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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().These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.