From b4ac7f030fdb467ee995a7e12314d80633a72668 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 6 Sep 2018 11:53:38 +0200 Subject: Static documentation rebuilt by pkgdown --- docs/articles/compiled_models.html | 90 +++++++++++++++++++------------------- 1 file changed, 45 insertions(+), 45 deletions(-) (limited to 'docs/articles/compiled_models.html') diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index 183c9658..17387187 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -84,7 +84,7 @@

Performance benefit by using compiled model definitions in mkin

Johannes Ranke

-

2018-07-18

+

2018-09-06

@@ -97,37 +97,37 @@

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)
-SFO_SFO <- mkinmod(
-  parent = mkinsub("SFO", "m1"),
-  m1 = mkinsub("SFO"))
+
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(
-    "deSolve, not compiled" = mkinfit(SFO_SFO, FOCUS_2006_D,
-                                      solution_type = "deSolve",
-                                      use_compiled = FALSE, quiet = TRUE),
-    "Eigenvalue based" = mkinfit(SFO_SFO, FOCUS_2006_D,
-                                 solution_type = "eigen", quiet = TRUE),
-    "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"])
-} else {
-  factor_SFO_SFO <- NA
-  print("R package benchmark is not available")
-}
+
if (require(rbenchmark)) {
+  b.1 <- benchmark(
+    "deSolve, not compiled" = mkinfit(SFO_SFO, FOCUS_2006_D,
+                                      solution_type = "deSolve",
+                                      use_compiled = FALSE, quiet = TRUE),
+    "Eigenvalue based" = mkinfit(SFO_SFO, FOCUS_2006_D,
+                                 solution_type = "eigen", quiet = TRUE),
+    "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"])
+} else {
+  factor_SFO_SFO <- NA
+  print("R package benchmark is not available")
+}
## Lade nötiges Paket: rbenchmark
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   2.044    1.000     2.043        0
-## 1 deSolve, not compiled            3  16.571    8.107    16.565        0
-## 2      Eigenvalue based            3   2.499    1.223     2.496        0
+## 3     deSolve, compiled            3   2.112    1.000     2.110        0
+## 1 deSolve, not compiled            3  16.633    7.875    16.624        0
+## 2      Eigenvalue based            3   2.637    1.249     2.635        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -138,31 +138,31 @@ SFO_SFO <- 
 Model that can not be solved with Eigenvalues
 
This evaluation is also taken from the example section of mkinfit.

-
if (require(rbenchmark)) {
-  FOMC_SFO <- mkinmod(
-    parent = mkinsub("FOMC", "m1"),
-    m1 = mkinsub( "SFO"))
-
-  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"])
-} else {
-  factor_FOMC_SFO <- NA
-  print("R package benchmark is not available")
-}

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

 
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   3.592    1.000     3.589        0
-## 1 deSolve, not compiled            3  35.340    9.839    35.324        0
+## 2     deSolve, compiled            3   3.720    1.000     3.718        0
+## 1 deSolve, not compiled            3  34.677    9.322    34.661        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

-
Here we get a performance benefit of a factor of 10 using the version of the differential equation model compiled from C code!

-
This vignette was built with mkin 0.9.47.1 on

+
Here we get a performance benefit of a factor of 9 using the version of the differential equation model compiled from C code!

+
This vignette was built with mkin 0.9.47.2 on

 
## R version 3.5.1 (2018-07-02)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 9 (stretch)

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