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polySegratioMM (version 0.6-3)

Bayesian mixture models for marker dosage in autopolyploids

Description

Fits Bayesian mixture models to estimate marker dosage for dominant markers on autopolyploids using JAGS (1.0 or greater) as outlined in Baker et al (2010). May be used in conjunction with polySegratio for simulation studies and comparison with standard methods.

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Version

Install

install.packages('polySegratioMM')

Monthly Downloads

156

Version

0.6-3

License

GPL-3

Maintainer

Peter Baker

Last Published

March 6th, 2014

Functions in polySegratioMM (0.6-3)

setPriors

Set prior distributions for parameters of Bayesian mixture model for dosages
plotFitted

Plot observed segregation ratios and fitted and theoretical models
dosagesJagsMix

Compute dosages under specified Bayesian mixture model
dumpData

Dumps segregation ratio data to file for subsequent JAGS run
print.runJags

Running JAGS
runJags

Run JAGS to create MCMC sample for segregation ratio mixture model
diagnosticsJagsMix

MCMC diagnostics for polyploid segregation ratio mixture models
calculateDIC

Compute DIC for fitted mixture model
DistributionPlotBinomial

Distribution Plot
writeControlFile

Write JAGS .cmd file for running JAGS
readJags

Read MCMC sample(s) from a JAGS run
mcmcHexRun

Results of MCMC estimation for simulated overdispersed markers
runSegratioMM

Run a Bayesian mixture model for marker dosage with minimal effort
writeJagsFile

Writes BUGS file for processing by JAGS
plot.segratioMCMC

MCMC plots for segregation ratio mixture models
setControl

Set up controls for a JAGS segregation ratio model run
setModel

Set characteristics of the Bayesian mixture model for dosages
summary.segratioMCMC

Summary statistics for an segratioMCMC object
hexmarkers.overdisp

Simulated overdispersed autopolyploid dominant markers from 200 hexaploid individuals
hexmarkers

Simulated autopolyploid dominant markers from 200 hexaploid individuals
setInits

Set up and dump initial values given the model and prior
print.dosagesMCMC

Doses from Bayesian mixture model
polySegratioMM-package

Marker dosage for autoployploids by Bayesian mixture models