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 |