I have counts of plants from different sites over a number of years. In each census year, all sites were surveyed, but the gaps between census years vary (between 1 and 4 years between consecutive surveys). I would like to use a GEE to account for the correlation structure of the data (but really, my purpose is just in estimating the long-term population trend, and some estimate of its uncertainty).

I think I can specify a model like this:

```
library(geepack)
model1<-geeglm(Count~Year,id=Site,family=poisson,data=mydata,corstr="ar1",waves=Year)

```

But I am not sure if this is quite right--I think the correlation parameter estimate it gives is the correlation between any two consecutive counts, i.e. without accounting for the time between counts. My question relates to a previous one below, but I could not comment on it. The waves argument makes no differences to my results (the data is already ordered by site, and time within site). Can anyone point me in the right direction? Or comment on how much I should worry about this?

[How to analyze GEE with unevenly spaced observations?](https://stats.stackexchange.com/questions/21480/how-to-analyze-gee-with-unevenly-spaced-observations)