BASiCS_diagPlot {BASiCS}R Documentation

Create diagnostic plots of MCMC parameters

Description

Plot parameter values and effective sample size. See effectiveSize for more details on this diagnostic measure.

Usage

BASiCS_diagPlot(object, Param = "mu", x = NULL, y = NULL,
  LogX = isTRUE(x %in% c("mu", "delta")), LogY = isTRUE(y %in%
  c("mu", "delta")), na.rm = TRUE)

Arguments

object

an object of class BASiCS_Summary

Param

Optional name of a chain parameter to restrict the histogram; if not supplied, all parameters will be assessed. Possible values: 'mu', 'delta', 'phi', 's', 'nu', 'theta', 'beta', 'sigma2' and 'epsilon'. Default Param = 'mu'

x, y

Optional MCMC parameter values to be plotted on the x or y axis, respectively. If neither is supplied, Param will be plotted on the x axis and coda::effectiveSize(Param) will be plotted on the y axis as a density plot.

LogX, LogY

A boolean value indicating whether to use a log10 transformation for the x or y axis, respectively.

na.rm

Logical value indicating whether NA values should be removed before calculating effective sample size.

Value

A ggplot object.

Author(s)

Alan O'Callaghan a.b.ocallaghan@sms.ed.ac.uk

See Also

BASiCS_Chain

Examples


# Built-in example chain
data(ChainSC)

# Point estimates versus effective sample size
BASiCS_diagPlot(ChainSC, Param = "mu")
# Effective sample size as colour, mu as x, delta as y.
BASiCS_diagPlot(ChainSC, x = "mu", y = "delta")


[Package BASiCS version 1.6.0 Index]