Package: pedmut 0.8.0

Magnus Dehli Vigeland

pedmut: Mutation Models for Pedigree Likelihood Computations

A collection of functions for modelling mutations in pedigrees with marker data, as used e.g. in likelihood computations with microsatellite data. Implemented models include equal, proportional and stepwise models, as well as random models for experimental work, and custom models allowing the user to apply any valid mutation matrix. Allele lumping is done following the lumpability criteria of Kemeny and Snell (1976), ISBN:0387901922.

Authors:Magnus Dehli Vigeland [aut, cre], Thore Egeland [ctb]

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pedmut.pdf |pedmut.html
pedmut/json (API)
NEWS

# Install 'pedmut' in R:
install.packages('pedmut', repos = c('https://magnusdv.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/magnusdv/pedmut/issues

On CRAN:

Conda:

5.03 score 2 stars 18 packages 5 scripts 591 downloads 21 exports 0 dependencies

Last updated 3 hours agofrom:d4bf4cd2eb. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKApr 01 2025
R-4.5-winOKApr 01 2025
R-4.5-macOKApr 01 2025
R-4.5-linuxOKApr 01 2025
R-4.4-winOKApr 01 2025
R-4.4-macOKApr 01 2025
R-4.4-linuxOKApr 01 2025
R-4.3-winOKApr 01 2025
R-4.3-macOKApr 01 2025

Exports:adjustRatealwaysLumpablefindStationarygetParamsisBoundedisLumpableisMutationMatrixisMutationModelisReversibleisStationarylumpedMatrixlumpedModelmakeReversiblemutationMatrixmutationModelmutRatesexEqualstabilizestepwiseReversiblevalidateMutationMatrixvalidateMutationModel

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
Adjust the overall mutation rate of a modeladjustRate
Find the stationary frequency distributionfindStationary
Get model parametersgetParams
Test for mutation matrix/modelisMutationMatrix isMutationModel
Combine alleles in a mutation matrixlumpedMatrix lumpedModel
Transformations to reversibilitymakeReversible
Upper limits for overall mutation rate for the stepwise reversible model.maxRate
Mutation model propertiesalwaysLumpable isBounded isLumpable isReversible isStationary model_properties
Mutation matrixmutationMatrix validateMutationMatrix
Mutation modelsmutationModel sexEqual validateMutationModel
Overall mutation ratemutRate
Stabilization of mutation matrixstabilize
Dawid's reversible stepwise modelstepwiseReversible