[R-sig-ME] MCMCglmm Starting Value structure

[Jarrod Hadfield]

Hi, 

A bug has crept into MCMCglmm at some point when specifying starting
values. The correct syntax should be start2c for which you get an error
message. I will update as soon I have finished some of the other updates
I am working on. As a work around you can add another matrix to the G
element:

start2c$G[[5]]<-diag(2)

It will be ignored but will alow the code to run.

Sorry,

Jarrod


 


On Tue, 2011-06-07 at 10:34 -0700, Robin Jeffries wrote:
> I am having some difficulty defining the correct structure for the
> starting values in MCMCglmm.
> Several prior google searches for examples of starting values for
> MCMCglmm resulted only in one unhelpful L-serv posting where the
> poster was subsequently told to RTM and quit posting. I hope that I
> show that I have spent time trying to find the answer on my own prior
> to posting.
> 
> 
> My prior structure is:
> 
> prior1 = list(R = list(V = 1, nu = .002),
>   G = list(
>    G1 = list(V = diag(3), n=4),
>    G2 = list(V = diag(3), n=4),
>    G3 = list(V = 1, nu=1),
>    G4 = list(V = 1, nu=1)
> ))
> 
> 
> To set up starting values I first set Rc and Gc to be vectors of
> length 1 and 20 respectively. I then tried the starting value
> structure as
> 
> start2a = list( R = Rc,
>   G = list(
>    G1 = Gc[1:9],
>    G2 = Gc[10:18],
>    G3 = Gc[19],
>    G4 = Gc[20]),
> QUASI=FALSE)
> 
> which gives me the error "V is the wrong dimension for some
> startG/startR elements"
> So I tried to structure it exactly as the priors (with lists and matricies)
> 
> start2b = list(R = list(V =Rc),
> G = list(
>  G1 = list(V = matrix(Gc[1:9], nrow=3, ncol=3)),
>  G2 = list(V = matrix(Gc[10:18], nrow=3, ncol=3)),
>  G3 = list(V = Gc[19]),
>  G4 = list(V = Gc[20])
> ))
> 
> and got the same error message.
> 
> Since the help file/notes/vignette says that "the starting values is a
> list of 4 possible elements, where G itself is also a list with as
> many elements as RE components" I tried a combination of the above
> two:
> 
> start2c = list(
> R = Rc,
> G = list(
>  G1 = matrix(Gc[1:9], nrow=3, ncol=3),
>  G2 = matrix(Gc[10:18], nrow=3, ncol=3),
>  G3 = Gc[19],
>  G4 = Gc[20]),
> QUASI=FALSE)
> 
> but then was greeted with the error "Error in start$G[[r]] : subscript
> out of bounds"
> 
> If someone could help me out with what the structure of the starting
> values is supposed to look like, it would be appreciated.
> 
> 
> Robin Jeffries
> MS, DrPH Candidate
> Department of Biostatistics
> UCLA
> 530-633-STAT(7828)
> 
> _______________________________________________
> R-sig-mixed-models at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> 



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