polySegratioMM: Bayesian mixture models for marker dosage in autopolyploids

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.

AuthorPeter Baker
Date of publication2014-03-06 07:37:23
MaintainerPeter Baker <p.baker1@uq.edu.au>
LicenseGPL-3
Version0.6-3

View on R-Forge

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

calculateDIC Man page
diagnosticsJagsMix Man page
DistributionPlotBinomial Man page
DistributionPlotGamma Man page
DistributionPlotNorm 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
plotFitted Man page
plot.runJagsWrapper Man page
plot.segratioMCMC Man page
plotTheoretical Man page
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

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

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