check.MethComp {MethComp}R Documentation

Functions to graphically assess the convergence of the MCMC-simulation in a MethComp object

Description

These functions display traces, posterior densities and autocorrelation functions for the relevant subset of the parameters in a MethComp object.

Usage

trace.MethComp( obj, what = "sd",
                   scales = c("same", "free"),
                   layout = "col",
                   aspect = "fill", ...)
post.MethComp( obj, what ="sd",
                   check = TRUE,
                  scales = "same",
                  layout = "row",
                     lwd = 2,
                     col,
             plot.points = FALSE,
                  aspect = "fill", ... )
pairs.MethComp( obj,
             subset,
                col = NULL,
                pch = 16,
                cex = 0.2 )

Arguments

obj A MethComp object.
what Character indicating what parameters to plot. Possible values are "sd" or "var" which gives plots for the variance components (on the sd. scale), "beta" or "slope", which gives plots for slope parameters and "alpha" or "int", which gives plost for the intercept parameters.
scales Character vector of length two, indicating whether x- and y-axes of the plots should be constrained to be the same across panels.
layout Character. If "col" parameters are displayed columnwise by method, if "row" they are displayed row-wise.
aspect How should the panels be scaled. Default ("fill") is to make a panels take up as much place as possible.
lwd Width of the lines used for plotting of the posterior densities.
col Color of the lines used for plotting of the posterior densities.
plot.points Logical. Should a rug with actual data points be plotted beneath the density.
pch Plot symbol for the points.
... Further aruments passed on to the lattice function called: trace calls coda:::xyplot, post calls coda:::densityplot, pairs calls graphics:::pairs.

Details

A lattice plot is returned, which means that it must printed when these functions are called in a batch program or inside another function or for-loop.

trace plots traces of the sampled chains, post plots posterior densities of the parameters and pairs plots a scatter-plot matrix of bivariate marginal posterior distributions.

Value

A lattice plot.

Author(s)

Bendix Carstensen.

See Also

MethComp,plot.MethComp

Examples

library( MethComp )
# Load a provided MethComp object
data( ox.MC )
trace.MethComp( ox.MC )
trace.MethComp( ox.MC, "beta" )
post.MethComp( ox.MC )
post.MethComp( ox.MC, "beta" )
pairs.MethComp( ox.MC, "sd" )

[Package MethComp version 0.3.0 Index]