# Bayesian Mixture Models for Marker Dosage in Autopolyploids

## Documentation for package ‘polySegratioMM’ version 0.6-5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

polySegratioMM-package | Bayesian Mixture Models for Marker Dosage in Autopolyploids
calculateDIC | Compute DIC for fitted mixture model
diagnosticsJagsMix | MCMC diagnostics for polyploid segregation ratio mixture models
DistributionPlotBinomial | Distribution Plot
DistributionPlotGamma | Distribution Plot
DistributionPlotNorm | Distribution Plot
dosagesJagsMix | Compute dosages under specified Bayesian mixture model
dosagesMCMC | Compute dosages under specified Bayesian mixture model
dumpData | Dumps segregation ratio data to file for subsequent JAGS run
dumpInits | Set up and dump initial values given the model and prior
hexmarkers | Simulated autopolyploid dominant markers from 200 hexaploid individuals
hexmarkers.overdisp | Simulated overdispersed autopolyploid dominant markers from 200 hexaploid individuals
mcmcHexRun | Results of MCMC estimation for simulated overdispersed markers
modelSegratioMM | Set characteristics of the Bayesian mixture model for dosages
plot.runJagsWrapper | Plot observed segregation ratios and fitted and theoretical models
plot.segratioMCMC | MCMC plots for segregation ratio mixture models
plotFitted | Plot observed segregation ratios and fitted and theoretical models
plotTheoretical | Plot observed segregation ratios and fitted and theoretical models
polySegratioMM | Bayesian Mixture Models for Marker Dosage in Autopolyploids
print.dosagesMCMC | Doses from Bayesian mixture model
print.runJags | Running JAGS
print.runJagsWrapper | Running JAGS
print.segratioMCMC | Doses from Bayesian mixture model
readJags | Read MCMC sample(s) from a JAGS run
runJags | Run JAGS to create MCMC sample for segregation ratio mixture model
runJagsWrapper | Run a Bayesian mixture model for marker dosage with minimal effort
runSegratioMM | Run a Bayesian mixture model for marker dosage with minimal effort
segratioMCMC | Read MCMC sample(s) from a JAGS run
setControl | Set up controls for a JAGS segregation ratio model run
setInits | Set up and dump initial values given the model and prior
setModel | Set characteristics of the Bayesian mixture model for dosages
setPriors | Set prior distributions for parameters of Bayesian mixture model for dosages
summary.segratioMCMC | Summary statistics for an segratioMCMC object
summarySegratioMCMC | Summary statistics for an segratioMCMC object
writeControlFile | Write JAGS .cmd file for running JAGS
writeJagsFile | Writes BUGS file for processing by JAGS