computeRSPs: Compute the relatedness summary parameters (RSPs) from a...
In jraffa/pedRSP: Calculates the Relatedness Summary Parameters (RSPs) in Pedigrees

Description Usage Arguments Details Value Author(s) See Also Examples

This function computes the RSPs from the eigenvalues of twice the kinship matrix either directly or via a pedigree object.

1 2	computeRSPs(ped = NULL, kmat = NULL, thresholderror = 0.01, forcePD = TRUE)

`ped`	a pedigree object from the 'kinship2' package. One of `ped` or `kmat` must be specified, but not both.
`kmat`	a kinship matrix
`thresholderror`	a scalar numeric of a permissible threshold that the mean eigenvalue is allowed to deviate from 1.
`forcePD`	logical of whether positive definiteness of kmat should be strictly enforced.

This function calculates the eigenvalues from a pedigree object or twice the kinship matrix, and using these computes the RSPs: the variance of the eigenvalue and log eigenvalues, and the geometric mean.

a pedRSP object with the calculated RSPs.

Jesse D. Raffa

pedigree kinship

require(kinship2)
# Example from kinship2 package
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, 2, 2, 4, 4, 6,  2,  0,  0, 12, 13),
dad =c(0, 0, 0, 0, 1, 1, 3, 3, 3,  7,  0,  0, 11, 10),
sex =c(1, 2, 1, 2, 1, 2, 1, 2, 1, 1, 1, 2, 2, 2))
tped <- with(test1, pedigree(id, dad, mom, sex))
computeRSPs(ped=tped)