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# Example from
# [R-sig-ME] Struggle with glmer().
# Sun, 16 Jul 2017 21:57:07 +1200
# Rolf Turner <r.turner@auckland.ac.nz>
# r-sig-mixed-models@r-project.org <r-sig-mixed-models@r-project.org>
# see also http://bbolker.github.io/mixedmodels-misc/notes/cloglogsim.html
cat(crayon::yellow("\ntest-cloglog:\n"))
if (spaMM.getOption("example_maxtime")>1.8) {
if (requireNamespace("MASS", quietly = TRUE)) {
artSim <- function(){
#
# Function to simulate "artificial" data which is at least superficially
# similar to some real data.
#
link <- "cloglog"
B <- binomial(link=link)
linkfun <- B$linkfun
linkinv <- B$linkinv
# Construct (artificial) treatment factor, covariate, and
# (random) replicate factor.
x <- seq(0,28,by=2)
Trt <- LETTERS[1:24]
Rep <- 1:3 # Three reps per treatment.
Xdat <- expand.grid(x=x,Trt=Trt,Rep=Rep)
uRep <- with(Xdat,factor(paste0(Rep,Trt)))
Xdat$Rep <- with(Xdat,factor(as.numeric(uRep)))
beta0 <- seq(-3,0.45,by=0.15)
beta1 <- rep(seq(0.05,0.3,by=0.05),4)
names(beta0) <- Trt
names(beta1) <- Trt
Sigma <- matrix(c(0.06,-0.001,-0.001,0.0001),nrow=2)
lb0 <- beta0[match(Xdat$Trt,names(beta0))]
lb1 <- beta1[match(Xdat$Trt,names(beta1))]
nrep <- 72
imat <- match(Xdat$Rep,1:nrep)
Z <- MASS::mvrnorm(nrep,c(0,0),Sigma)[imat,]
linpr <- lb0 + Z[,1] + (lb1 + Z[,2])*Xdat$x
p <- linkinv(linpr)
nsize <- 25
Dead <- rbinom(nrow(Xdat),nsize,p)
Alive <- nsize - Dead
x0 <- (linkfun(0.99) - beta0)/beta1
Xdat$Dead <- Dead
Xdat$Alive <- Alive
attr(Xdat,"trueLD99") <- x0
return(Xdat)
}
set.seed(42)
artsim <- artSim()
fit1 <- fitme(cbind(Dead,Alive) ~ (Trt + 0)/x + (x | Rep),
family=binomial(link="cloglog"),
data=artsim, method="ML",verbose=c(TRACE=FALSE))
testthat::expect_equal(logLik(fit1)[[1]],-1413.207,tolerance=1e-4)
if (FALSE) { ## not useful in routine tests
if (file.exists((privtest <- "D:/home/francois/travail/stats/spaMMplus/spaMM/package/tests_other_pack/test-cloglog-lme4-glmmTMB.R"))) {
source(privtest)
}
}
} else cat("test cloglog random slope: increase example_maxtime (1.8) to run this test.\n")
}
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