From 7faf98ac5475bb2041d7e434478c58c2f2cec0fd Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 28 Jun 2016 08:23:38 +0200 Subject: Static documentation rebuilt by staticdocs::build_site() --- vignettes/compiled_models.html | 51 +++++++++++++++++++----------------------- 1 file changed, 23 insertions(+), 28 deletions(-) (limited to 'vignettes/compiled_models.html') diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html index c3ffb035..cec76ef9 100644 --- a/vignettes/compiled_models.html +++ b/vignettes/compiled_models.html @@ -226,13 +226,8 @@ div.tocify { 
##            gcc 
 ## "/usr/bin/gcc"

First, we build a simple degradation model for a parent compound with one metabolite.

-
library("mkin")
-
## Loading required package: minpack.lm
-
## Loading required package: rootSolve
-
## Loading required package: inline
-
## Loading required package: methods
-
## Loading required package: parallel
-
SFO_SFO <- mkinmod(
+
library("mkin")
+SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"))

 
## Successfully compiled differential equation model from auto-generated C code.

@@ -255,22 +250,22 @@ mb.1 <- microbenchmark(
 print(mb.1)
## Unit: seconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 13.694897 13.774112 13.820936 13.853327 13.883956
-##       Eigenvalue based  2.087861  2.089503  2.116323  2.091145  2.130555
-##      deSolve, compiled  1.794975  1.799892  1.814653  1.804808  1.824492
-##        max neval cld
-##  13.914585     3   c
-##   2.169964     3  b 
-##   1.844177     3 a
+## deSolve, not compiled 25.422123 25.889685 26.065978 26.357247 26.387905 +## Eigenvalue based 2.243667 2.254539 2.277770 2.265412 2.294821 +## deSolve, compiled 1.849468 1.865343 1.871339 1.881219 1.882274 +## max neval cld +## 26.41856 3 b +## 2.32423 3 a +## 1.88333 3 a 
autoplot(mb.1)
-

-

We see that using the compiled model is by a factor of 7.7 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:

+

+

We see that using the compiled model is by a factor of 14 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:

rownames(smb.1) <- smb.1$expr
 smb.1["median"]/smb.1["deSolve, compiled", "median"]
-
##                         median
-## deSolve, not compiled 7.675788
-## Eigenvalue based      1.158652
-## deSolve, compiled     1.000000
+
##                          median
+## deSolve, not compiled 14.010730
+## Eigenvalue based       1.204226
+## deSolve, compiled      1.000000

Benchmark for a model that can not be solved with Eigenvalues

@@ -290,20 +285,20 @@ smb.1["median"]/smb.1["deSolve, compiled", "median" 
smb.2 <- summary(mb.2)
 print(mb.2)
## Unit: seconds
-##                   expr       min        lq      mean   median        uq
-##  deSolve, not compiled 29.120048 29.170013 29.246607 29.21998 29.309886
-##      deSolve, compiled  3.338458  3.343954  3.379437  3.34945  3.399926
+##                   expr       min       lq      mean    median        uq
+##  deSolve, not compiled 54.386189 54.39423 54.477986 54.402271 54.523884
+##      deSolve, compiled  3.424205  3.53522  3.574587  3.646236  3.649778
 ##        max neval cld
-##  29.399796     3   b
-##   3.450402     3  a
+## 54.645498 3 b +## 3.653319 3 a 
smb.2["median"]/smb.2["deSolve, compiled", "median"]
##   median
 ## 1     NA
 ## 2     NA
autoplot(mb.2)
-

-

Here we get a performance benefit of a factor of 8.7 using the version of the differential equation model compiled from C code!

-

This vignette was built with mkin 0.9.43 on

+

+

Here we get a performance benefit of a factor of 14.9 using the version of the differential equation model compiled from C code!

+

This vignette was built with mkin 0.9.43.9000 on

## R version 3.3.1 (2016-06-21)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 8 (jessie)
-- cgit v1.2.3