Choice of test in R. Repeated measurements, binary response and missing data...

I have two treatments and one co-variate (affect the response variable but is also correlated with one of the treatments). Each replicate has been examined for the presence/absence of morphological characters at several time point but there are unfortunately a lot of missing data. What would be the best way of analyzing this data? GLMM? GEE?
Hmmm...Because my data is repeated measures I think glmer would suit the data better. Or do you beg to differ? I guess I need to pick only one time-point to include in the time to event analysis or can I use all of my data (from all 4 time points)?