plotQuant: Plot MCMC Quantiles

In plotMCMC: MCMC Diagnostic Plots

Description

Plot quantiles of multiple Markov chain Monte Carlo chains, using bars, boxes, or lines.

Usage

plotQuant(mcmc, style="boxes", probs=c(0.025,0.975), axes=TRUE,
          names=NULL, ylim=NULL, yaxs="i", div=1, log=FALSE, base=10,
          main=NULL, xlab=NULL, ylab=NULL, cex.axis=0.8, las=1,
          tck=-0.015, tick.number=8, lty.median=1*(style!="bars"),
          lwd.median=1+1*(style!="boxes"), col.median="black",
          lty.outer=1+2*(style=="lines"), lwd.outer=1,
          col.outer="black", pch=16, cex=0.8, col="black",
          boxfill="darkgray", boxwex=0.5, staplewex=0.5, sfrac=0.005,
          mai=c(0.8,1,1,0.6),
          mgp=list(bottom=c(2,0.4,0),left=c(3,0.6,0),top=c(0,0.6,0),
          right=c(0,0.6,0)), ...)

Arguments

mcmc	MCMC chains as a data frame or mcmc object.
style	how quantiles should be drawn: "bars", "boxes", or "lines".
probs	vector of outer quantiles to draw, besides the median.
axes	numeric vector indicating which axis labels should be drawn: 1=bottom, 2=left, 3=top, 4=right, or TRUE to display all (default).
names	x-axis labels.
ylim	y-axis limits.
yaxs	y-axis style: "i" to truncate exactly at limits (default) or "r" to extend the axis slightly beyond the limits.
div	denominator to shorten values on the y axis.
log	whether values should be log-transformed.
base	logarithm base.
main	main title.
xlab	x-axis label.
ylab	y-axis label.
cex.axis	size of tick 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.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	size of points.
col	color of points.
boxfill	color of boxes.
boxwex	width of boxes.
staplewex	width of error bar staples when style="boxes", as a fraction of box width.
sfrac	width of error bar staples when style="bars", as a fraction of plot region.
mai	margins around plot as a vector of four numbers (bottom, left, top, right).
mgp	margins around axis titles, labels, and lines as a list of four vectors (bottom, left, top, right).
...	passed to plot, bxp, plotCI, lines, matplot, axis, and title.

Value

List containing:

x	midpoint coordinates on the x axis.
y	quantile coordinates on the y axis.

Note

With style="boxes", the quartiles are shown as boxes.

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

See Also

bxp, plotCI, and matplot are the underlying drawing functions.

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

plotDens and plotQuant are posterior plots.

plotMCMC-package gives an overview of the package.

Examples

plotQuant(xrec, names=substring(names(xrec),3), div=1000, xlab="Year",
          ylab="Recruitment (million one-year-olds)")
plotQuant(xbio, div=1000, xlab="Year", ylab="Biomass age 4+ (kt)")
plotQuant(xbio, style="bars", div=1000, sfrac=0, xlab="Year",
          ylab="Biomass age 4+ (kt)")
plotQuant(xbio, style="lines", div=1000, xlab="Year",
          ylab="Biomass age 4+ (kt)")
plotQuant(xpro, axes=1:2, div=1000, xlab="Year",
          ylab="Biomass age 4+ (kt)")

Example output

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