Rename twa to max_twa_parent, update docs

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")