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.

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]]))

+}

+```