diff options
Diffstat (limited to 'vignettes')
| -rw-r--r-- | vignettes/FOCUS_Z.pdf | bin | 224802 -> 224775 bytes | |||
| -rw-r--r-- | vignettes/compiled_models.html | 34 | ||||
| -rw-r--r-- | vignettes/mkin.pdf | bin | 160268 -> 160268 bytes |
3 files changed, 17 insertions, 17 deletions
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf Binary files differindex 1234de20..31480019 100644 --- a/vignettes/FOCUS_Z.pdf +++ b/vignettes/FOCUS_Z.pdf diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html index 92919da9..7722d95a 100644 --- a/vignettes/compiled_models.html +++ b/vignettes/compiled_models.html @@ -99,18 +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 9307.3194 9319.9546 9332.8171 9332.5899 9345.5659 -## Eigenvalue based 855.3608 855.8081 869.4725 856.2555 876.5283 -## deSolve, compiled 686.6143 687.9256 698.0279 689.2369 703.7346 +## deSolve, not compiled 9442.5119 9447.2060 9458.3420 9451.9001 9466.2571 +## Eigenvalue based 868.6312 872.4552 895.3422 876.2792 908.6977 +## deSolve, compiled 691.9663 697.5653 701.1004 703.1643 705.6674 ## max neval cld -## deSolve, not compiled 9358.5420 3 c -## Eigenvalue based 896.8012 3 b -## deSolve, compiled 718.2324 3 a</code></pre> -<p>We see that using the compiled model is by a factor of 13.5 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 9480.6141 3 c +## Eigenvalue based 941.1163 3 b +## deSolve, compiled 708.1706 3 a</code></pre> +<p>We see that using the compiled model is by a factor of 13.4 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 13.540468 -## Eigenvalue based 1.242324 +## deSolve, not compiled 13.441951 +## Eigenvalue based 1.246194 ## deSolve, compiled 1.000000</code></pre> </div> <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2"> @@ -127,17 +127,17 @@ print(smb.1)</code></pre> 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 20.130709 20.147223 20.180429 20.163737 20.205289 -## deSolve, compiled 1.235864 1.255748 1.267458 1.275632 1.283255 -## max neval cld -## deSolve, not compiled 20.246841 3 b -## deSolve, compiled 1.290878 3 a</code></pre> +<pre><code>## min lq mean median uq +## deSolve, not compiled 20.444632 20.48824 20.557595 20.531857 20.614077 +## deSolve, compiled 1.251733 1.25179 1.275227 1.251846 1.286973 +## max neval cld +## deSolve, not compiled 20.6963 3 b +## deSolve, compiled 1.3221 3 a</code></pre> <pre class="r"><code>smb.2["median"]/smb.2["deSolve, compiled", "median"]</code></pre> <pre><code>## median -## deSolve, not compiled 15.80686 +## deSolve, not compiled 16.40126 ## deSolve, compiled 1.00000</code></pre> -<p>Here we get a performance benefit of a factor of 15.8 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 16.4 using the version of the differential equation model compiled from C code using the inline package!</p> <p>This vignette was built with mkin 0.9.41 on</p> <pre><code>## R version 3.2.2 (2015-08-14) ## Platform: x86_64-pc-linux-gnu (64-bit) diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf Binary files differindex 9c1a03f3..9f9f9af0 100644 --- a/vignettes/mkin.pdf +++ b/vignettes/mkin.pdf |