From 05ca1ca375414b974b13da3bdb565e20d0cd46d6 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 8 Dec 2016 08:18:52 +0100 Subject: Static documentation articles rebuilt by pkgdown::build_articles() Split out an extra pd_articles target in the Makefile --- docs/articles/compiled_models.html | 37 +++++++++++++++++++++---------------- 1 file changed, 21 insertions(+), 16 deletions(-) (limited to 'docs/articles/compiled_models.html') diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index d39caf12..2850a9ae 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -67,8 +67,13 @@ 
##            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.

@@ -91,21 +96,21 @@ mb.1 <- micr
 print(mb.1)
## Unit: milliseconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 6263.2932 6273.5107 6286.8574 6283.7283 6298.6394
-##       Eigenvalue based  865.5257  872.4146  892.2705  879.3036  905.6429
-##      deSolve, compiled  716.7534  717.9075  724.6869  719.0617  728.6537
+##  deSolve, not compiled 4973.8901 4975.2320 5000.4065 4976.5739 5013.6648
+##       Eigenvalue based  848.4335  859.7111  886.9766  870.9887  906.2481
+##      deSolve, compiled  702.8916  705.1930  706.2696  707.4944  707.9587
 ##        max neval cld
-##  6313.5506     3   c
-##   931.9821     3  b 
-##   738.2457     3 a
+## 5050.7556 3 c +## 941.5075 3 b +## 708.4229 3 a 
autoplot(mb.1)

-

We see that using the compiled model is by a factor of 8.7 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 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:

rownames(smb.1) <- smb.1$expr
 smb.1["median"]/smb.1["deSolve, compiled", "median"]
##                         median
-## deSolve, not compiled 8.738789
-## Eigenvalue based      1.222849
+## deSolve, not compiled 7.034082
+## Eigenvalue based      1.231089
 ## deSolve, compiled     1.000000
@@ -127,18 +132,18 @@ smb.1["median"]/smbprint(mb.2)
## Unit: seconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 13.487097 13.492149 13.528060 13.497201 13.548541
-##      deSolve, compiled  1.307845  1.318979  1.322967  1.330114  1.330528
+##  deSolve, not compiled 10.819486 10.846433 10.863732 10.873381 10.885855
+##      deSolve, compiled  1.300192  1.301168  1.304769  1.302144  1.307058
 ##        max neval cld
-##  13.599881     3   b
-##   1.330941     3  a
+## 10.898330 3 b +## 1.311972 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 10.1 using the version of the differential equation model compiled from C code!

+

Here we get a performance benefit of a factor of 8.4 using the version of the differential equation model compiled from C code!

This vignette was built with mkin 0.9.44.9000 on

## R version 3.3.2 (2016-10-31)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
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