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()

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]]))
+}
+