 --> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 2f7dcb5d..43b6028a 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -60,12 +60,7 @@ </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 --> diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 82a0b039..8e491bc9 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 6ff7ac36..a3716060 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -61,12 +61,7 @@ </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 @@ with the advantage that the SFORB model can also be used for metabolites.</p> <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> - <p>The function is used internally by <code>summary.mkinfit</code>.</p> + <p>The function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index a4b661e2..633e0865 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -60,12 +60,7 @@ </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 --> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index d2551059..955b5c58 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/index.html b/docs/reference/index.html index 23eb608b..b7d59a21 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -60,12 +60,7 @@ </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 --> @@ -115,7 +110,7 @@ </ul> <p><a href="mkinparplot.html">Function to plot the confidence intervals obtained using - mkinfit</a></p> + list(list("mkinfit"))</a></p> <ul> <li><code><a href="mkinparplot.html">mkinparplot</a></code></li> </ul> @@ -124,6 +119,16 @@ <ul> <li><code><a href="mkinresplot.html">mkinresplot</a></code></li> </ul> + + <p><a href="plot.mkinfit.html">Plot the observed data and the fitted model of an mkinfit object</a></p> + <ul> + <li><code><a href="plot.mkinfit.html">plot.mkinfit</a></code></li><li><code><a href="plot.mkinfit.html">plot_sep</a></code></li> + </ul> + + <p><a href="summary.mkinfit.html">Summary method for class "mkinfit"</a></p> + <ul> + <li><code><a href="summary.mkinfit.html">summary.mkinfit</a></code></li><li><code><a href="summary.mkinfit.html">print.summary.mkinfit</a></code></li> + </ul> <h2 id="section-work-with-mmkin-objects" class="hasAnchor"><a href="#section-work-with-mmkin-objects" class="anchor"></a>Work with mmkin objects</h2> <p class="section-desc"><p>Functions working with aggregated results</p></p> @@ -176,6 +181,11 @@ <li><code><a href="print.mkinds.html">print.mkinds</a></code></li> </ul> + <p><a href="schaefer07_complex_case.html">Metabolism data set used for checking the software quality of KinGUI</a></p> + <ul> + <li><code><a href="schaefer07_complex_case.html">schaefer07_complex_case</a></code></li><li><code><a href="schaefer07_complex_case.html">schaefer07_complex_results</a></code></li> + </ul> + <p><a href="synthetic_data_for_UBA.html">Synthetic datasets for one parent compound with two metabolites</a></p> <ul> <li><code><a href="synthetic_data_for_UBA.html">synthetic_data_for_UBA_2014</a></code></li> @@ -189,6 +199,11 @@ <li><code><a href="geometric_mean.html">geometric_mean</a></code></li> </ul> + <p><a href="ilr.html">Function to perform isometric log-ratio transformation</a></p> + <ul> + <li><code><a href="ilr.html">ilr</a></code></li><li><code><a href="ilr.html">invilr</a></code></li> + </ul> + <p><a href="mkin_long_to_wide.html">Convert a dataframe from long to wide format</a></p> <ul> <li><code><a href="mkin_long_to_wide.html">mkin_long_to_wide</a></code></li> @@ -213,6 +228,11 @@ <ul> <li><code><a href="print.mkinmod.html">print.mkinmod</a></code></li> </ul> + + <p><a href="transform_odeparms.html">Functions to transform and backtransform kinetic parameters for fitting</a></p> + <ul> + <li><code><a href="transform_odeparms.html">transform_odeparms</a></code></li><li><code><a href="transform_odeparms.html">backtransform_odeparms</a></code></li> + </ul> <h2 id="section-analytical-solutions" class="hasAnchor"><a href="#section-analytical-solutions" class="anchor"></a>Analytical solutions</h2> <p class="section-desc"><p>Parent only model solutions</p></p> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 8309a23e..d32acb5b 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -61,12 +61,7 @@ </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 --> @@ -124,8 +119,8 @@ <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: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Thu Nov 3 17:46:24 2016 -#> Date of summary: Thu Nov 3 17:46:24 2016 +#> Date of fit: Fri Nov 4 15:36:38 2016 +#> Date of summary: Fri Nov 4 15:36:38 2016 #> #> Equations: #> d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -135,7 +130,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.662 s +#> Fitted with method Port using 246 model solutions performed in 1.886 s #> #> Weighting: none #> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 0385ccbb..21a8a8f8 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 965262ce..fe6e47e4 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 522aab33..f5dd4c88 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -60,12 +60,7 @@ </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 --> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 4e1be39c..8d420165 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -61,12 +61,7 @@ </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 --> @@ -110,7 +105,7 @@ as defined in the FOCUS kinetics report from 2006.</p> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - <p>This function is used internally by <code>summary.mkinfit</code>.</p> + <p>This function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 867fb9ff..b298d90a 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -61,12 +61,7 @@ </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 --> @@ -256,7 +251,7 @@ to do transformations. If TRUE, the g parameter of the DFOP and HS models are also transformed, as they can also be seen as compositional data. The transformation used for these transformations is the - <code>ilr</code> transformation. + <code><a href='ilr.html'>ilr</a></code> transformation. </dd> <dt>plot</dt> <dd> @@ -332,11 +327,11 @@ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>A list with "mkinfit" and "modFit" in the class attribute. - A summary can be obtained by <code>summary.mkinfit</code>.</p> + A summary can be obtained by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <p>Plotting methods <code>plot.mkinfit</code> and + <p>Plotting methods <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and <code><a href='mkinparplot.html'>mkinparplot</a></code>.</p> <p>Fitting of several models to several datasets in a single call to <code><a href='mmkin.html'>mmkin</a></code>.