Static documentation rebuilt by pkgdown::build_site()

1 files changed, 42 insertions, 0 deletions

diff --git a/docs/articles/compiled_models.R b/docs/articles/compiled_models.R
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+++ b/docs/articles/compiled_models.R
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+## ----benchmark_SFO_SFO, fig.height = 3-----------------------------------
+library("microbenchmark")
+library("ggplot2")
+mb.1 <- microbenchmark(
+  "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),
+  times = 3, control = list(warmup = 0))
+
+smb.1 <- summary(mb.1)
+print(mb.1)
+autoplot(mb.1)
+
+## ------------------------------------------------------------------------
+rownames(smb.1) <- smb.1$expr
+smb.1["median"]/smb.1["deSolve, compiled", "median"]
+
+## ----benchmark_FOMC_SFO, fig.height = 3----------------------------------
+FOMC_SFO <- mkinmod(
+  parent = mkinsub("FOMC", "m1"),
+  m1 = mkinsub( "SFO"))
+
+mb.2 <- microbenchmark(
+  "deSolve, not compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, 
+                                    use_compiled = FALSE, quiet = TRUE),
+  "deSolve, compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE),
+  times = 3, control = list(warmup = 0))
+smb.2 <- summary(mb.2)
+print(mb.2)
+smb.2["median"]/smb.2["deSolve, compiled", "median"]
+autoplot(mb.2)
+
+## ----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]]))
+}
+