ribd 1.4.0

Breaking changes

• The function idcoefs() was removed, since it relied on the no-longer-available package identity.

• The deprecated kinshipX(), inbreedingX() and kappaIbdX() were removed, being replaced with an argument Xchrom in kinship(), inbreeding() and kappaIBD() respectively. This is also consistent with the new identityCoefs() (see below).

• The function generalisedKinship() has been replaced with the much more versatile gKinship() (see below).

New features

• New function identityCoefs() for computing condensed and detailed identity coefficients ("Jacquard coefficients"). Both autosomal and X-chromosomal versions are supported. This function supersedes condensedIdentity() and condensedIdentityX(), which will continue to exist, nonetheless.

• condensedIdentity() gains arguments simplify and self, to match the new identityCoefs().

• Computation of identity coefficients by MERLIN (via the "--extended" feature) is implemented in identityCoefs() with the option method = "merlin". Note that MERLIN rounds the output to 3 decimal places, reducing its utility somewhat.

• New function gKinship() for computing generalised kinship coefficients. Several algorithms are implemented, supporting various flavours (random vs. deterministic; distinct vs. non-distinct groups; autosomal vs. X).

• New container class gip for generalised IBD patterns. Includes a print method.

• New function coeffTable() collecting various pedigree coefficients in a single table.

• New function kin2deg() computing the degree of relatedness, as used e.g. by the software KING.

Bug fixes

• Fixed bug in kinship() affecting pedigrees in nonstandard order.