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## ---- include = FALSE----------------------------------------------------
library(knitr)
opts_chunk$set(tidy = FALSE, cache = FALSE)
## ----check_gcc-----------------------------------------------------------
Sys.which("gcc")
## ----create_SFO_SFO------------------------------------------------------
library("mkin", quietly = TRUE)
SFO_SFO <- mkinmod(
parent = mkinsub("SFO", "m1"),
m1 = mkinsub("SFO"))
## ----benchmark_SFO_SFO, fig.height = 3-----------------------------------
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")
}
## ----benchmark_FOMC_SFO, fig.height = 3----------------------------------
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")
}
## ----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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