[R-sig-ME] MCMCglmm bivariate with offset

[Walid Mawass]

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 using 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
>>
>>
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>>
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>

-- 
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