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Diffstat (limited to 'vignettes/compiled_models.html')
| -rw-r--r-- | vignettes/compiled_models.html | 42 |
1 files changed, 21 insertions, 21 deletions
diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html index 2f2a6edb..e6f21b09 100644 --- a/vignettes/compiled_models.html +++ b/vignettes/compiled_models.html @@ -77,7 +77,7 @@ img { --> <div id="benchmark-for-a-model-that-can-also-be-solved-with-eigenvalues" class="section level1"> <h1>Benchmark for a model that can also be solved with Eigenvalues</h1> -<p>This evaluation is taken from the example section of mkinfit. When using an mkin version greater than 0.9-36 and the ccSolve package is installed and functional, you will get a message that the model is being compiled when defining a model using mkinmod.</p> +<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 compiler (gcc) is installed, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod.</p> <pre class="r"><code>library("mkin") SFO_SFO <- mkinmod( parent = list(type = "SFO", to = "m1", sink = TRUE), @@ -94,20 +94,20 @@ mb.1 <- microbenchmark( 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 6192.0125 6195.3470 6211.0309 6198.6816 6220.5401 -## Eigenvalue based 956.7604 1008.7224 1026.2572 1060.6844 1061.0055 -## deSolve, compiled 869.6880 871.9315 883.4929 874.1751 890.3953 +<pre><code>## min lq mean median uq +## deSolve, not compiled 4969.585 5033.7311 5092.7389 5097.8773 5154.3160 +## Eigenvalue based 868.731 891.7239 909.6449 914.7169 930.1018 +## deSolve, compiled 4935.049 4935.4796 4968.2150 4935.9097 4984.7978 ## max neval -## deSolve, not compiled 6242.3986 3 -## Eigenvalue based 1061.3266 3 -## deSolve, compiled 906.6155 3</code></pre> +## deSolve, not compiled 5210.7547 3 +## Eigenvalue based 945.4867 3 +## deSolve, compiled 5033.6858 3</code></pre> <p>We see that using the compiled model is almost a factor of 8 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 7.120877 -## Eigenvalue based 1.205328 -## deSolve, compiled 1.000000</code></pre> +<pre><code>## median +## deSolve, not compiled 1.0328141 +## Eigenvalue based 0.1853188 +## deSolve, compiled 1.0000000</code></pre> </div> <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level1"> <h1>Benchmark for a model that can not be solved with Eigenvalues</h1> @@ -124,16 +124,16 @@ 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 13.297283 13.427702 13.481155 13.558121 13.573092 -## deSolve, compiled 1.486926 1.526887 1.546851 1.566848 1.576813 -## max neval -## deSolve, not compiled 13.588063 3 -## deSolve, compiled 1.586778 3</code></pre> +## deSolve, not compiled 11.745276 11.754288 11.820726 11.763300 11.858451 +## deSolve, compiled 1.385829 1.386407 1.400841 1.386985 1.408347 +## max neval +## deSolve, not compiled 11.95360 3 +## deSolve, compiled 1.42971 3</code></pre> <pre class="r"><code>smb.2["median"]/smb.2["deSolve, compiled", "median"]</code></pre> -<pre><code>## median -## deSolve, not compiled 8.653119 -## deSolve, compiled 1.000000</code></pre> -<p>Here we get a performance benefit of more than a factor of 8 using the version of the differential equation model compiled from C code using the ccSolve package!</p> +<pre><code>## median +## deSolve, not compiled 8.4812 +## deSolve, compiled 1.0000</code></pre> +<p>Here we get a performance benefit of more than a factor of 10 using the version of the differential equation model compiled from C code using the inline package!</p> </div> |