# [R-sig-Geo] ANOVA with correlated errors

Ole F. Christensen olefc at daimi.au.dk
Thu May 13 18:48:16 CEST 2004

```Paulo

I think you need to provide a few more details here about how to fit
those models using your function in geoR.
* note the r_i term, which means that the replications have different
means. How would you specify this in your function ?
* I Assume the quantity of interest are the contrasts in T_j. Guess some
manual fiddling is needed to obtain confidence intervals for these
contrast ?

Alternatively, since the model is a multivariate Guassian, so it is
definetely possible to do inference by figuring out what the mean vector
and covariance matrix of the vector Y={Y_ij | i,j= ....} looks like,
write down the likelihood function and use the nlm or optim function for
maximising it.

Best regards Ole

Paulo Justiniano Ribeiro Jr wrote:

>Hi Jose
>The function likfit() in the package geoR will fit those models.
>Actually there is a data-set in the package with a similar structure
>see:
>
>require(geoR)
>data(hoef)
>help(hoef)
>
>best
>P.J.
>
>
>
>On Thu, 13 May 2004, Jose A. Hernandez wrote:
>
>
>
>>Dear R colleagues,
>>
>>My name is Jose Hernandez and work in the analysis of on-farm experiments.
>>
>>I've been a R user for sometime now, however am still struggling figuring
>>out some of my spatial analysis using R.
>>
>>Most of my experiments have the following model:
>>
>>Y_ij = Mu + r_i + T_j + e_ij
>>
>>Where:
>>r_i is some replication and T_j some fixed treatment effect.
>>
>>I many cases there is significant within block heterogeneity and therefore
>>I can't assume that e_ij are iid.
>>
>>An alternative is to use:
>>
>>Y_ij = Mu + T_j + e_ij
>>
>>And assume that:
>>
>>e_ij follows some spatial covariance model such as exponential, spherical, etc.
>>
>>
>>Are there any R packages that will integrate spatial variability into the
>>model ?
>>
>>Thanks and advance and best regards !
>>
>>Jose
>>
>>
>>--
>>Jose A. Hernandez
>>Ph.D. Candidate
>>Precision Agriculture Center
>>
>>Department of Soil, Water, and Climate
>>University of Minnesota
>>1991 Upper Buford Circle
>>St. Paul, MN 55108
>>
>>Ph. (612) 625-0445, Fax. (612) 625-2208
>>
>>_______________________________________________
>>R-sig-Geo mailing list
>>R-sig-Geo at stat.math.ethz.ch
>>https://www.stat.math.ethz.ch/mailman/listinfo/r-sig-geo
>>
>>
>>
>>
>
>Paulo Justiniano Ribeiro Jr
>Departamento de Estatística
>Universidade Federal do Paraná
>Caixa Postal 19.081
>CEP 81.531-990
>Curitiba, PR  -  Brasil
>Tel: (+55) 41 361 3471
>Fax: (+55) 41 361 3141
>e-mail: pj at est.ufpr.br
>http://www.est.ufpr.br/~paulojus
>
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>
>
>
>

--
Ole F. Christensen
BiRC - Bioinformatics Research Center
University of Aarhus
Høegh-Guldbergs Gade 10, Building 090
DK-8000 Aarhus C
Denmark

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