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authorJohannes Ranke <jranke@uni-bremen.de>2015-06-22 06:09:00 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2015-06-22 20:31:22 +0200
commit01d9de6ff165c64ffc4366f2eeb3d2649b5c74c0 (patch)
tree87d586590a1b94e5915cdd51394caef7eaf51ed1 /vignettes/compiled_models.Rmd
parent5bd8716b2e4c880b798d1e5e231d49816bbdebd1 (diff)
Version bump, correct benchmark in vignette/compiled_models
Reorganisation of the vignette generation in the Makefile. Improved YAML header in the R markdown vignettes. Rebuilt vignettes with the package installed.
Diffstat (limited to 'vignettes/compiled_models.Rmd')
-rw-r--r--vignettes/compiled_models.Rmd47
1 files changed, 29 insertions, 18 deletions
diff --git a/vignettes/compiled_models.Rmd b/vignettes/compiled_models.Rmd
index 3b24acbb..9aa8b133 100644
--- a/vignettes/compiled_models.Rmd
+++ b/vignettes/compiled_models.Rmd
@@ -1,34 +1,41 @@
---
-title: "Performance benefit by using compiled model definitions in mkin"
+title: "`r (vignette_title <- 'Performance benefit by using compiled model definitions in mkin')`"
+author: "Johannes Ranke"
+date: "`r Sys.Date()`"
output:
html_document:
css: mkin_vignettes.css
toc: true
mathjax: null
theme: united
+vignette: >
+ %\VignetteIndexEntry{`r vignette_title`}
+ %\VignetteEngine{knitr::rmarkdown}
+ \usepackage[utf8]{inputenc}
---
-<!--
-%\VignetteEngine{knitr::rmarkdown}
-%\VignetteIndexEntry{Performance benefit by using compiled model definitions in mkin}
--->
```{r, include = FALSE}
library(knitr)
opts_chunk$set(tidy = FALSE, cache = TRUE)
```
-# Benchmark for a model that can also be solved with Eigenvalues
+## Benchmark for a 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 compiler (gcc) is installed, you will see
a message that the model is being compiled from autogenerated C code when
-defining a model using mkinmod.
+defining a model using mkinmod. The package tests for presence of the gcc compiler using
+
+```{r check_gcc}
+Sys.which("gcc")
+```
+First, we build a simple degradation model for a parent compound with one metabolite.
```{r create_SFO_SFO}
library("mkin")
SFO_SFO <- mkinmod(
- parent = list(type = "SFO", to = "m1", sink = TRUE),
- m1 = list(type = "SFO"))
+ parent = mkinsub("SFO", "m1"),
+ m1 = mkinsub("SFO"))
```
We can compare the performance of the Eigenvalue based solution against the
@@ -36,11 +43,7 @@ compiled version and the R implementation of the differential equations using
the microbenchmark package.
-```{r benchmark_SFO_SFO, echo=-(1:2)}
-# Redefining the model, in order not to confuse the knitr cache which leads to segfaults
-suppressMessages(SFO_SFO <- mkinmod(
- parent = list(type = "SFO", to = "m1", sink = TRUE),
- m1 = list(type = "SFO")))
+```{r benchmark_SFO_SFO}
library("microbenchmark")
mb.1 <- microbenchmark(
mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", use_compiled = FALSE,
@@ -63,14 +66,14 @@ iterative solution of the ODEs:
smb.1["median"]/smb.1["deSolve, compiled", "median"]
```
-# Benchmark for a model that can not be solved with Eigenvalues
+## Benchmark for a model that can not be solved with Eigenvalues
This evaluation is also taken from the example section of mkinfit.
```{r benchmark_FOMC_SFO}
FOMC_SFO <- mkinmod(
- parent = list(type = "FOMC", to = "m1", sink = TRUE),
- m1 = list(type = "SFO"))
+ parent = mkinsub("FOMC", "m1"),
+ m1 = mkinsub( "SFO"))
mb.2 <- microbenchmark(
mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet = TRUE),
@@ -80,10 +83,18 @@ smb.2 <- summary(mb.2)[-1]
rownames(smb.2) <- c("deSolve, not compiled", "deSolve, compiled")
print(smb.2)
smb.2["median"]/smb.2["deSolve, compiled", "median"]
-
```
Here we get a performance benefit of a factor of
`r round(smb.2["deSolve, not compiled", "median"]/smb.2["deSolve, compiled", "median"], 1)`
using the version of the differential equation model compiled from C code using
the inline package!
+
+This vignette was built with mkin `r packageVersion("mkin")` on
+
+```{r sessionInfo, echo = FALSE}
+cat(capture.output(sessionInfo())[1:3], sep = "\n")
+if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) {
+ cat(gsub("model name\t: ", "CPU model: ", cpuinfo[grep("model name", cpuinfo)[1]]))
+}
+```

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