[R] Correlation structures in gls with repeated measurements

[ONKELINX, Thierry]

Emma,

It looks like there is at least one location that has been sampled at
least twice in some year. A co-worker of me got similar errors. After
checking his data carefully he found a duplicate row. Removing the
duplicate row solved his problem.

HTH,

Thierry


------------------------------------------------------------------------
----
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium 
tel. + 32 54/436 185
Thierry.Onkelinx op inbo.be 
www.inbo.be 

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
data.
~ John Tukey

-----Oorspronkelijk bericht-----
Van: r-help-bounces op r-project.org [mailto:r-help-bounces op r-project.org]
Namens t03eh7 op abdn.ac.uk
Verzonden: woensdag 2 juli 2008 12:29
Aan: r-help op r-project.org
Onderwerp: [R] Correlation structures in gls with repeated measurements

Hi,

I am trying include a spatial correlation structure into a gls model but
keep getting the following error:

> ocean<-read.table("C:\\oceanography2.txt",header=TRUE)
> library(nlme)

> YEAR<-as.factor(ocean$YEAR)

>group<-groupedData(san_dens~temp_grad*pyc_grad*start_thermo|YEAR,data=o
cean)

> model1<-gls(san_dens~temp_grad*pyc_grad*start_thermo,data=group)

> model2<-update(model1,corr=corSpher(form=~MIDLONGDEC+MIDLATDEC|YEAR))
Error in getCovariate.corSpatial(object, data = data) :
  Cannot have zero distances in "corSpatial"


The measurements have been repeated over 10 years so the coordinates are
repeated which I assume is the reason for this error. I thought grouping
by YEAR should remove this but it doesnt seem to work, or I am making a
mistake when I am trying to group it? I have noticed a couple of other
posts with the same problem but I have still not managed to solve this.

I would be really grateful if anyone has any ideas or has had this
problem
before.


Thanks in advance,
Emma Hazard

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