pedmut 0.9.0

New features

• 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").

Bug fixes

• Fixed a bug in makeReversible(..., method = "PR") failing to catch non-reversible inputs.

• Various minor fixes and code simplifications.

pedmut 0.8.0

New features

• 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.

Other

• 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.

pedmut 0.7.1

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

• New function lumpedModel() which is a convenient wrapper of lumpedMatrix().

• New function sexEqual() for reading the sexEqual attribute of a mutation model.

Other

• 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.

pedmut 0.4.0

New features

• mutationModel() gains a new parameter validate, making it possible to disable validation of the model.
• validateMutationModel() and validateMutationMatrix() are significantly faster, due to various code improvements.

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.