MCMCglmm Bivariate Binary Model - R-SIG-mixed-models

Thu, Jul 23, 2009 5:18 AM #

Hi Chuck
I think you need to fix residual variance and covariance to 1 and 0 for 
both traits because they are both binary traits. With your actual prior, 
you fix it only for the second trait.
So I think it should work with

prior = list(R = list(V = diag(2), n = 0, fix = 1),
             G = list(G1 = list(V = diag(2), n = 1)))


Hope this would work
Sincerely

Julien

Julien Martin, Ph.D. Candidate
Universit? de Sherbrooke
Sherbrooke, Qc
J1A 2R1
Canada



> Date: Wed, 22 Jul 2009 15:13:00 -0400
> From: Chuck Cleland <ccleland at optonline.net>
> Subject: [R-sig-ME] MCMCglmm Bivariate Binary Model
> To: r-sig-mixed-models at r-project.org
> Message-ID: <4A6764BC.8080106 at optonline.net>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi All,
>
>   I attempted to fit a bivariate binary model similar to the example in
> the Tutorial:
>
> prior = list(R = list(V = diag(2), n = 0, fix = 2),
>              G = list(G1 = list(V = diag(2), n = 1)))
>
> model5 <- MCMCglmm(cbind(ANYHR, ANYPO) ~ trait - 1, random =
> ~us(trait):PROGRAM, rcov = ~idh(trait):units, family=c("categorical",
> "categorical"), data = radars, prior = prior, verbose = FALSE)
>
> Error in MCMCglmm(cbind(ANYHR, ANYPO) ~ trait - 1, random =
> ~us(trait):PROGRAM,  :
>   ill-conditioned G/R structure: use proper priors if you haven't or
> rescale data if you have
>
>   In this dataset, one of the four cells in the 2x2 table is empty:
>
>    Cell Contents
> |-------------------------|
> |                   Count |
> |-------------------------|
>
> Total Observations in Table:  21335
>
>              | ANYPO
>        ANYHR |        0  |        1  | Row Total |
> -------------|-----------|-----------|-----------|
>            0 |        0  |     8999  |     8999  |
> -------------|-----------|-----------|-----------|
>            1 |     6458  |     5878  |    12336  |
> -------------|-----------|-----------|-----------|
> Column Total |     6458  |    14877  |    21335  |
> -------------|-----------|-----------|-----------|
>
>   Is there a way to change the specification for prior to make this work?
>
> thanks,
>
> Chuck
>