From 19997986f7ee5b6274c9a06796b97a5610c4f888 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 26 Jun 2015 14:52:22 +0200 Subject: Pass R CMD check --as-cran, vignette rebuild --- vignettes/compiled_models.html | 47 +++++++++++++++++++++++------------------- 1 file changed, 26 insertions(+), 21 deletions(-) (limited to 'vignettes/compiled_models.html') diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html index 8d4c36a4..12454559 100644 --- a/vignettes/compiled_models.html +++ b/vignettes/compiled_models.html @@ -10,7 +10,7 @@ - + Performance benefit by using compiled model definitions in mkin @@ -65,7 +65,7 @@ img {
@@ -82,8 +82,13 @@ img { 
##            gcc 
 ## "/usr/bin/gcc"

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

-
library("mkin")
-SFO_SFO <- mkinmod(
+
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(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"))

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

@@ -99,18 +104,18 @@ smb.1 <- summary(mb.1)[-1]
 rownames(smb.1) <- c("deSolve, not compiled", "Eigenvalue based", "deSolve, compiled")
 print(smb.1)
##                             min        lq      mean    median        uq
-## deSolve, not compiled 6555.9044 6654.5464 6693.6732 6753.1885 6762.5577
-## Eigenvalue based       941.4496  949.4094  972.3045  957.3693  987.7320
-## deSolve, compiled      743.6684  756.3411  761.1512  769.0139  769.8926
+## 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
 ##                             max neval
-## deSolve, not compiled 6771.9268     3
-## Eigenvalue based      1018.0946     3
-## deSolve, compiled      770.7713     3
-

We see that using the compiled model is by a factor of 8.8 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:

+## deSolve, not compiled 5466.1959 3 +## Eigenvalue based 966.1282 3 +## deSolve, compiled 759.7404 3 +

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:

smb.1["median"]/smb.1["deSolve, compiled", "median"]
##                         median
-## deSolve, not compiled 8.781621
-## Eigenvalue based      1.244931
+## deSolve, not compiled 7.132304
+## Eigenvalue based      1.267853
 ## deSolve, compiled     1.000000
@@ -128,17 +133,17 @@ smb.2 <- summary(mb.2)[-1] rownames(smb.2) <- c("deSolve, not compiled", "deSolve, compiled") print(smb.2) 
##                             min        lq      mean    median        uq
-## deSolve, not compiled 14.202106 14.342265 14.430352 14.482424 14.544475
-## deSolve, compiled      1.363102  1.367979  1.377016  1.372857  1.383973
+## 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
 ##                             max neval
-## deSolve, not compiled 14.606526     3
-## deSolve, compiled      1.395088     3
+## deSolve, not compiled 11.505901 3 +## deSolve, compiled 1.367025 3 
smb.2["median"]/smb.2["deSolve, compiled", "median"]
##                         median
-## deSolve, not compiled 10.54912
-## deSolve, compiled      1.00000
-

Here we get a performance benefit of a factor of 10.5 using the version of the differential equation model compiled from C code using the inline package!

-

This vignette was built with mkin 0.9.38 on

+## deSolve, not compiled 8.465368 +## deSolve, compiled 1.000000 +

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!

+

This vignette was built with mkin 0.9.39 on

## R version 3.2.1 (2015-06-18)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 8 (jessie)
-- cgit v1.2.1