New function lumpMutSpecial() implementing special
lumping of mutation models. Only some cases are implemented so far, more
may be added in the future.
mutationMatrix() gains argument
validate.
New function makeStationary() replaces the previous
stabilize() for PM-transformation to stationarity.
As a shortcut for makeStationary(), the PM
transformation may also be applied directly with
mutationMatrix(..., transform = "PM") or
mutationModel(..., transform = "PM").
Fixed a bug in makeReversible(..., method = "PR")
failing to catch non-reversible inputs.
Various minor fixes and code simplifications.
New function makeReversible() implementing three
transformations to reversibility.
mutationMatrix() and mutationModel()
gain a transform argument for applying transformations to
reversibility on the fly.
New function adjustRate() for adjusting the overall
mutation rate of a mutation matrix.
mutationModel(model = "dawid", ...) replaces the
function stepwiseReversible().
Random mutation models can now condition on a fixed overall mutation rate.
Include info on boundedness in the print method for mutation models.
Refactored mutationMatrix() for better code
maintainability.
Bug fix: Don’t trivialise model name when there is only 1 allele.
Several minor improvements in documentation and examples.
Use rhub v2.
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
pedsuite, 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().
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