Just make sure it IS help. Following Dieter's advice I checked to see what format V&R use to pass data as success/failure and now wonder if the the proper invocation following their examples on pg 49, 59 and 134 in <http://cran.r-project.org/web/packages/VR/VR.pdf> would be: mod<-glmmBUGS( cbind(y, not.y = tot - y) ~ Newsect + Newdist, effects="Newtree", family="binomial", data=Newdat) That invocation runs without complaint, but this two step one does not: > Newdat$not.y <- with(Newdat, tot - y) > mod<-glmmBUGS(cbind(y, not.y) ~ Newsect + Newdist, effects="Newtree", family="binomial", data=Newdat) Error in family$linkfun(mustart) : Value 0 out of range (0, 1) It worries me when two submission that I would expect to be equivalent produce different results. It's not that the failure vector has zeros, but I cannot immediately see the source of the problem: > Newdat$not.y [1] 13 11 7 5 4 13 10 6 6 5 9 12 9 5 5 10 10 8 6 5 12 10 8 6 5 14 7 8 5 4 11 11 9 8 3 [36] 10 7 9 8 1 13 11 9 6 6 11 10 7 7 2 13 10 9 5 6 10 8 8 7 2 You probably need either to consult a reference that is more authoritative or to construct an example for which you are certain of the correct result with your chosen package.
David Winsemius
Heritage Labs
On Feb 8, 2009, at 12:48 PM, John Poulsen wrote:
> Thanks for your help! -- John
>
> David Winsemius wrote:
>> Installing the glmmBUGS package and a bit of experimentation
>> produces this minor modification of your code that seems to run
>> without error. It's back to you to see if the output is sensible.
>>
>> library(glmmBUGS)
>> Newdat<-data.frame(Newtree=rep(1:3, each=20), Newsect=rep(c("a","b"),
>> each=10), Newdist=rep(1:5, 2),
>> y=rpois(60,2), tot=rep(c(14,12,10,8,6), 12))
>>
>> yseed<-cbind(Newdat$y, Newdat$tot)
>>
>> mod<-glmmBUGS(y/tot~Newsect + Newdist, effects="Newtree",
>> family="binomial", data=Newdat)
>>
>> I am guessing that the interpreter was looking for a variable yseed
>> within Newdat and not finding it. It, however, is able to "see" y
>> and tot within Newdat. Also appears that using cbind(y, tot) on the
>> LHS of hte formula will avoid the error you were getting.
>>
>