[R-sig-eco] temporal autocorrelation with lme

[Jean-Yves BARNAGAUD]

Dear all,

I'm trying to fit lme models on spatial-temporal data with strong 
inter-annual autocorrelation.
The response variable is a bird diversity measure sampled on several 
plots during 10 to 40 years, which I want to relate to environmental 
covariates. To give an idea of the sample size, there are appr. 800 plots.

Here is the temporal autocorrelation of the response variable (averaged 
over years, x axis=years)


Based on AIC, the best model I tried is a model with a corAR1 structure, 
as compared with ARMA models with different p and q lags.

x1=corAR1(form=~year | plot)
m2=lme(y~cov1+cov2+cov3,random=list(plot=~1),correlation=x1,data=d1)

Below are residual plots. The first plot is a plot of residuals over 
years, the 2nd and third are plots of mean residuals per year vs years. 
The third plot is from the acf function. Looks like the AR structure 
does not correct temporal autocorrelation, and the ARMA models don't do 
better. I've tried other things, including adding a "year" covariate to 
remove the apparent linear trend, without making it with a better 
correction.


Any advice or alternative solution?

Many thanks,

Best

JYB




-- 
Jean-Yves Barnagaud
Vertebrate Biogeography & Ecology group
EPHE - CEFE - Montpellier, Fr.
+0033(0)467613326
http://sites.google.com/site/jybarnagaud