plot.bim.mcmc {bim}R Documentation

Bayesian MCMC sequence plots for burnin and iterations.

Description

Plot MCMC burnin and iteration sequences for number of QTL, LOD score, environmental SD, and heritability.

Usage

plot.bim.mcmc(x, element = c("burnin","iter"),
  xlab = c("burnin sequence","mcmc sequence"),
  items = <<see below>>, ylabs = items,
  types = <<see below>>, ... )

Arguments

x object of class bim
element elements of x to plot
xlab x-axis labels for elements
items diagnostic item names to be plotted as time series (default is all names in x$iter
ylabs labels for items
types line types (default is both for first item–usually number of QTL–and lines for the rest)
... graphical parameters can be given as arguments to plot

Details

Plots show grey line for saved sequences, usually nearly vertical due to mixing, plus a smoothed curve (blue). Burnin plots should show initial jump in number of QTL during pre-burnin sequence, ideally settling into a well-behaved Markov chain by the end of the burn-in. That is, look for visual evidence of stationarity as flat blue line and even spread of grey. Trend or cyclic pattern indicates Markov chain is not mixing well and needs to be run much longer. No formal assessment is provided.

Author(s)

Brian S. Yandell, yandell@stat.wisc.edu

References

http://www.stat.wisc.edu/~yandell/qtl/software/Bmapqtl

See Also

run.bmapqtl

Examples

data( verngeo.bim )

plot.bim.mcmc( verngeo.bim )

[Package bim version 1.01-1 Index]