likelihood() function now handles multiple marker inputs. For example, the call likelihood(x, 1:nMarkers(x)) results in a vector with the likelihood of each marker attached to x.For likelihoods involving linked markers, e.g., likelihood(x, marker1, marker2, rho),marker1may be a vector of marker indices, whilemarker2` must still refer to a single marker.
theta is renamed to rho everywhere, to align with other ped suite packages. theta still works, though.Many input checks have been added, giving more useful error messages
The data structure used in likelihood calculations is simplified and more efficient.
Likelihood computation of two linked markers (and therefore also twoMarkerDistribution()) is much faster now.
New general MERLIN wrapper, merlin().
Both likelihoodMerlin() and the new merlin() now accepts ped lists.