From e05656d57668688b971c28e32b4cfd4d3eac4662 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 18 Sep 2019 13:03:50 +0200 Subject: Correct and rebuild docs - Reconcile docs and code for max_twa_parent - Correct links to docs in twa vignette - Static documentation rebuilt by pkgdown --- docs/articles/web_only/compiled_models.html | 49 ++++++++++++++++------------- 1 file changed, 27 insertions(+), 22 deletions(-) (limited to 'docs/articles/web_only/compiled_models.html') diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 0bb564ad..89977591 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -7,8 +7,9 @@ Performance benefit by using compiled model definitions in mkin • mkin - - + + + @@ -82,13 +83,14 @@ +

Performance benefit by using compiled model definitions in mkin

Johannes Ranke

-

2019-07-09

+

2019-09-18

@@ -101,18 +103,18 @@

Model that can also be solved with Eigenvalues

This evaluation is taken from the example section of mkinfit. When using an mkin version equal to or greater than 0.9-36 and a C compiler (gcc) is available, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod. The mkinmod() function checks for presence of the gcc compiler using

-
Sys.which("gcc")
+
Sys.which("gcc")
##            gcc 
 ## "/usr/bin/gcc"

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

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

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

 
We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the benchmark package.

-
if (require(rbenchmark)) {
-  b.1 <- benchmark(
+
if (require(rbenchmark)) {
+  b.1 <- benchmark(
     "deSolve, not compiled" = mkinfit(SFO_SFO, FOCUS_2006_D,
                                       solution_type = "deSolve",
                                       use_compiled = FALSE, quiet = TRUE),
@@ -121,11 +123,11 @@
     "deSolve, compiled" = mkinfit(SFO_SFO, FOCUS_2006_D,
                                   solution_type = "deSolve", quiet = TRUE),
     replications = 3)
-  print(b.1)
-  factor_SFO_SFO <- round(b.1["1", "relative"])
+  print(b.1)
+  factor_SFO_SFO <- round(b.1["1", "relative"])
 } else {
   factor_SFO_SFO <- NA
-  print("R package rbenchmark is not available")
+  print("R package rbenchmark is not available")
 }

 
## Lade nötiges Paket: rbenchmark

 
## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve",
@@ -163,9 +165,9 @@
 ## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet
 ## = TRUE): Observations with value of zero were removed from the data

 
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   3.127    1.000     3.125        0
-## 1 deSolve, not compiled            3  28.337    9.062    28.322        0
-## 2      Eigenvalue based            3   4.320    1.382     4.317        0
+## 3     deSolve, compiled            3   3.124    1.000     3.122        0
+## 1 deSolve, not compiled            3  28.822    9.226    28.807        0
+## 2      Eigenvalue based            3   4.416    1.414     4.413        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -176,21 +178,21 @@
 

 Model that can not be solved with Eigenvalues

 
This evaluation is also taken from the example section of mkinfit.

-
if (require(rbenchmark)) {
+
if (require(rbenchmark)) {
   FOMC_SFO <- mkinmod(
     parent = mkinsub("FOMC", "m1"),
     m1 = mkinsub( "SFO"))
 
-  b.2 <- benchmark(
+  b.2 <- benchmark(
     "deSolve, not compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D,
                                       use_compiled = FALSE, quiet = TRUE),
     "deSolve, compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE),
     replications = 3)
-  print(b.2)
-  factor_FOMC_SFO <- round(b.2["1", "relative"])
+  print(b.2)
+  factor_FOMC_SFO <- round(b.2["1", "relative"])
 } else {
   factor_FOMC_SFO <- NA
-  print("R package benchmark is not available")
+  print("R package benchmark is not available")
 }

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

 
## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet =
@@ -214,14 +216,14 @@
 ## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
 ## value of zero were removed from the data

 
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.783    1.000     4.780        0
-## 1 deSolve, not compiled            3  52.761   11.031    52.733        0
+## 2     deSolve, compiled            3   4.878    1.000     4.875        0
+## 1 deSolve, not compiled            3  53.602   10.989    53.568        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

 
Here we get a performance benefit of a factor of 11 using the version of the differential equation model compiled from C code!

 
This vignette was built with mkin 0.9.49.6 on

-
## R version 3.6.0 (2019-04-26)
+
## R version 3.6.1 (2019-07-05)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 10 (buster)

 
## CPU model: AMD Ryzen 7 1700 Eight-Core Processor

@@ -242,17 +244,20 @@
 

 
 
+
       

   
Developed by Johannes Ranke.

 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.4.1.

 

+
       

 

 
   
 
+
   
 
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