## ---- include = FALSE---------------------------------------------------------
library(knitr)
opts_chunk$set(tidy = FALSE, cache = FALSE)
## ----check_gcc, eval = FALSE--------------------------------------------------
# pkgbuild::has_compiler()
## ----Rprofile, eval = FALSE---------------------------------------------------
# Sys.setenv(PATH = paste("C:/Rtools/bin", Sys.getenv("PATH"), sep=";"))
## ----HOME, eval = FALSE-------------------------------------------------------
# Sys.getenv("HOME")
## ----create_SFO_SFO-----------------------------------------------------------
library("mkin", quietly = TRUE)
SFO_SFO <- mkinmod(
parent = mkinsub("SFO", "m1"),
m1 = mkinsub("SFO"))
FOCUS_D <- subset(FOCUS_2006_D, value != 0)
## ----benchmark_SFO_SFO, fig.height = 3, message = FALSE, warning = FALSE------
if (require(rbenchmark)) {
b.1 <- benchmark(
"deSolve, not compiled" = mkinfit(SFO_SFO, FOCUS_D,
solution_type = "deSolve",
use_compiled = FALSE, quiet = TRUE),
"Eigenvalue based" = mkinfit(SFO_SFO, FOCUS_D,
solution_type = "eigen", quiet = TRUE),
"deSolve, compiled" = mkinfit(SFO_SFO, FOCUS_D,
solution_type = "deSolve", quiet = TRUE),
"analytical" = mkinfit(SFO_SFO, FOCUS_D,
solution_type = "analytical",
use_compiled = FALSE, quiet = TRUE),
replications = 1, order = "relative",
columns = c("test", "replications", "relative", "elapsed"))
print(b.1)
} else {
print("R package rbenchmark is not available")
}
## ----benchmark_FOMC_SFO, fig.height = 3, warning = FALSE----------------------
if (require(rbenchmark)) {
FOMC_SFO <- mkinmod(
parent = mkinsub("FOMC", "m1"),
m1 = mkinsub( "SFO"))
b.2 <- benchmark(
"deSolve, not compiled" = mkinfit(FOMC_SFO, FOCUS_D,
use_compiled = FALSE, quiet = TRUE),
"deSolve, compiled" = mkinfit(FOMC_SFO, FOCUS_D, quiet = TRUE),
replications = 1, order = "relative",
columns = c("test", "replications", "relative", "elapsed"))
print(b.2)
factor_FOMC_SFO <- round(b.2["1", "relative"])
} else {
factor_FOMC_SFO <- NA
print("R package benchmark is not available")
}
## ----sessionInfo, echo = FALSE------------------------------------------------
cat(utils::capture.output(utils::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]]))
}