extended.shared: Compute a common shared environment matrix

In MESS: Miscellaneous Esoteric Statistical Scripts

Compute a common shared environment matrix

Description

Compute the common shared environment matrix for a set of related subjects. The function is generic, and can accept a pedigree, or pedigreeList as the first argument.

Usage

extended.shared(id, rho = 1, theta = 1, ...)

## S3 method for class 'pedigreeList'
extended.shared(id, rho = 1, theta = 1, ...)

## S3 method for class 'pedigree'
extended.shared(id, rho = 1, theta = 1, ...)

Arguments

id	either a pedigree object or pedigreeList object
rho	The correlation between spouses
theta	The partial path coefficient from parents to offspring
...	Any number of optional arguments. Not used at the moment

Details

When called with a pedigreeList, i.e., with multiple families, the routine will create a block-diagonal-symmetric ‘bdsmatrix’ object. Since the [i,j] value of the result is 0 for any two unrelated individuals i and j and a ‘bdsmatix’ utilizes sparse representation, the resulting object is often orders of magnitude smaller than an ordinary matrix. When called with a single pedigree and ordinary matrix is returned.

Value

a matrix of shared environment coefficients

Author(s)

Claus Ekstrom [e-mail]

See Also

pedigree, kinship,

Examples

library(kinship2)
test1 <- data.frame(id  =c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14),
                    mom =c(0, 0, 0, 0, 0, 2, 2, 4, 0,  6,  8,  0, 10, 11),
                    dad =c(0, 0, 0, 0, 0, 1, 1, 3, 0,  5,  7,  0,  9, 12),
                    sex =c(1, 2, 1, 2, 1, 2, 1, 2, 1,  2,  2,  1,  2,  2))

tped <- with(test1, pedigree(id, dad, mom, sex))
extended.shared(tped)

MESS documentation built on Aug. 21, 2023, 1:05 a.m.