bdsmatrix-class {bdsmatrix}R Documentation

Class "bdsmatrix"

Description

Representation for a Block Diagonal Sparse matrix

Objects from the Class

Objects of this class are usually created using the bdsmatrix, bdsI or bdsBlock functions. The result is a symmetrix matrix whose upper left portion is block-diagonal, with an optional border on the right and bottom that is dense. The matrices were originally created to represent familial correlation structures, which have a block for each family but no connection between families.

Slots

blocksize:
An integer vector containing the sizes of the diagonal blocks
blocks:
A numeric vector containing the contents of the block portion. Only the lower triangle of each block is stored.
rmat:
An optional numeric matrix containing the dense portion
offdiag:
A single numeric element, default zero, which is the value for elements off the block-diagonal
Dim:
The dimension of the matrix, an integer vector of length 2
Dimnames:
The dimnames of the matrix, a list with 2 elements

Methods

%*%
signature(x = "matrix", y = "bdsmatrix"): the result will be an ordinary matrix
%*%
signature(x = "numeric", y = "bdsmatrix"): the result will be a vector
%*%
signature(x = "bdsmatrix", y = "matrix"): the result will be an ordinary matrix
%*%
signature(x = "bdsmatrix", y = "numeric"): the result will be a vector
Math2
signature(x = "bdsmatrix"):
Math
signature(x = "bdsmatrix"):
Ops
signature(e1 = "bdsmatrix", e2 = "numeric"):
Ops
signature(e1 = "bdsmatrix", e2 = "bdsmatrix"):
Ops
signature(e1 = "bdsmatrix", e2 = "matrix"):
Ops
signature(e1 = "numeric", e2 = "bdsmatrix"):
Ops
signature(e1 = "matrix", e2 = "bdsmatrix"):
[
signature(x = "bdsmatrix"): if the subscripts are a set of increasing integers, and the row and column subscripts are identical, then the result is aslo a bdsmatrix. This is useful for example to create the kinship matrix for all females from an overall kinship matrix. If the subscripts do not match, then an ordinary matrix is created
all
signature(x = "bdsmatrix"): ...
any
signature(x = "bdsmatrix"): ...
coerce
signature(from = "bdsmatrix", to = "matrix"): ...
coerce
signature(from = "bdsmatrix", to = "vector"): ...
diag
signature(x = "bdsmatrix"): retrieve the diagonal of the matrix
diag<-
signature(x = "bdsmatrix"): set the diagonal of the matrix to a given value
dim
signature(x = "bdsmatrix"): dimension of the matrix
dimnames
signature(x = "bdsmatrix"): dimnames of the matrix
dimnames<-
signature(x = "bdsmatrix"): set the dimnames of the matrix
gchol
signature(x = "bdsmatrix"): generalized cholesky decomposition of the matrix
max
signature(x = "bdsmatrix"): maximum of the matrix
min
signature(x = "bdsmatrix"): minimum of the matrix
prod
signature(x = "bdsmatrix"):
range
signature(x = "bdsmatrix"):
show
signature(object = "bdsmatrix"): print out the matrix
sum
signature(x = "bdsmatrix"):

Note

Many of the actions above will result in conversion to an ordinary matrix object, including print, addition to an ordinary matrix, etc. This can easily create objects that are too large for system memory. By default the value of options('bdsmatrixsize') is consulted first, and if the resulting object would be have a length greater than this option the conversion an error is generated and conversion is not attempted. The default value for the option is 1000.

Author(s)

Terry Therneau

See Also

gchol

Examples

showClass("bdsmatrix")

[Package bdsmatrix version 1.0 Index]