</p> @@ -361,15 +356,15 @@ <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: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Thu Nov 3 17:46:27 2016 -#> Date of summary: Thu Nov 3 17:46:27 2016 +#> Date of fit: Fri Nov 4 15:36:41 2016 +#> Date of summary: Fri Nov 4 15:36:41 2016 #> #> Equations: #> d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.147 s +#> Fitted with method Port using 64 model solutions performed in 0.156 s #> #> Weighting: none #> @@ -438,7 +433,7 @@ <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 -#> 1.204 1.244 0.932 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 1.244 1.208 0.933 </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 bdfd0e09..7dba1b6d 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index f8151c16..923abc6d 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 9ed92dd0..5fe94a8a 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -61,12 +61,7 @@ </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 --> @@ -83,7 +78,7 @@ </div> - <p>Deprecated function. It now only calls the plot method <code>plot.mkinfit</code>.</p> + <p>Deprecated function. It now only calls the plot method <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p> <pre><span class='fu'>mkinplot</span>(<span class='no'>fit</span>, <span class='no'>...</span>)</pre> @@ -96,7 +91,7 @@ </dd> <dt>&#8230;</dt> <dd> - further arguments passed to <code>plot.mkinfit</code>. + further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>. </dd> </dl> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 57bb747c..f7eb950a 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -61,12 +61,7 @@ </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 --> @@ -277,17 +272,17 @@ <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.004 0.024 0.004 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.008 0.024 0.005 </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.004 0.016 0.003 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.000 0.020 0.003 </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.036 0.000 0.033 </div></pre> +#> 0.036 0.000 0.037 </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index 53c4f62f..a0dcd06d 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -61,12 +61,7 @@ </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 --> @@ -85,7 +80,7 @@ <p>This function plots the residuals for the specified subset of the observed variables from an mkinfit object. A combined plot of the fitted - model and the residuals can be obtained using <code>plot.mkinfit</code> + model and the residuals can be obtained using <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> using the argument <code>show_residuals = TRUE</code>.</p> diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index 86374e4b..8424eaab 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 21461986..5613a720 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 61a597e7..e7158180 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index b107ca70..ef5c04b7 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -61,12 +61,7 @@ </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 --> @@ -124,7 +119,7 @@ </dd> <dt>&#8230;</dt> <dd> - Further arguments passed to <code>plot.mkinfit</code> and <code><a href='mkinresplot.html'>mkinresplot</a></code>. + Further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and <code><a href='mkinresplot.html'>mkinresplot</a></code>. </dd> </dl> diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index 9bd088b1..c578f4ee 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index 11b96036..3f653971 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 526dde10..c63ba490 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 46d078bf..241964a7 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -61,12 +61,7 @@ </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 --> @@ -144,15 +139,15 @@ <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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Thu Nov 3 17:46:35 2016 -#> Date of summary: Thu Nov 3 17:46:35 2016 +#> Date of fit: Fri Nov 4 15:36:49 2016 +#> Date of summary: Fri Nov 4 15:36:49 2016 #> #> Equations: #> d_parent = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.08 s +#> Fitted with method Port using 35 model solutions performed in 0.086 s #> #> Weighting: none #> diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index a46a5781..333b3dbf 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index ccd56ca4..5ee1e9cc 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -61,12 +61,7 @@ </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 --> @@ -88,7 +83,7 @@ constants and other paramters that can only take on positive values, a simple log transformation is used. For compositional parameters, such as the formations fractions that should always sum up to 1 and can not be - negative, the <code>ilr</code> transformation is used.</p> + negative, the <code><a href='ilr.html'>ilr</a></code> transformation is used.</p> <p>The transformation of sets of formation fractions is fragile, as it supposes the same ordering of the components in forward and backward transformation. @@ -114,7 +109,7 @@ <dd> The kinetic model of class <code><a href='mkinmod.html'>mkinmod</a></code>, containing the names of the model variables that are needed for grouping the formation fractions - before <code>ilr</code> transformation, the parameter names and + before <code><a href='ilr.html'>ilr</a></code> transformation, the parameter names and the information if the pathway to sink is included in the model. </dd> <dt>transform_rates</dt> @@ -133,7 +128,7 @@ assumption of normal distribution of the estimator. The default (TRUE) is to do transformations. The g parameter of the DFOP and HS models are also transformed, as they can also be seen as compositional data. The - transformation used for these transformations is the <code>ilr</code> + transformation used for these transformations is the <code><a href='ilr.html'>ilr</a></code> transformation. </dd> </dl> @@ -151,8 +146,8 @@ <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Thu Nov 3 17:46:36 2016 -#> Date of summary: Thu Nov 3 17:46:36 2016 +#> Date of fit: Fri Nov 4 15:36:50 2016 +#> Date of summary: Fri Nov 4 15:36:50 2016 #> #> Equations: #> d_parent = - k_parent_sink * parent - k_parent_m1 * parent @@ -160,7 +155,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.657 s +#> Fitted with method Port using 153 model solutions performed in 0.663 s #> #> Weighting: none #> |
