Nothing
library(lme4)
gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd),
family = binomial, data = cbpp)
X <- model.matrix(~period,data=cbpp)
Zherd <- model.matrix(~herd-1,data=cbpp)
library(R2admb)
setup_admb()
tmpdat <- list(X=X,Zherd=Zherd,
incidence=cbpp$incidence,size=cbpp$size,
nobs=nrow(cbpp))
d1 <- do_admb("toy1",
data=tmpdat,
re=TRUE,
params=list(beta=rep(0,ncol(X)),sigma_herd=0.1),
bounds=list(sigma_herd=c(0.0001,20)),
re_vectors=c(u_herd=ncol(Zherd)),
checkdata="write",checkparam="write",
mcmc=TRUE,
mcmcpars=c("beta","sigma_herd"),
clean=FALSE)
save("d1",file="toy1_runs.RData")
unlink(c("toy1","toy1_gen.tpl"))
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