diff options
Diffstat (limited to 'vignettes/compiled_models.html')
| -rw-r--r-- | vignettes/compiled_models.html | 24 |
1 files changed, 15 insertions, 9 deletions
diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html index 53c5647f..67d0f658 100644 --- a/vignettes/compiled_models.html +++ b/vignettes/compiled_models.html @@ -229,8 +229,13 @@ div.tocify { <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</code></pre> +<pre><code>## Loading required package: rootSolve</code></pre> +<pre><code>## Loading required package: inline</code></pre> +<pre><code>## Loading required package: methods</code></pre> +<pre><code>## 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> @@ -251,15 +256,16 @@ SFO_SFO <- mkinmod( factor_SFO_SFO <- NA print("R package benchmark is not available") }</code></pre> +<pre><code>## Loading required package: rbenchmark</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 3 deSolve, compiled 3 2.742 1.000 2.740 0.000 -## 1 deSolve, not compiled 3 24.467 8.923 24.344 0.124 -## 2 Eigenvalue based 3 3.050 1.112 3.044 0.004 +## 3 deSolve, compiled 3 2.040 1.000 2.040 0 +## 1 deSolve, not compiled 3 14.622 7.168 14.624 0 +## 2 Eigenvalue based 3 2.478 1.215 2.480 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 ## 2 0 0</code></pre> -<p>We see that using the compiled model is by a factor of around 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> +<p>We see that using the compiled model is by a factor of around 7 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs.</p> </div> <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2"> <h2>Model that can not be solved with Eigenvalues</h2> @@ -282,12 +288,12 @@ SFO_SFO <- mkinmod( }</code></pre> <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 4.038 1.000 4.036 0.000 -## 1 deSolve, not compiled 3 55.209 13.672 54.888 0.324 +## 2 deSolve, compiled 3 3.500 1.000 3.500 0 +## 1 deSolve, not compiled 3 29.932 8.552 29.932 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> -<p>Here we get a performance benefit of a factor of 14 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 using the version of the differential equation model compiled from C code!</p> <p>This vignette was built with mkin 0.9.45 on</p> <pre><code>## R version 3.4.0 (2017-04-21) ## Platform: x86_64-pc-linux-gnu (64-bit) |