[R-sig-Geo] testing nlme models for spatial correlation

[Javier Moreira]

​​Sorry, the error is

Error in corFactor.corSpatial(object) :
  NA/NaN/Inf in foreign function call (arg 1)
In addition: Warning messages:
1: In min(unlist(attr(object, "covariate"))) :
  no non-missing arguments to min; returning Inf
2: In min(unlist(attr(object, "covariate"))) :
  no non-missing arguments to min; returning Inf

and i attach the data to this mail.
​
 base_modelo3.csv
<https://drive.google.com/file/d/0B6YImu-ZATe4bEFKTlAxci1PNW8/view?usp=drive_web>
​
thanks!

2017-08-01 11:42 GMT-03:00 Thierry Onkelinx <thierry.onkelinx at inbo.be>:

> Dear Javier,
>
> Your problem is hard to understand without a reproducible example. You
> only gives the code, not the data nor the error message.
>
> 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 16:36 GMT+02:00 Javier Moreira <javiermoreira at gmail.com>:
>
>> Thanks Thierry,
>> I would check that info.
>> Any ideas why if i choose the finest level of random effects as
>> /SUBMUESTREO and run model 4 (with correlation) wont let me?
>> If i undesrtand you wel, you adress more the second question i made, im
>> all right?
>> Thanks!
>>
>>
>> El 1 ago. 2017 8:10 a. m., "Thierry Onkelinx" <thierry.onkelinx at inbo.be>
>> escribió:
>>
>> 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 <javiermoreira at 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 at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>>
>>
>>
>


-- 
Javier Moreira de Souza
Ingeniero Agrónomo
099 406 006

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