[R] Zero distance error in corSpatial - correlation structure using lme

[John Poulsen]

Hello,

I am having a problem specifying the correlation structure in lme which 
leads to the error: Error in getCovariate.corSpatial(object, data = 
data) : Cannot have zero distances in "corSpatial".  I have specified a 
grouping variable which is the only fix I could find by searching this 
error on R-help.

ISee the below example.  When my samples (tran) - which are transects 
sampled several times - have different coordinates (STX1 and STY1), 
everything seems to work fine.  But in my actual data set, there are 
multiple observations per sample and the coordinates are the same for 
the same sample.  This is demonstrated below using the coordinates STX2 
and STY2, which are the same for a single transect.  How can I properly 
specify this structure in Variogram() and corSpatial()?

library(nlme)

set.seed(1001)
ntrans <- 30
npertrans <- 5
ntot <- ntrans*npertrans
STX1<-runif(ntot, min=16.0921, max=16.4823)
STY1<-runif(ntot, min=1.9812, max=2.3932)
STX2<-rep(runif(ntrans, min=16.0921, max=16.4823), each=npertrans)
STY2<-rep(runif(ntrans, min=1.9812, max=2.3932), each=npertrans)
site<-rep(c(1,2,3), each=ntot/3)
tran<-rep(1:ntrans,each=npertrans)
log<-rep(rbinom(n=ntrans, 1, 0.5), each=npertrans)
yabund<-rnorm(ntot, 5, 0.4)
dat<-data.frame(STX1, STY1, STX2, STY2, site, tran, log, yabund)

test1<-lme(yabund~factor(log)+STX1+STY1, random=~1|tran,data=dat)
test2<-lme(yabund~factor(log)+STX2+STY2, random=~1|tran,data=dat)

Variogram(test1, form=~STX1+STY1|tran)
plot(Variogram(test1, form=~STX1+STY1|tran))

Variogram(test2, form=~STX2+STY2|tran)   # Varigoram has distance of 0!
plot(Variogram(test2, form=~STX2+STY2|tran))


mod1<-lme(log(yabund)~factor(log)+STX1+STY1, random=~1|tran, data=dat,
               corr=corSpatial(form=~STY1+STX1|tran, type="exponential", 
nugget=T), method="REML")

mod2<-lme(log(yabund)~factor(log)+STX2+STY2, random=~1|tran, data=dat,
               corr=corSpatial(form=~STY2+STX2, type="exponential", 
nugget=T), method="REML")

# Error in getCovariate.corSpatial(object, data = data) :
# Cannot have zero distances in "corSpatial"