diff options
Diffstat (limited to 'vignettes')
| -rw-r--r-- | vignettes/FOCUS_D.html | 4 | ||||
| -rw-r--r-- | vignettes/FOCUS_L.html | 4 | ||||
| -rw-r--r-- | vignettes/FOCUS_Z.pdf | bin | 225057 -> 224819 bytes | |||
| -rw-r--r-- | vignettes/compiled_models.html | 53 | ||||
| -rw-r--r-- | vignettes/mkin.pdf | bin | 160258 -> 160268 bytes |
5 files changed, 33 insertions, 28 deletions
diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index 23cfe0fb..557ceb03 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -10,7 +10,7 @@ <meta name="author" content="Johannes Ranke" /> -<meta name="date" content="2015-07-22" /> +<meta name="date" content="2015-11-09" /> <title>Example evaluation of FOCUS Example Dataset D</title> @@ -64,7 +64,7 @@ img { <div id="header"> <h1 class="title">Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author"><em>Johannes Ranke</em></h4> -<h4 class="date"><em>2015-07-22</em></h4> +<h4 class="date"><em>2015-11-09</em></h4> </div> diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index 98e38924..9bb60153 100644 --- a/vignettes/FOCUS_L.html +++ b/vignettes/FOCUS_L.html @@ -10,7 +10,7 @@ <meta name="author" content="Johannes Ranke" /> -<meta name="date" content="2015-07-22" /> +<meta name="date" content="2015-11-09" /> <title>Example evaluation of FOCUS Laboratory Data L1 to L3</title> @@ -65,7 +65,7 @@ img { <div id="header"> <h1 class="title">Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author"><em>Johannes Ranke</em></h4> -<h4 class="date"><em>2015-07-22</em></h4> +<h4 class="date"><em>2015-11-09</em></h4> </div> <div id="TOC"> diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf Binary files differindex 21f6db98..a84b8c94 100644 --- a/vignettes/FOCUS_Z.pdf +++ b/vignettes/FOCUS_Z.pdf diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html index a8f6e3ef..3d92a7b8 100644 --- a/vignettes/compiled_models.html +++ b/vignettes/compiled_models.html @@ -10,7 +10,7 @@ <meta name="author" content="Johannes Ranke" /> -<meta name="date" content="2015-06-26" /> +<meta name="date" content="2015-11-09" /> <title>Performance benefit by using compiled model definitions in mkin</title> @@ -65,7 +65,7 @@ img { <div id="header"> <h1 class="title">Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author"><em>Johannes Ranke</em></h4> -<h4 class="date"><em>2015-06-26</em></h4> +<h4 class="date"><em>2015-11-09</em></h4> </div> <div id="TOC"> @@ -82,8 +82,13 @@ img { <pre><code>## gcc ## "/usr/bin/gcc"</code></pre> <p>First, we build a simple degradation model for a parent compound with one metabolite.</p> -<pre class="r"><code>library("mkin") -SFO_SFO <- mkinmod( +<pre class="r"><code>library("mkin")</code></pre> +<pre><code>## Loading required package: minpack.lm +## Loading required package: rootSolve +## Loading required package: inline +## Loading required package: methods +## Loading required package: parallel</code></pre> +<pre class="r"><code>SFO_SFO <- mkinmod( parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))</code></pre> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> @@ -99,18 +104,18 @@ smb.1 <- summary(mb.1)[-1] rownames(smb.1) <- c("deSolve, not compiled", "Eigenvalue based", "deSolve, compiled") print(smb.1)</code></pre> <pre><code>## min lq mean median uq -## deSolve, not compiled 6767.3728 6834.5128 6879.5969 6901.6528 6935.7090 -## Eigenvalue based 977.5545 1161.8591 1225.1262 1346.1637 1348.9120 -## deSolve, compiled 761.0689 761.8958 772.3379 762.7228 777.9724 -## max neval -## deSolve, not compiled 6969.7653 3 -## Eigenvalue based 1351.6603 3 -## deSolve, compiled 793.2221 3</code></pre> -<p>We see that using the compiled model is by a factor of 9 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> +## deSolve, not compiled 4920.5498 4957.8305 5073.8005 4995.1112 5150.4259 +## Eigenvalue based 792.7603 820.6244 849.2773 848.4885 877.5358 +## deSolve, compiled 663.5431 673.4949 678.4844 683.4468 685.9551 +## max neval cld +## deSolve, not compiled 5305.7406 3 b +## Eigenvalue based 906.5832 3 a +## deSolve, compiled 688.4634 3 a</code></pre> +<p>We see that using the compiled model is by a factor of 7.3 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> <pre class="r"><code>smb.1["median"]/smb.1["deSolve, compiled", "median"]</code></pre> <pre><code>## median -## deSolve, not compiled 9.048704 -## Eigenvalue based 1.764945 +## deSolve, not compiled 7.308706 +## Eigenvalue based 1.241484 ## deSolve, compiled 1.000000</code></pre> </div> <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2"> @@ -128,18 +133,18 @@ smb.2 <- summary(mb.2)[-1] rownames(smb.2) <- c("deSolve, not compiled", "deSolve, compiled") print(smb.2)</code></pre> <pre><code>## min lq mean median uq -## deSolve, not compiled 14.161917 14.189080 14.201763 14.216243 14.221687 -## deSolve, compiled 1.358691 1.366613 1.393306 1.374535 1.410614 -## max neval -## deSolve, not compiled 14.227131 3 -## deSolve, compiled 1.446693 3</code></pre> +## deSolve, not compiled 10.710141 10.757988 10.810178 10.805835 10.860196 +## deSolve, compiled 1.200581 1.203966 1.211877 1.207351 1.217525 +## max neval cld +## deSolve, not compiled 10.914558 3 b +## deSolve, compiled 1.227699 3 a</code></pre> <pre class="r"><code>smb.2["median"]/smb.2["deSolve, compiled", "median"]</code></pre> <pre><code>## median -## deSolve, not compiled 10.34258 -## deSolve, compiled 1.00000</code></pre> -<p>Here we get a performance benefit of a factor of 10.3 using the version of the differential equation model compiled from C code using the inline package!</p> -<p>This vignette was built with mkin 0.9.39 on</p> -<pre><code>## R version 3.2.1 (2015-06-18) +## deSolve, not compiled 8.950036 +## deSolve, compiled 1.000000</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 using the inline package!</p> +<p>This vignette was built with mkin 0.9.40.900 on</p> +<pre><code>## R version 3.2.2 (2015-08-14) ## Platform: x86_64-pc-linux-gnu (64-bit) ## Running under: Debian GNU/Linux 8 (jessie)</code></pre> <pre><code>## CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz</code></pre> diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf Binary files differindex 3c9ea903..ce628c0e 100644 --- a/vignettes/mkin.pdf +++ b/vignettes/mkin.pdf |