Changes in version 0.9.1 (2026-05-17)                  

New features

  - New output format (format = 4) in getParams(). This produces a list
    of lists, suitable for programmatic use.

                 Changes in version 0.9.0 (2025-04-29)                  

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.

                 Changes in version 0.8.0 (2025-04-01)                  

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.

                        Changes in version 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.

                 Changes in version 0.6.0 (2023-04-12)                  

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.

                 Changes in version 0.5.0 (2023-02-11)                  

New features

  - 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.

                 Changes in version 0.4.0 (2022-11-16)                  

New features

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

                 Changes in version 0.3.0 (2021-10-22)                  

This is maintenance release with mostly minor changes.

                 Changes in version 0.2.0 (2020-07-30)                  

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.

                 Changes in version 0.1.0 (2019-10-01)                  

  - Initial CRAN release