From d852e9e000f57f280deb84611ae1af58daa883cc Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 18 Nov 2016 23:08:45 +0100 Subject: Fix links in README, configure navbar, rebuild docs --- vignettes/compiled_models.html | 43 +++++++++++++++++++++--------------------- 1 file changed, 22 insertions(+), 21 deletions(-) (limited to 'vignettes/compiled_models.html') diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html index 2cb73ac7..c9501b11 100644 --- a/vignettes/compiled_models.html +++ b/vignettes/compiled_models.html @@ -11,7 +11,7 @@ - + Performance benefit by using compiled model definitions in mkin @@ -24,7 +24,7 @@ - + @@ -187,8 +187,9 @@ div.tocify { } .tocify-subheader .tocify-item { - font-size: 0.9em; - padding-left: 5px; + font-size: 0.90em; + padding-left: 25px; + text-indent: 0; } .tocify .list-group-item { @@ -216,7 +217,7 @@ div.tocify {

Performance benefit by using compiled model definitions in mkin

Johannes Ranke

-

2016-11-17

+

2016-11-18

@@ -257,21 +258,21 @@ mb.1 <- microbenchmark( print(mb.1) 
## Unit: milliseconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 4925.0009 4957.6694 4974.0652 4990.3379 4998.5974
-##       Eigenvalue based  838.9741  839.6651  857.4679  840.3561  866.7149
-##      deSolve, compiled  695.5858  709.3905  717.8062  723.1951  728.9163
+##  deSolve, not compiled 4919.3703 4922.1463 4957.6695 4924.9224 4976.8191
+##       Eigenvalue based  824.0317  840.7962  861.2648  857.5608  879.8813
+##      deSolve, compiled  691.8755  701.7453  706.2023  711.6151  713.3657
 ##        max neval cld
-##  5006.8569     3   c
-##   893.0736     3  b 
-##   734.6375     3 a
+## 5028.7158 3 c +## 902.2019 3 b +## 715.1164 3 a 
autoplot(mb.1)
-

+

We see that using the compiled model is by a factor of 6.9 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 6.900403
-## Eigenvalue based      1.162005
+## deSolve, not compiled 6.920767
+## Eigenvalue based      1.205091
 ## deSolve, compiled     1.000000
@@ -292,19 +293,19 @@ 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 10.905262 11.007527 11.335389 11.109791 11.55045
-##      deSolve, compiled  1.297428  1.304999  1.327356  1.312569  1.34232
+##                   expr       min        lq      mean    median        uq
+##  deSolve, not compiled 10.667049 10.692450 10.719555 10.717851 10.745808
+##      deSolve, compiled  1.279783  1.280014  1.281444  1.280244  1.282274
 ##        max neval cld
-##  11.991114     3   b
-##   1.372071     3  a
+## 10.773765 3 b +## 1.284305 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 8.5 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)
-- 
cgit v1.2.1