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author | Johannes Ranke <jranke@uni-bremen.de> | 2020-04-03 17:40:55 +0200 |
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committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-04-03 17:40:55 +0200 |
commit | 8c19fc5261dc53dc7880b3f54f8f2adf413de996 (patch) | |
tree | 193aad4a3b2920ad6bff1d54cd18e992ac179bdd /vignettes/web_only/compiled_models.R | |
parent | 312255078d2529f485a81df2a53d5928622ae81f (diff) | |
parent | 47ba9ea512b82fb8b31da8ec5558f3c0952d86d4 (diff) |
Merge branch 'master' into mxkin
Merge DESCRIPTION manually to combine dependencies and rerun check to
update check.log
Diffstat (limited to 'vignettes/web_only/compiled_models.R')
-rw-r--r-- | vignettes/web_only/compiled_models.R | 61 |
1 files changed, 61 insertions, 0 deletions
diff --git a/vignettes/web_only/compiled_models.R b/vignettes/web_only/compiled_models.R new file mode 100644 index 00000000..691037ec --- /dev/null +++ b/vignettes/web_only/compiled_models.R @@ -0,0 +1,61 @@ +## ---- 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")) + +## ----benchmark_SFO_SFO, fig.height = 3, message = FALSE, warning = FALSE------ +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 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_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(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]])) +} + |