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authorJohannes Ranke <jranke@uni-bremen.de>2020-04-02 10:58:34 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-04-03 10:53:07 +0200
commit47ba9ea512b82fb8b31da8ec5558f3c0952d86d4 (patch)
tree775b56488b5f040132d00a962c6f7f876ed15b7c /vignettes/web_only/compiled_models.R
parent1d01aa6e40bdb3e338638b9239153cf82713d634 (diff)
Compiled models article, reduce distractions
- Added a section with platform specific notes on getting compiled models to work to the compiled models article - Don't return empty SFORB parameter list from endpoints() if there is no SFORB model - Avoid warnings when using standardized = TRUE in plot.mmkin()
Diffstat (limited to 'vignettes/web_only/compiled_models.R')
-rw-r--r--vignettes/web_only/compiled_models.R61
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
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+++ b/vignettes/web_only/compiled_models.R
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+## ---- 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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