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MasterBayes (version 2.57)

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

420

Version

2.57

License

GPL (>= 2)

Maintainer

Jarrod Hadfield

Last Published

June 24th, 2020

Functions in MasterBayes (2.57)

GdataPed

GdataPed Object
PdataPed

PdataPed Object
MLE.ped

Maximum Likelihood Estimation of the Pedigree
MLE.popsize

Maximum Likelihood Estimation of the Unsampled Population Size
extractA

Allele Frequencies
mismatches

Parent-Offspring Genotype Mismatches
orderPed

Orders a Pedigree
legalG

Legal Genotype Configurations
beta.loglik

Log-Likelihood of Beta
genotype.list

Genotype Objects for all Loci
popsize.loglik

Log-Likelihood of Unsampled Population Size
fillX.G

Mendelian Transition Probabilities
genotypeD

genotypeD Object
reordXlist

Reorders Design Matrices
autocorrP

Autocorrelation Function for Parenatge Assignment
summary.genotypeD

genotypeD Object
modeG

Posterior Mode of Genotypes
consensusG

Obtains a consensus genotype from duplicate samples
simgenotypes

Genotype and Genotyping Error Simulation
tunePed

tunePed Object
simpedigree

Simulates a Pedigree given a Log-Linear Model
getXlist

Design Matrices for the Multinomial Log-Linear Model
startPed

startPed Object
insertPed

Inserts Founders into a Pedigree
modeP

Posterior Mode of Parents
post.pairs

Returns pairs of individuals that fall into specific relatedness categories
varPed

Transforms Variables for a Multinomial Log-Linear Model
priorPed

priorPed Object
WarblerG

Seychelles Warbler Genotypes
WarblerP

Seychelles Warbler Phenotypes
MCMCped

Markov chain Monte Carlo Methods for Pedigree Reconstruction and Analysis
MLE.beta

Maximum Likelihood Estimation of Beta
MasterBayes

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