diff options
author | Johannes Ranke <jranke@uni-bremen.de> | 2015-06-26 16:08:04 +0200 |
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committer | Johannes Ranke <jranke@uni-bremen.de> | 2015-06-26 16:08:04 +0200 |
commit | cc0d7a44cccac46ea1c71cf663aadee0efb2bba7 (patch) | |
tree | 146d1cbcb29ce4831f9ff013bf03a8637b348e8f /vignettes/compiled_models.html | |
parent | 4cc13bcd8305611cb730faecae3511acf7c92043 (diff) |
Vignettes rebuilt by staticdocs::build_site() for static documentation on r-forge
Diffstat (limited to 'vignettes/compiled_models.html')
-rw-r--r-- | vignettes/compiled_models.html | 39 |
1 files changed, 17 insertions, 22 deletions
diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html index 12454559..a62f3826 100644 --- a/vignettes/compiled_models.html +++ b/vignettes/compiled_models.html @@ -82,13 +82,8 @@ 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")</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( +<pre class="r"><code>library("mkin") +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> @@ -104,18 +99,18 @@ 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 5292.0165 5313.7620 5364.5733 5335.5075 5400.8517 -## Eigenvalue based 893.9459 921.1984 936.1750 948.4509 957.2895 -## deSolve, compiled 742.7723 745.4243 750.1963 748.0763 753.9083 +## deSolve, not compiled 7047.6039 7083.3201 7123.5962 7119.0364 7161.5924 +## Eigenvalue based 901.5593 924.3357 968.8689 947.1121 1002.5238 +## deSolve, compiled 765.7604 770.7657 786.8638 775.7709 797.4156 ## max neval -## deSolve, not compiled 5466.1959 3 -## Eigenvalue based 966.1282 3 -## deSolve, compiled 759.7404 3</code></pre> -<p>We see that using the compiled model is by a factor of 7.1 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 7204.1483 3 +## Eigenvalue based 1057.9355 3 +## deSolve, compiled 819.0602 3</code></pre> +<p>We see that using the compiled model is by a factor of 9.2 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 7.132304 -## Eigenvalue based 1.267853 +## deSolve, not compiled 9.176725 +## Eigenvalue based 1.220866 ## deSolve, compiled 1.000000</code></pre> </div> <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2"> @@ -133,16 +128,16 @@ 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 11.277340 11.336373 11.392883 11.395407 11.450654 -## deSolve, compiled 1.339204 1.342662 1.350783 1.346121 1.356573 +## deSolve, not compiled 14.080456 14.209689 14.287313 14.338922 14.390742 +## deSolve, compiled 1.467266 1.521451 1.555168 1.575636 1.599119 ## max neval -## deSolve, not compiled 11.505901 3 -## deSolve, compiled 1.367025 3</code></pre> +## deSolve, not compiled 14.442561 3 +## deSolve, compiled 1.622601 3</code></pre> <pre class="r"><code>smb.2["median"]/smb.2["deSolve, compiled", "median"]</code></pre> <pre><code>## median -## deSolve, not compiled 8.465368 +## deSolve, not compiled 9.100402 ## deSolve, compiled 1.000000</code></pre> -<p>Here we get a performance benefit of a factor of 8.5 using the version of the differential equation model compiled from C code using the inline package!</p> +<p>Here we get a performance benefit of a factor of 9.1 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) ## Platform: x86_64-pc-linux-gnu (64-bit) |