[R-sig-ME] glmmTMB and foreach parallel adaptor

[João Veríssimo]

Hi Sophia,

Not sure why this happens, but using <<- assignment seems to work.
(i.e., dat <<- ..., rather than dat <- ...)

João

On Fri, 2017-03-17 at 00:34 +0200, Sophia Kyriakou wrote:
> Dear members,
> 
> I am trying to set some code running on Windows, which calculates and
> returns the Laplace-based maximum likelihood estimates of a generalized
> linear mixed model.
> Both glmer and glmmTMB functions work on R 3.3.3 when the code is executed
> sequentially.
> However, when I use the parallel algorithm, then glmer still works, but
> glmmTMB does not.
> The error I get is Error in { : task 1 failed - "object 'dat' not found" ,
> where dat is the simulated dataset in each replication.
> 
> Any ideas on how to tackle this error? I am interested in using glmmTMB
> instead of lme4, because I need some of glmmTMB output components.
> 
> Below is a sample code that illustrates the above:
> 
> 
> library(doParallel)
> library(glmmTMB)
> library(lme4)
> 
> simSamples <- matrix(sample(0:6,300,replace=TRUE),30,10)
> 
> ## Sequential version
> LA <- LA2 <- matrix(NA,3,10)
> for (i in 1:10){
> dat <-
> data.frame(subject=rep(1:15,each=2),x=-14:15,m=rep(6,30),y=simSamples[,i],yprop=simSamples[,i]/6)
> fitLA <- glmmTMB(yprop ~ x +(1|subject),family=binomial,weights=m,data=dat)
> LA[,i] <- fitLA$fit$par
> fitLA2 <- glmer(cbind(y,6-y) ~ x +(1|subject),family=binomial,data=dat)
> LA2[,i] <- c(fixef(fitLA2),sqrt(unlist(VarCorr(fitLA2))))
> }
> 
> 
> ## Parallel version
> cl <- makeCluster(3)
> registerDoParallel(cl)
> TMBfit <- foreach(i=1:10, .combine= cbind, .packages=c("glmmTMB")) %dopar% {
> dat <-
> data.frame(subject=rep(1:15,each=2),x=-14:15,m=rep(6,30),yprop=simSamples[,i]/6)
> fitLA <- glmmTMB(yprop ~ x +(1|subject),family=binomial,weights=m,data=dat)
> fitLA$fit$par
> }
> stopCluster(cl)
> 
> 
> cl <- makeCluster(3)
> registerDoParallel(cl)
> LME4fit <- foreach(i=1:10, .combine= cbind, .packages=c("lme4")) %dopar% {
> dat <-
> data.frame(subject=rep(1:15,each=2),x=-14:15,m=rep(6,30),y=simSamples[,i])
> fitLA <- glmer(cbind(y,6-y) ~ x +(1|subject),family=binomial,data=dat)
> c(fixef(fitLA),sqrt(unlist(VarCorr(fitLA))))
> }
> stopCluster(cl)
> 
> Any help is much appreciated.
> Thanks in advance!
> Sophia
> 
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