Resolves a Prior Specification in MCMCglmm

Generates the (co)variance matrix prior parameters in MCMCglmm given a prior specification that might utilise a prior_generator.

Usage

resolve_prior(prior_element, k=NULL)

Arguments

prior_element: prior spefictaion for a (co)variance matrix
k: dimension of the (co)variance matrix
vtype: type of covariance structure used: currently only us and idh are allowed

Details

Primarily used internally to generate the (co)variance matrix prior parameters used in MCMCglmm: V, nu, alpha.mu and alpha.V. If these are already passed as a list, the list is simply returned. If a prior_generator is used then the prior parameters are generated given dimension of the (co)variance matrix, k and its stucture type vtype.

Value

list of prior parameters for MCMCglmm

Author

Jarrod Hadfield j.hadfield@ed.ac.uk

Examples

prior_element1<-list(V=diag(2)/2, nu=2, alpha.mu=c(0,0), alpha.V=diag(2)*1000)

resolve_prior(prior_element1)
#> $V
#>      [,1] [,2]
#> [1,]  0.5  0.0
#> [2,]  0.0  0.5
#> 
#> $nu
#> [1] 2
#> 
#> $alpha.mu
#> [1] 0 0
#> 
#> $alpha.V
#>      [,1] [,2]
#> [1,] 1000    0
#> [2,]    0 1000
#> 

prior_element2<-F(df2=1, scale=1000)

resolve_prior(prior_element2, k=2, vtype="us")
#> $V
#>      [,1] [,2]
#> [1,]  0.5  0.0
#> [2,]  0.0  0.5
#> 
#> $nu
#> [1] 2
#> 
#> $alpha.mu
#> [1] 0 0
#> 
#> $alpha.V
#>      [,1] [,2]
#> [1,] 1000    0
#> [2,]    0 1000
#> 

resolve_prior(prior_element2, k=2, vtype="idh")
#> $V
#>      [,1] [,2]
#> [1,]    1    0
#> [2,]    0    1
#> 
#> $nu
#> [1] 1
#> 
#> $alpha.mu
#> [1] 0 0
#> 
#> $alpha.V
#>      [,1] [,2]
#> [1,] 1000    0
#> [2,]    0 1000
#>