Bayesian Mixture Models for Marker Dosage in Autopolyploids

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Documentation for package ‘polySegratioMM’ version 0.6-4

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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