You posted the same message to r-sig-geo, please avoid cross-posting.
Anyway, on that list there has been a useful reply by Edzer Pebesma:

http://r-sig-geo.2731867.n2.nabble.com/Need-help-understanding-the-spatial-correlation-structure-applied-in-lme-tp6049193p7580220.html

the relevant part is:

###########################################################

 > *My first question is*: the variogram of soil.gaus indicates a range 
of 40,
 > but the estimated range is 20.43725. Does this mean the model "soil.gaus"
 > failed?

<http://r-sig-geo.2731867.n2.nabble.com/Need-help-understanding-the-spatial-correlation-structure-applied-in-lme-td6049193.html#>

no, it means that the range parameter is not identical to the value you
interpret from the plot as range. This is usual for Gaussian and
exponential models and some others, try:

library(gstat)
show.vgms(range=20, model="Gau", max=50)

###########################################################



Cheers,
Luca

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Le 16/06/2012 18:56, Gary Dong a écrit :
> Dear R users,
>
> I need some help in understanding the spatial correlation structure in
> mixed models. I'm wondering if there is a document or paper that explains
> how to use spatial correlation structure such as "corExp" or "corGaus"?
>
> Let me use the example and data posted on UCLA's R FAQ webpage to explain
> my problems. The link for the webpage is:
> http://www.ats.ucla.edu/stat/r/faq/spatial_regression.htm
>
> First, following the instructions on the webpage, I do the followingï¼s(
>
> install.packages("nlme")
> library(nlme)
>
> spdata <- read.table("http://www.ats.ucla.edu/stat/R/faq/thick.csv", header
> = T, sep = ",")
> dummy <- rep(1, 75)
> spdata <- cbind(spdata, dummy)
>
> ### estimate the null model ###
>
> soil.model <- lme(fixed = thick ~ soil, data = spdata, random = ~ 1 |
> dummy, method = "ML")
> summary(soil.model)
> plot(Variogram(soil.model,form=~north+east))
>
> ### I then updated the model by the spatial correlation structure ####
>
> soil.gaus <- update(soil.model, correlation=corGaus(1,form=~north+east))
> summary(soil.gaus)
> plot(Variogram(soil.gaus,form=~north+east))
>
> *My first question is*: the variogram of soil.gaus indicates a range of 40,
> but the estimated range is 20.43725. Does this mean the model "soil.gaus"
> failed?
>
> Next, I define the range and nugget manually as below. The variogram of
> soil.model indicates a range at 40 and nugget at about 0.1.
>
> soil.gaus.1 <- update(soil.model,
> correlation=corGaus(c(40,0.1),form=~north+east,nugget=T))
> summary(soil.gaus.1)
> plot(Variogram(soil.gaus.1,form=~north+east))
>
> The estimated range looks right (very close to 40). But the estimated
> nugget and variogram plot still look weird. *So my question is*: what I can
> do next step to improve the model?
>
> Any advice would be greatly appreciated!
>
> Best
> Gary
>
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>
>
>
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