New function mutRate() computing the overall mutation rate of a mutation model.
New function isBounded() checking if a mutation matrix M is bounded by the allele frequencies, i.e., that M[i,j] <= afreq[j] for all i != j.
New function stepwiseReversible().
Added Thore Egeland as package contributor.
Fixed a floating point bug in the creation of stepwise models.
Fix broken URLs.
Implement the PM stabilisation method of Simonsson & Mostad; liftover from Familias:::stabilize.
Implement more general lumping (multiple lumps!) under strong lumpability.
New utility getParams() for extracting model parameters.
Extend isStationary(), isReversible() and alwaysLumpable() to full models.
New functions isMutationMatrix() and isMutationModel().
New S3 method as.matrix() for classes mutationMatrix and mutationModel.
New function findStationary() for obtaining the stationary distribution of a mutation matrix.
Various speedups, mainly concerning lumped models. These improvements should give better performance in other parts of the ped suite, especially in likelihood calculations with many markers.
New function lumpedModel() which is a convenient wrapper of lumpedMatrix().
New function sexEqual() for reading the sexEqual attribute of a mutation model.
mutationModel() gains a new parameter validate.validateMutationModel() and validateMutationMatrix(), making them significantly faster.This is maintenance release with mostly minor changes.
onestep model.toString() method producing a short description of a mutation model.
This is used in pedtools::print.marker().