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Construct a ginverse Object from Precision Matrices

Source: R/ginverse.R
as.ginverse.Rd

Creates a ginverse object from a named list of precision (inverse covariance) matrices. These matrices are typically used to specify the inverse of covariance structures for random effects in LMMsolve.

Usage

as.ginverse(precisionMatrices, levels = NULL, tol = 1e-10)

Arguments

precisionMatrices

A named list of square matrices. Each element must be a base matrix, an object inheriting from Matrix, or a spam object. Each element represents a precision matrix corresponding to a random effect.

levels

An optional named list giving the levels corresponding to the rows and columns of the precision matrices. This is required for spam objects, which do not have row and column names. For matrix and Matrix objects, levels are obtained from the row names; if supplied, they are checked for consistency with the row and column names.

tol

A numeric tolerance used for numerical stability (e.g. during inversion or eigenvalue truncation). Stored as an attribute of the resulting object.

Value

An object of class "ginverse" (a named list) containing the supplied precision matrices, with attributes "levels" and "tol".

Details

Each precision matrix must be square. For matrix and Matrix objects, the row and column names define the corresponding levels. For spam objects, which do not use row and column names, the corresponding levels must be supplied through levels.

The function performs basic validation:

  • precisionMatrices must be a named list.

  • If supplied, levels must be a named list with matching names.

  • Each precision matrix must be square.

  • For matrix and Matrix objects, row and column names must be present and identical.

  • For spam objects, levels must be supplied.

  • Levels must be a character vector with length equal to the corresponding matrix dimension and contain no duplicates.

  • If levels is supplied for a matrix or Matrix object, it must agree with its row and column names.

No reordering or alignment with the data is performed at this stage. This is handled internally by LMMsolve.

See also

LMMsolve

Examples

K <- diag(1, 5)
dimnames(K) <- list(as.character(1:5), as.character(1:5))

# Construct ginverse object from a matrix with names
g <- as.ginverse(list(id = K))
g
#> $id
#>   1 2 3 4 5
#> 1 1 0 0 0 0
#> 2 0 1 0 0 0
#> 3 0 0 1 0 0
#> 4 0 0 0 1 0
#> 5 0 0 0 0 1
#> 
#> attr(,"class")
#> [1] "ginverse" "list"    
#> attr(,"levels")
#> attr(,"levels")$id
#> [1] "1" "2" "3" "4" "5"
#> 
#> attr(,"tol")
#> [1] 1e-10

# A spam matrix requires levels to be supplied
# Kspam <- spam::as.spam(K)
# g <- as.ginverse(list(id = Kspam),
#                  levels = list(id = as.character(1:5)))