polySegratioMM: Bayesian mixture models for marker dosage in autopolyploids

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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.

Author
Peter Baker
Date of publication
2014-03-06 22:09:58
Maintainer
Peter Baker <p.baker1@uq.edu.au>
License
GPL-3
Version
0.6-3

View on CRAN

Man pages

calculateDIC
Compute DIC for fitted mixture model
diagnosticsJagsMix
MCMC diagnostics for polyploid segregation ratio mixture...
DistributionPlotBinomial
Distribution Plot
dosagesJagsMix
Compute dosages under specified Bayesian mixture model
dumpData
Dumps segregation ratio data to file for subsequent JAGS run
hexmarkers
Simulated autopolyploid dominant markers from 200 hexaploid...
hexmarkers.overdisp
Simulated overdispersed autopolyploid dominant markers from...
mcmcHexRun
Results of MCMC estimation for simulated overdispersed...
plotFitted
Plot observed segregation ratios and fitted and theoretical...
plot.segratioMCMC
MCMC plots for segregation ratio mixture models
polySegratioMM-package
Marker dosage for autoployploids by Bayesian mixture models
print.dosagesMCMC
Doses from Bayesian mixture model
print.runJags
Running JAGS
readJags
Read MCMC sample(s) from a JAGS run
runJags
Run JAGS to create MCMC sample for segregation ratio mixture...
runSegratioMM
Run a Bayesian mixture model for marker dosage with minimal...
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...
summary.segratioMCMC
Summary statistics for an segratioMCMC object
writeControlFile
Write JAGS .cmd file for running JAGS
writeJagsFile
Writes BUGS file for processing by JAGS

Files in this package

polySegratioMM
polySegratioMM/TODO
polySegratioMM/inst
polySegratioMM/inst/CITATION
polySegratioMM/inst/doc
polySegratioMM/inst/doc/polySegratioMM-overview.pdf
polySegratioMM/inst/doc/polySegratioMM-overview.R
polySegratioMM/inst/doc/polySegratioMM-overview.Rnw
polySegratioMM/NAMESPACE
polySegratioMM/CHANGELOG
polySegratioMM/data
polySegratioMM/data/hexmarkers.overdisp.RData
polySegratioMM/data/mcmcHexRun.RData
polySegratioMM/data/hexmarkers.RData
polySegratioMM/R
polySegratioMM/R/DistributionPlotBinomial.R
polySegratioMM/R/DistributionPlotGamma.R
polySegratioMM/R/readJags.R
polySegratioMM/R/setControl.R
polySegratioMM/R/DistributionPlotNorm.R
polySegratioMM/R/runJags.R
polySegratioMM/R/print.dosagesMCMC.R
polySegratioMM/R/setPriors.R
polySegratioMM/R/writeJagsFile.R
polySegratioMM/R/writeControlFile.R
polySegratioMM/R/calculateDIC.R
polySegratioMM/R/diagnosticsJagsMix.R
polySegratioMM/R/print.runJagsWrapper.R
polySegratioMM/R/setModel.R
polySegratioMM/R/setInits.R
polySegratioMM/R/dumpData.R
polySegratioMM/R/runSegratioMM.R
polySegratioMM/R/summary.segratioMCMC.R
polySegratioMM/R/plot.segratioMCMC.R
polySegratioMM/R/dumpInits.R
polySegratioMM/R/dosagesJagsMix.R
polySegratioMM/R/plot.runJagsWrapper.R
polySegratioMM/R/print.segratioMCMC.R
polySegratioMM/R/plotTheoretical.R
polySegratioMM/R/plotFitted.R
polySegratioMM/R/print.runJags.R
polySegratioMM/vignettes
polySegratioMM/vignettes/polySegratioMM-overview.bib
polySegratioMM/vignettes/auto
polySegratioMM/vignettes/auto/_region_.el
polySegratioMM/vignettes/auto/polySegratioMM-overview.el
polySegratioMM/vignettes/tmp
polySegratioMM/vignettes/tmp/tmp-016.pdf
polySegratioMM/vignettes/tmp/tmp-006.eps
polySegratioMM/vignettes/tmp/tmp-017.eps
polySegratioMM/vignettes/tmp/tmp-016.eps
polySegratioMM/vignettes/tmp/tmp-006.pdf
polySegratioMM/vignettes/tmp/tmp-009.pdf
polySegratioMM/vignettes/tmp/tmp-009.eps
polySegratioMM/vignettes/tmp/tmp-017.pdf
polySegratioMM/vignettes/polySegratioMM-overview.Rnw
polySegratioMM/MD5
polySegratioMM/build
polySegratioMM/build/vignette.rds
polySegratioMM/DESCRIPTION
polySegratioMM/man
polySegratioMM/man/runSegratioMM.Rd
polySegratioMM/man/setPriors.Rd
polySegratioMM/man/polySegratioMM-package.Rd
polySegratioMM/man/setControl.Rd
polySegratioMM/man/hexmarkers.Rd
polySegratioMM/man/diagnosticsJagsMix.Rd
polySegratioMM/man/dumpData.Rd
polySegratioMM/man/hexmarkers.overdisp.Rd
polySegratioMM/man/print.runJags.Rd
polySegratioMM/man/setInits.Rd
polySegratioMM/man/setModel.Rd
polySegratioMM/man/readJags.Rd
polySegratioMM/man/writeJagsFile.Rd
polySegratioMM/man/writeControlFile.Rd
polySegratioMM/man/calculateDIC.Rd
polySegratioMM/man/dosagesJagsMix.Rd
polySegratioMM/man/DistributionPlotBinomial.Rd
polySegratioMM/man/summary.segratioMCMC.Rd
polySegratioMM/man/mcmcHexRun.Rd
polySegratioMM/man/plotFitted.Rd
polySegratioMM/man/plot.segratioMCMC.Rd
polySegratioMM/man/print.dosagesMCMC.Rd
polySegratioMM/man/runJags.Rd