pedprobr 1.0.0

• Methods for allele lumping have been rewritten and expanded. In particular, markers with an un-lumpable mutation model (in the Kemeny-Snell sense) can now, in certain cases, be lumped using the special lumping recently implemented in pedmut. To activate this, set special = TRUE in likelihood() and likelihood2(). By default, special is FALSE in the former and TRUE in the latter.

• likelihood() and likelihood2() also gain a new argument alleleLimit, limiting the number of alleles in unlumpable markers. If the limit is exceeded, the mutation model is replaced with the simpler equal model, which always permits lumping. By default, this behaviour is disabled (i.e., alleleLimit = Inf).

• Improve structure of likelihood() and likelihood2(), to avoid redundant calculations.

• Skip unneeded checks in [one/two]MarkerDistribution().