pedtools 2.11.0

New features

• The loop breaking algorithm has been revamped and extended to allow founders to act as loop breakers, and to use the same individual as loop breaker for several loops. This enables loop breaking (and therefore likelihood calculations etc.) in many pedigrees that were previously intractable. The new algorithm is also faster than the previous one, especially in large pedigrees.

  Awaiting updates in downstream packages, the new loop breaking methods are disabled by default, but may be activated by breakLoops(x, allowFounder = TRUE, allowRepeated = TRUE).

• The ped() constructor now always checks for the presence of loops, ignoring the previous argument detectLoops, which is now deprecated. The previous internal loop detection algorithm, which was optional because it was slow in large pedigrees, has been replaced by a faster one which scales better.

• Several methods have been revised and made more efficient, including randomPed(), peelingOrder(), connectedComponents().

• New function children2(), similar to children() but requiring both parents as input.

• children() gains argument bySpouse, which if TRUE gives a list of children for each spouse, instead of a single vector with all children.

Other

• Fix bug in summary.list() handling ped lists.
• Handle NULLs in the internal split_genotype_cols().
• Various vector code cleanups.