1) I think that the repeated measure is not "years", but, as you said, the
"count of birds". If you are interested with the effect of the time variable
(years), perhaps you need to introduce it as a fixed effect ?

2) See ?corARMA.

2008/8/22 mtb954 <mtb954@gmail.com>

> We are attempting to use nlme to fit a linear mixed model to explain bird
> abundance as a function of habitat:
>
>     lme(abundance~habitat-1,data=data,method="ML",random=~1|sampleunit)
>
> The data consist of repeated counts of birds in sample units across
> multiple
> years, and we have two questions:
>
> 1) Is it necessary (and, if so, how) to specify the repeated measure
> (years)?
>
> 2) How can we specify a Toeplitz heterogeneous covariance structure for
> this
> model? We have searched the help file for lme, and the R-help archives, but
> cannot find any pertinent information.
>
> Any help would be appreciated.
>
> Thanks, Mark
>
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>
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