I am working with presence-absence data and want to use a GEE, fitting splines to my environmental co-variates, in order to account for non-linear response to my parameters and the fact that within individual non-independance between sequential observations is apparent. Essentially the goal is to estimate the effect of environmental variables on the presence of a population.
What is the best correlation structure to use when I want to assume independence between individuals but non-independence within individuals?
I am using the R package geepack to fit the GEEs and my current working model looks like this:
geeglm(used ~ ns(temp) + ns(temp2), id=id, data=data, corstr = "independent", family=binomial)