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R package: polySegratioMM

polySegratioMM: Bayesian mixture models for marker dosage in autopolyploids

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.

Maintenance release: I am no longer working in polyploids.

NB: Migrated from r-forge to better manage project

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Install

install.packages('polySegratioMM')

Monthly Downloads

182

Version

0.6-4

License

GPL-3

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Maintainer

Peter Baker

Last Published

March 23rd, 2018

Functions in polySegratioMM (0.6-4)

mcmcHexRun

Results of MCMC estimation for simulated overdispersed markers
plot.segratioMCMC

MCMC plots for segregation ratio mixture models
dosagesJagsMix

Compute dosages under specified Bayesian mixture model
DistributionPlotBinomial

Distribution Plot
dumpData

Dumps segregation ratio data to file for subsequent JAGS run
calculateDIC

Compute DIC for fitted mixture model
print.runJags

Running JAGS
hexmarkers

Simulated autopolyploid dominant markers from 200 hexaploid individuals
runSegratioMM

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

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

Doses from Bayesian mixture model
setControl

Set up controls for a JAGS segregation ratio model run
runJags

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

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

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

Summary statistics for an segratioMCMC object
polySegratioMM-package

Bayesian Mixture Models for Marker Dosage in Autopolyploids
readJags

Read MCMC sample(s) from a JAGS run
writeControlFile

Write JAGS .cmd file for running JAGS
writeJagsFile

Writes BUGS file for processing by JAGS
hexmarkers.overdisp

Simulated overdispersed autopolyploid dominant markers from 200 hexaploid individuals
diagnosticsJagsMix

MCMC diagnostics for polyploid segregation ratio mixture models
plotFitted

Plot observed segregation ratios and fitted and theoretical models