pedtools 2.8.0

Breaking changes

• Pedtools previously included igraph in the Suggests field, for the sole purpose of finding loop breakers in pedigrees with marriage loops (in breakLoops()). This functionality has now been replaced with a custom implementation, allowing to drop the igraph dependency. The new method is slightly faster than the previous, but it may select different loop breakers in some cases.

New features

• New plot argument miscarriage for indicating miscarriages as triangles.

• New function harmoniseMarkers().

• New functions niblings() (= nephews & nieces) and piblings() (= aunts & uncles, i.e. siblings of parents).

• getLocusAttributes() gains argument simplify.

• In getGenotypes(), allow ids to be a function.

Other

• Improved error messages in father(), mother() etc.
• Better handling of ped lists in father(), mother() etc.
• Remove deprecated offspring(). Use children() instead.