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MasterBayes (version 2.58)

ML and MCMC Methods for Pedigree Reconstruction and Analysis

Description

The primary aim of 'MasterBayes' is to use MCMC techniques to integrate over uncertainty in pedigree configurations estimated from molecular markers and phenotypic data. Emphasis is put on the marginal distribution of parameters that relate the phenotypic data to the pedigree. All simulation is done in compiled 'C++' for efficiency.

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Version

Install

install.packages('MasterBayes')

Monthly Downloads

439

Version

2.58

License

GPL (>= 2)

Maintainer

Jarrod Hadfield

Last Published

June 22nd, 2022

Functions in MasterBayes (2.58)

MLE.popsize

Maximum Likelihood Estimation of the Unsampled Population Size
GdataPed

GdataPed Object
WarblerP

Seychelles Warbler Phenotypes
PdataPed

PdataPed Object
getXlist

Design Matrices for the Multinomial Log-Linear Model
MasterBayes

Maximum Likelihood and Markov chain Monte Carlo methods for Pedigree Reconstruction, Analysis and Simulation.
extractA

Allele Frequencies
fillX.G

Mendelian Transition Probabilities
beta.loglik

Log-Likelihood of Beta
MLE.ped

Maximum Likelihood Estimation of the Pedigree
WarblerG

Seychelles Warbler Genotypes
genotype.list

Genotype Objects for all Loci
genotypeD

genotypeD Object
modeG

Posterior Mode of Genotypes
priorPed

priorPed Object
varPed

Transforms Variables for a Multinomial Log-Linear Model
post.pairs

Returns pairs of individuals that fall into specific relatedness categories
reordXlist

Reorders Design Matrices
simgenotypes

Genotype and Genotyping Error Simulation
modeP

Posterior Mode of Parents
simpedigree

Simulates a Pedigree given a Log-Linear Model
startPed

startPed Object
mismatches

Parent-Offspring Genotype Mismatches
legalG

Legal Genotype Configurations
consensusG

Obtains a consensus genotype from duplicate samples
popsize.loglik

Log-Likelihood of Unsampled Population Size
insertPed

Inserts Founders into a Pedigree
orderPed

Orders a Pedigree
tunePed

tunePed Object
summary.genotypeD

genotypeD Object
MCMCped

Markov chain Monte Carlo Methods for Pedigree Reconstruction and Analysis
autocorrP

Autocorrelation Function for Parenatge Assignment
MLE.beta

Maximum Likelihood Estimation of Beta