[R-sig-ME] correlation structure in nlme

[Juliette Chamagne]

That's weird, no attachment. Let me try again
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Le Jun 28, 2011 ? 5:25 PM, Juliette Chamagne a ?crit :

> Hi all,
> 
> 
> I have a dataset of dbh increment (Cum.TRW) against Age. Here is attached a subset of my data, with only 6 trees.
> I performed a very simple nlme (no fixed or random effects), estimating the parameters of a monomolecular growth model based on log(Cum.TRW), for every individual.
> I then looked at the residuals of this model, and plotted acf and pacf on those. There is a strong autocorrelation at lag 1, for every individual.
> I thought I would put a correlation structure into my model. So I made the exact same model, but with the corAR1(). The AIC is much better, but when I look at the fit (I plot real data super imposed with both models: without correlation structure in green and with in red).
> 
> When I calculate myself the autocorrelation coefficients for the 6 individuals and take an average, and then force it into CorAR1(), R crashes (see code below).
> 
> Any ideas why is the fit with autocorrelation better based on AIC? And why does R crash when I fix the correlation parameter?
> 
> 
> 
> 
> 
> 
> library(nlme)
> 
> sub <- read.table("data_subset.txt", h=T)
> 
> model.data <- groupedData(log(Cum.TRW) ~ Age | IndID,  data=sub)
> 
> fit.nlme.NoCor <- nlme(log(Cum.TRW) ~ SSasymp (Age, Asym, M0, lrc), fixed=Asym + lrc + M0 ~ 1, data = model.data, random=(Asym + lrc ~ 1), verbose=T, start=c(4.7, -3, 2.5))
> 
> fit.nlme.CorAR <- nlme(log(Cum.TRW) ~ SSasymp (Age, Asym, M0, lrc), fixed=Asym + lrc + M0 ~ 1, data = model.data, random=(Asym + lrc ~ 1), verbose=T, start=c(4.7, -3, 2.5), correlation=corAR1())
> 
> fit.nlme.FixCorAR <- nlme(log(Cum.TRW) ~ SSasymp (Age, Asym, M0, lrc), fixed=Asym + lrc + M0 ~ 1, data = model.data, random=(Asym + lrc ~ 1), verbose=T, start=c(4.7, -3, 2.5), correlation=corAR1(0.9398526, fixed=TRUE))
> 
> 
> 
> Thanks a lot,
> 
> Juliette Chamagne
> 
> 
> --
> PhD student
> Institute for Evolution Biology and Environmental Studies
> University of Z?rich
> Winterthurerstrasse 190
> 8057 Z?rich, Switzerland
> office: +41 (0)44 635 61 21
> 
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