Package: pedmut 0.9.1

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]

pedmut_0.9.1.tar.gz
pedmut_0.9.1.zip(r-4.7)pedmut_0.9.1.zip(r-4.6)pedmut_0.9.1.zip(r-4.5)
pedmut_0.9.1.tgz(r-4.6-any)pedmut_0.9.1.tgz(r-4.5-any)
pedmut_0.9.1.tar.gz(r-4.7-any)pedmut_0.9.1.tar.gz(r-4.6-any)
pedmut_0.9.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
pedmut/json (API)

# 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:

mutation-modeling pedigree-analysis pedsuite

5.43 score 3 stars 20 packages 7 scripts 997 downloads 23 exports 1 dependencies

Last updated from:ebf096743d. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	130
source / vignettes	OK	177
linux-release-x86_64	OK	105
macos-release-arm64	OK	88
macos-oldrel-arm64	OK	110
windows-devel	OK	87
windows-release	OK	76
windows-oldrel	OK	68
wasm-release	OK	92

Exports:adjustRate alwaysLumpable findStationary getParams isBounded isLumpable isMutationMatrix isMutationModel isReversible isStationary lumpedMatrix lumpedModel lumpMutSpecial makeReversible makeStationary mutationMatrix mutationModel mutRate sexEqual stabilize stepwiseReversible validateMutationMatrix validateMutationModel

Dependencies:lpSolve

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Adjust the overall mutation rate of a model	adjustRate
Find the stationary frequency distribution	findStationary
Get model parameters	getParams
Test for mutation matrix/model	isMutationMatrix isMutationModel
Combine alleles in a mutation matrix	lumpedMatrix lumpedModel
Special lumping of mutation models	lumpMutSpecial
Transformations to reversibility	makeReversible
Transformation (stabilisation) to stationarity	makeStationary
Upper limits for overall mutation rate for the stepwise reversible model.	maxRate
Mutation model properties	alwaysLumpable isBounded isLumpable isReversible isStationary model_properties
Mutation matrix	mutationMatrix validateMutationMatrix
Mutation models	mutationModel sexEqual validateMutationModel
Overall mutation rate	mutRate
Stabilization of mutation matrix	stabilize
Dawid's reversible stepwise model	stepwiseReversible