diagnosticsJagsMix: MCMC diagnostics for polyploid segregation ratio mixture...

In polySegratioMM: Bayesian mixture models for marker dosage in autopolyploids

Description

Produce and/or plot various diagnostic measures from coda package for Bayesian mixture models for assessing marker dosage in autopolyploids

Usage

diagnosticsJagsMix(mcmc.mixture, diagnostics = TRUE, plots = FALSE,
 index = -c( grep("T\\[",varnames(mcmc.mixture$mcmc.list)),
             grep("b\\[",varnames(mcmc.mixture$mcmc.list)) ),
 trace.plots = FALSE, auto.corrs = FALSE, density.plots = FALSE,
 xy.plots = FALSE, hpd.intervals = FALSE, hdp.prob = 0.95,
 return.results = FALSE)

Arguments

mcmc.mixture	Object of class segratioMCMC or runJagsWrapper after JAGS run produced by coda
diagnostics	if TRUE then print several coda dignostic tests
plots	if TRUE then produce several coda dignostic plots
index	index of parameters for disgnostic tests/plots (Default: mixture model (and random effects) parameters)
trace.plots	if TRUE plot mcmc traces (default: FALSE)
auto.corrs	if TRUE produce autocorrelations of mcmc's (default: FALSE)
density.plots	if TRUE plot parameter densities (default: FALSE)
xy.plots	if TRUE plot traces using 'lattice' (default: FALSE)
hpd.intervals	if TRUE print and return highest posterior density intervals for parameters specified by index
hdp.prob	probability for hpd.intervals
return.results	if TRUE return results as list

Value

If return.results is TRUE then a list is returned with components depending on various settings of arguments

Author(s)

Peter Baker [e-mail]

See Also

mcmc autocorr.diag raftery.diag geweke.diag gelman.diag trellisplots

Examples

## simulate small autooctaploid data set
a1 <- sim.autoMarkers(8,c(0.7,0.2,0.1),n.markers=100,n.individuals=50)
##print(a1)
sr <-  segregationRatios(a1$markers)
x <- setModel(3,8)

## Not run: 
## fit simple model in one hit

x.run <- runSegratioMM(sr, x, burn.in=200, sample=500)
print(x.run)
diagnosticsJagsMix(x.run)
diagnosticsJagsMix(x.run, plot=TRUE)

## End(Not run)

polySegratioMM documentation built on May 2, 2019, 4:41 p.m.