Bayesian Mixture Models for Marker Dosage in Autopolyploids
Compute DIC for fitted mixture model
MCMC diagnostics for polyploid segregation ratio mixture models
Distribution Plot
Compute dosages under specified Bayesian mixture model
Dumps segregation ratio data to file for subsequent JAGS run
MCMC plots for segregation ratio mixture models
Plot observed segregation ratios and fitted and theoretical models
Bayesian Mixture Models for Marker Dosage in Autopolyploids
Doses from Bayesian mixture model
Running JAGS
Read MCMC sample(s) from a JAGS run
Run JAGS to create MCMC sample for segregation ratio mixture model
Run a Bayesian mixture model for marker dosage with minimal effort
Set up controls for a JAGS segregation ratio model run
Set up and dump initial values given the model and prior
Set characteristics of the Bayesian mixture model for dosages
Set prior distributions for parameters of Bayesian mixture model for d...
Summary statistics for an segratioMCMC object
Write JAGS .cmd file for running JAGS
Writes BUGS file for processing by JAGS
Fits Bayesian mixture models to estimate marker dosage for dominant markers in autopolyploids using JAGS (1.0 or greater) as outlined in Baker et al "Bayesian estimation of marker dosage in sugarcane and other autopolyploids" (2010, <doi:10.1007/s00122-010-1283-z>). May be used in conjunction with polySegratio for simulation studies and comparison with standard methods.
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