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authorJohannes Ranke <jranke@uni-bremen.de>2020-04-04 16:46:37 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-04-04 16:46:37 +0200
commit68f5f5c17e3e1c3f9272b9b663a4d7380433b530 (patch)
treeca0c3837b1144368b67bb86a3192675f10212b97 /vignettes/web_only/compiled_models.R
parent8c19fc5261dc53dc7880b3f54f8f2adf413de996 (diff)
Add three functions to facilitate the use of nlme
Diffstat (limited to 'vignettes/web_only/compiled_models.R')
-rw-r--r--vignettes/web_only/compiled_models.R61
1 files changed, 0 insertions, 61 deletions
diff --git a/vignettes/web_only/compiled_models.R b/vignettes/web_only/compiled_models.R
deleted file mode 100644
index 691037ec..00000000
--- a/vignettes/web_only/compiled_models.R
+++ /dev/null
@@ -1,61 +0,0 @@
-## ---- 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]]))
-}
-

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