polySegratioMM: Bayesian mixture models for marker dosage in autopolyploids
Version 0.6-3

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.

Browse man pages Browse package API and functions Browse package files

AuthorPeter Baker
Date of publication2014-03-06 22:09:58
MaintainerPeter Baker <p.baker1@uq.edu.au>
LicenseGPL-3
Version0.6-3
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("polySegratioMM")

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

Functions

DistributionPlotBinomial Man page
DistributionPlotGamma Man page
DistributionPlotNorm Man page
calculateDIC Man page
diagnosticsJagsMix Man page
dosagesJagsMix Man page
dosagesMCMC Man page
dumpData Man page
dumpInits Man page
hexmarkers Man page
hexmarkers.overdisp Man page
mcmcHexRun Man page
modelSegratioMM Man page
plot.runJagsWrapper Man page
plot.segratioMCMC Man page
plotFitted Man page Source code
plotTheoretical Man page Source code
polySegratioMM Man page
polySegratioMM-package Man page
print.dosagesMCMC Man page
print.runJags Man page
print.runJagsWrapper Man page
print.segratioMCMC Man page
readJags Man page
runJags Man page
runJagsWrapper Man page
runSegratioMM Man page
segratioMCMC Man page
setControl Man page
setInits Man page
setModel Man page
setPriors Man page
summary.segratioMCMC Man page
summarySegratioMCMC Man page
writeControlFile Man page
writeJagsFile Man page

Files

TODO
inst
inst/CITATION
inst/doc
inst/doc/polySegratioMM-overview.pdf
inst/doc/polySegratioMM-overview.R
inst/doc/polySegratioMM-overview.Rnw
NAMESPACE
CHANGELOG
data
data/hexmarkers.overdisp.RData
data/mcmcHexRun.RData
data/hexmarkers.RData
R
R/DistributionPlotBinomial.R
R/DistributionPlotGamma.R
R/readJags.R
R/setControl.R
R/DistributionPlotNorm.R
R/runJags.R
R/print.dosagesMCMC.R
R/setPriors.R
R/writeJagsFile.R
R/writeControlFile.R
R/calculateDIC.R
R/diagnosticsJagsMix.R
R/print.runJagsWrapper.R
R/setModel.R
R/setInits.R
R/dumpData.R
R/runSegratioMM.R
R/summary.segratioMCMC.R
R/plot.segratioMCMC.R
R/dumpInits.R
R/dosagesJagsMix.R
R/plot.runJagsWrapper.R
R/print.segratioMCMC.R
R/plotTheoretical.R
R/plotFitted.R
R/print.runJags.R
vignettes
vignettes/polySegratioMM-overview.bib
vignettes/auto
vignettes/auto/_region_.el
vignettes/auto/polySegratioMM-overview.el
vignettes/tmp
vignettes/tmp/tmp-016.pdf
vignettes/tmp/tmp-006.eps
vignettes/tmp/tmp-017.eps
vignettes/tmp/tmp-016.eps
vignettes/tmp/tmp-006.pdf
vignettes/tmp/tmp-009.pdf
vignettes/tmp/tmp-009.eps
vignettes/tmp/tmp-017.pdf
vignettes/polySegratioMM-overview.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/runSegratioMM.Rd
man/setPriors.Rd
man/polySegratioMM-package.Rd
man/setControl.Rd
man/hexmarkers.Rd
man/diagnosticsJagsMix.Rd
man/dumpData.Rd
man/hexmarkers.overdisp.Rd
man/print.runJags.Rd
man/setInits.Rd
man/setModel.Rd
man/readJags.Rd
man/writeJagsFile.Rd
man/writeControlFile.Rd
man/calculateDIC.Rd
man/dosagesJagsMix.Rd
man/DistributionPlotBinomial.Rd
man/summary.segratioMCMC.Rd
man/mcmcHexRun.Rd
man/plotFitted.Rd
man/plot.segratioMCMC.Rd
man/print.dosagesMCMC.Rd
man/runJags.Rd
polySegratioMM documentation built on May 19, 2017, 7:40 a.m.