NEWS.md

In pedmut: Mutation Models for Pedigree Likelihood Computations

pedmut 0.7.0

New features

• 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.

Bug fixes

• Fixed a floating point bug in the creation of stepwise models.

• Fix broken URLs.

pedmut 0.6.0

New features

• 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.

pedmut 0.5.0

New features

• 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.

pedmut 0.4.0

New features

• mutationModel() gains a new parameter validate.
• Various code improvements in validateMutationModel() and validateMutationMatrix(), making them significantly faster.

pedmut 0.3.0

This is maintenance release with mostly minor changes.

pedmut 0.2.0

New features

• Added onestep model.
• Added toString() method producing a short description of a mutation model. This is used in pedtools::print.marker().

Other changes

• Updated README.
• Minor bug fixes.

pedmut 0.1.0

• Initial CRAN release

pedmut documentation built on Nov. 5, 2023, 1:10 a.m.