Patrick Giraudoux
2006-Jul-01 16:57 UTC
[R] nlme: correlation structure in gls and zero distance
Dear listers,
I am trying to model the distribution of fox density over years in the
Doubs department. Measurements have been taken on 470 plots in March
each year and georeferenced. Average density is supposed to be different
each year.
In a first approach, I would like to use a general model of this type,
taking spatial correlation into account:
gls(IKAfox~an,correlation=corExp(2071,form=~x+y,nugget=1.22),data=renliev)
but I get
>
gls(IKAfox~an,correlation=corExp(2071,form=~x+y,nugget=1.22),data=renliev)
Error in getCovariate.corSpatial(object, data = data) :
Cannot have zero distances in "corSpatial"
I understand that the 470 geographical coordinates are repeated three
times (measurement are taken each of the three years at the same place)
which obviously cannot be handled there.
Does anybody know a way to work around that except jittering slightly
the geographical coordinates?
Thanks in advance,
Patrick
Patrick Giraudoux
2006-Jul-02 13:36 UTC
[R] nlme: correlation structure in gls and zero distance
Joris De Wolf a ?crit :> Have you tried to define 'an' as a group? Like in > > gls(IKAfox~an,correlation=corExp(2071,form=~x+y|an,nugget=1.22),data=renliev) > > > A small data set might help to explain the problem. > > JorisThanks. Seems to work with a small artificial data set: an<-as.factor(rep(2001:2004,each=10)) x<-rep(rnorm(10),times=4) y<-rep(rnorm(10),times=4) IKA<-rpois(40,2) site<-as.factor(rep(letters[1:10],times=4)) library(nlme) mod1<-gls(IKA~an-1,correlation=corExp(form=~x+y)) >Error in getCovariate.corSpatial(object, data = data) : Cannot have zero distances in "corSpatial" mod2<-gls(IKA~an-1,correlation=corExp(form=~x+y|an)) > mod2 Generalized least squares fit by REML Model: IKA ~ an - 1 Data: NULL Log-restricted-likelihood: -73.63998 Coefficients: an2001 an2002 an2003 an2004 1.987611 2.454520 2.429907 2.761011 Correlation Structure: Exponential spatial correlation Formula: ~x + y | an Parameter estimate(s): range 0.4304012 Degrees of freedom: 40 total; 36 residual Residual standard error: 1.746205> > Joris > > Patrick Giraudoux wrote: >> Dear listers, >> >> I am trying to model the distribution of fox density over years in >> the Doubs department. Measurements have been taken on 470 plots in >> March each year and georeferenced. Average density is supposed to be >> different each year. >> >> In a first approach, I would like to use a general model of this >> type, taking spatial correlation into account: >> >> gls(IKAfox~an,correlation=corExp(2071,form=~x+y,nugget=1.22),data=renliev) >> >> >> but I get >> >> > >> gls(IKAfox~an,correlation=corExp(2071,form=~x+y,nugget=1.22),data=renliev) >> >> Error in getCovariate.corSpatial(object, data = data) : >> Cannot have zero distances in "corSpatial" >> >> I understand that the 470 geographical coordinates are repeated three >> times (measurement are taken each of the three years at the same >> place) which obviously cannot be handled there. >> >> Does anybody know a way to work around that except jittering slightly >> the geographical coordinates? >> >> Thanks in advance, >> >> Patrick >> >> ______________________________________________ >> R-help at stat.math.ethz.ch mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide! >> http://www.R-project.org/posting-guide.html > > > confidentiality notice: > The information contained in this e-mail is confidential a...{{dropped}}