Dear Javier, The correlation structure in nlme only works on the residuals within the finest level of random effect. Observations in different random effect are independent.
Have a look at the INLA package (http://www.r-inla.org). INLA allows for correlated random effects. So you have spatial correlation among the random effects (instead of among residuals). INLA has options for correlations along a 2D regular grid, a neighbourhood graph or a mesh. If you want an book on this, I recommend Zuur et al (2017) Beginner's Guide to Spatial, Temporal and Spatial-Temporal Ecological Data Analysis with R-INLA. Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium 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 2017-08-01 11:31 GMT+02:00 Javier Moreira <javiermore...@gmail.com>: > hi, > im trying to generate different models to account for spatial correlation. > Im using nlme package, and mixed models, in order to compare two models, > one that doesnt include the spatial correlation and one that does. > > Its a nested design, one that has 4 leves, > BLOQUE/ AMBIENTE/ TRATAMIENTO/ SUBMUESTREO > Its a harvest set data, with multiple point of data/ treatment, so the last > level account for another term in the error for "sub-muestreo". > > My first problem its, when i try to add de correlation term to the model, i > cant, when the random effects are taken to the level /SUBMUESTREO, and i > have to leave it to the level of TRATAMIENTO. > When i do that, i have 2 differences between models, the term accounting > for sub-muestreo, and the spatial correlation. > > #MODELO 2## > attach(base_modelo3) > str(base_modelo3) > data1=base_modelo3 > str(data1) > data1=groupedData(REND.~1|BLOQUE/AMBIENTE/TRATAMIENTO/SUBMUESTREO, > data=data1, units=list(y="(ton/ha)")) > data1$TRATAMIENTO =factor(data1$TRATAMIENTO) > data1$BLOQUE =factor(data1$BLOQUE) > data1$AMBIENTE =factor(data1$AMBIENTE) > > modelo2_MM<-lme(REND.~1+TRATAMIENTO*AMBIENTE, > random=~1|BLOQUE/AMBIENTE/TRATAMIENTO/SUBMUESTREO, > weights=varComb(varIdent(form=~1|TRATAMIENTO)), > data=data1, > control=lmeControl(niterEM=150,msMaxIter=200)) > summary(modelo2_MM) > anova(modelo2_MM) > > ##MODELO 4## > > modelo4_MM<-lme(REND.~1+TRATAMIENTO*AMBIENTE, > random=~1|BLOQUE/AMBIENTE/TRATAMIENTO, > weights=varComb(varIdent(form=~1|TRATAMIENTO)), > correlation=corExp(form=~X+Y,nugget=T), > data=data1, > control=lmeControl(niterEM=150,msMaxIter=200)) > summary(modelo4_MM) > anova(modelo4_MM) > > My second problem is, that i need to get the specific parameter for the > error term that belongs to the spatial correlation, in order to map it. For > what i watch, what lme does is send it to the general error, and so, what i > could do is make the differences between the residuals of these two models. > so, its essetial to get the exact same model, except for the correlation > structure. > If anybody knows how to get the specific term of error accounting for the > correlation, it would be wonderful. > > E24=residuals(modelo24_3,type = "response") > E40=residuals(modelo4_MM,type = "response") > EE=E24-E40 > post=data.frame(E24,E40,EE,data1$X,data1$Y) > > coordinates(post)<-c("data1.X","data1.Y") > coor_post<-coordinates(post) > > bubble(post,"E24",main="residuos modelo 2") > bubble(post,"E40",main="residuos modelo 4") > bubble(post,"EE",main="Est.espacial removida por Modelo 4") > > thanks! > > -- > Javier Moreira de Souza > Ingeniero Agrónomo > 099 406 006 > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-Geo mailing list > R-sig-Geo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-geo [[alternative HTML version deleted]] _______________________________________________ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo