aboutsummaryrefslogtreecommitdiff
path: root/docs/articles/compiled_models.R
diff options
context:
space:
mode:
Diffstat (limited to 'docs/articles/compiled_models.R')
-rw-r--r--docs/articles/compiled_models.R64
1 files changed, 32 insertions, 32 deletions
diff --git a/docs/articles/compiled_models.R b/docs/articles/compiled_models.R
index dd450e0d..25c39dac 100644
--- a/docs/articles/compiled_models.R
+++ b/docs/articles/compiled_models.R
@@ -12,40 +12,40 @@ SFO_SFO <- mkinmod(
m1 = mkinsub("SFO"))
## ----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"]
+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 benchmark is not available")
+}
## ----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)
+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(capture.output(sessionInfo())[1:3], sep = "\n")

Contact - Imprint