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List:       r-sig-mixed-models
Subject:    Re: [R-sig-ME] MCMCglmm bivariate with offset
From:       Walid Mawass <walidmawass10 () gmail ! com>
Date:       2018-06-13 18:51:37
Message-ID: 09117a52-3f10-712c-0be5-f2f1afb98303 () gmail ! com
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Thank you Jarrod, the model finally ran with your advice. I am aware of 
the sensitivity of the posterior distribution, this is just my first 
prior. I am going to use another one with nu = 1.002.

Cheers

Walid


On 6/13/2018 2:08 PM, HADFIELD Jarrod wrote:
> Hi,
> 
> I think you have 11 fixed effects, not 5. Replace 5 with 11 and then it should \
> work. Also, you should expect the posterior to be sensitive to the prior if you \
> have nu=3 unless there is a lot of information in the data. 
> Cheers,
> 
> Jarrod
> 
> 
> > On 13 Jun 2018, at 15:28, Walid Mawass <walidmawass10@gmail.com> wrote:
> > 
> > Hello everyone,
> > 
> > I am working on a bivariate MCMCglmm model and I want to include an
> > offset term for my second response variable. I already know that for the
> > offset, i have to fix the coefficient to 1 through the prior but it is
> > not working in my case. I have 4 fixed effects fitted for both response
> > variables and the offset is fitted for the second one using
> > /at.level(trait,2)/.
> > 
> > prior1 <- list(B=list(V=diag(5)*1e8, mu=rep(0,5)), R=list(V=diag(2),
> > nu=3), G=list(G1=list(V=diag(2), nu=3),G2=list(V=diag(2), nu=3)))
> > prior1$B$mu[5]<- 1
> > prior1$B$V[5,5]<- 1e-8
> > 
> > is this the proper way to set the prior? or should the fixed effects
> > matrix have different dimensions since my model is bivariate:
> > 
> > model_multi <- MCMCglmm(cbind(AFR, OffMortality)~trait-1 + trait:COEFPAR
> > + trait:I(COEFPAR*COEFPAR) + trait:TWIN + trait:YEARM+
> > at.level(trait,2):log(FERTILITY), random =
> > ~us(trait):animal+us(trait):MOTHERW, rcov = ~us(trait):units, data =
> > IAC, pedigree = prunedPed, family = c("gaussian", "poisson"), nitt =
> > 3500000, burnin = 500000, thin = 3000, prior = prior1, verbose = FALSE,
> > pr=TRUE)
> > 
> > Thank you in advance for any advice.
> > 
> > -- 
> > Walid Mawass
> > 
> > Ph.D. candidate in Cellular and Molecular Biology
> > 
> > Population Genetics Laboratory
> > 
> > University of Québec at Trois-Rivières
> > 3351, boul. des Forges, C.P. 500
> > Trois-Rivières (Québec) G9A 5H7
> > Telephone: 819-376-5011 poste 3384
> > 
> > 
> > 	[[alternative HTML version deleted]]
> > 
> > _______________________________________________
> > R-sig-mixed-models@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> 

-- 
Walid Mawass

Ph.D. candidate in Cellular and Molecular Biology

Population Genetics Laboratory

University of Québec at Trois-Rivières
3351, boul. des Forges, C.P. 500
Trois-Rivières (Québec) G9A 5H7
Telephone: 819-376-5011 poste 3384

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