plotDens: Plot MCMC Density

In plotMCMC: MCMC Diagnostic Plots

Description

Plot Markov chain Monte Carlo density. This is an approximation of the posterior probability density function.

Usage

plotDens(mcmc, probs=c(0.025,0.975), points=FALSE, axes=TRUE,
         same.limits=FALSE, between=list(x=axes,y=axes), div=1,
         log=FALSE, base=10, main=NULL, xlab=NULL, ylab=NULL,
         cex.main=1.2, cex.lab=1, cex.axis=0.8, cex.strip=0.8,
         col.strip="gray95", las=0, tck=0.5, tick.number=5,
         lty.density=1, lwd.density=3, col.density="black",
         lty.median=2, lwd.median=1, col.median="darkgray", lty.outer=3,
         lwd.outer=1, col.outer="darkgray", pch="|", cex.points=1,
         col.points="black", plot=TRUE, ...)

Arguments

mcmc	MCMC chain(s) as a vector, data frame or mcmc object.
probs	vector of outer quantiles to draw, besides the median.
points	whether individual points should be plotted along the x axis.
axes	whether axis values should be plotted.
same.limits	whether panels should have same x-axis limits.
between	list with x and y indicating panel spacing.
div	denominator to shorten values on the x axis.
log	whether values should be log-transformed.
base	logarithm base.
main	main title.
xlab	x-axis label.
ylab	y-axis label.
cex.main	size of main title.
cex.lab	size of axis labels.
cex.axis	size of tick labels.
cex.strip	size of strip labels.
col.strip	color of strip labels.
las	orientation of tick labels: 0=parallel, 1=horizontal, 2=perpendicular, 3=vertical.
tck	tick mark length.
tick.number	number of tick marks.
lty.density	line type of density curve.
lwd.density	line width of density curve.
col.density	color of density curve.
lty.median	line type of median.
lwd.median	line width of median.
col.median	color of median.
lty.outer	line type of outer quantiles.
lwd.outer	line width of outer quantiles.
col.outer	color of outer quantiles.
pch	symbol for points.
cex.points	size of points.
col.points	color of points.
plot	whether to draw plot.
...	passed to densityplot and panel.densityplot.

Value

When plot=TRUE, a trellis plot is drawn and a data frame is returned, containing the data used for plotting. When plot=FALSE, a trellis object is returned.

Note

The Args function from the gdata package is recommended for reviewing the arguments, instead of args.

See Also

xyplot and panel.densityplot are the underlying drawing functions, and link[coda]{densplot} is a similar non-trellis plot.

plotTrace, plotAuto, plotCumu, and plotSplom are diagnostic plots.

plotDens and plotQuant are posterior plots.

plotMCMC-package gives an overview of the package.

Examples

plotDens(xbio$"2004", points=TRUE, div=1000, main="2004\n",
         xlab="Biomass age 4+ (kt)", tick.number=6, strip=FALSE)
plotDens(xpar, xlab="Parameter value", ylab="Posterior density\n")

Example output

plotMCMC documentation built on Nov. 23, 2020, 5:08 p.m.