vignettes/timingContraception.R

In glmmTMB: Generalized Linear Mixed Models using Template Model Builder

if (file.exists("timingFuns.R")) {
  ## don't run if this utility file can't be found
  ## (_should_ exist if source()ing from vignettes directory, but
  ## not found on r-hub Debian platform ...)
  source("timingFuns.R")
  data(Contraception,package="mlmRev")
  library("lme4")
  library("glmmTMB")
  library("glmmADMB")
  library("plyr")  ## load before dplyr; for ldply()
  library("tidyr")
  library("dplyr")

  ## make sure this is run with optimized build of glmmTMB,
  ## i.e. "make install" rather than "make quick-install/quick-check"
  ## (or at least document)
  nmax <- 40     ## max replications for glmer/glmmTMB
  nmaxADMB <- 2  ## max reps for glmmadmb (much slower)

  ## slow enough that I should consider using something with
  ## checkpointing instead ...
  tmat <- ldply(seq(nmax),getTimes)
  tmatADMB <- ldply(seq(nmaxADMB),getTimes,which="glmmadmb")

  ## reshape: wide-to-long, add n values
  ff <- function(dd,n=seq(nrow(dd))) {
    mutate(dd,n=n) %>%
      gather(pkg,time,-n)
  }
  tmatContraception <- rbind(ff(tmat),ff(tmatADMB))

  save("tmatContraception",file="contraceptionTimings.rda")
}  ## if auxiliary file available