R2BayesX (version 0.1-2)

plotblock: Factor Variable and Random Effects Plots

Description

Function to plot effects for model terms including factor, or group variables for random effects, typically used for objects created within bayesx or read.bayesx.output.

Usage

plotblock(x, residuals = FALSE, range = c(0.3, 0.3), 
  col.residuals = "black", col.lines = "black", c.select = NULL, 
  fill.select = NULL , col.polygons = NULL, data = NULL, ...)

Arguments

x

either a list of length of the unique factors, where each list element contains the estimated effects for one factor as a matrix, see fitted.bayesx, or one data mat

residuals

if set to TRUE, partial residuals will be plotted if available. Partial residuals may be set as an attribute of x named "partial.resids", where the partial r

range

numeric vector, specifying the left and right bound of the block.

col.residuals

the color of the partial residuals.

col.lines

vector of maximum length of columns of x minus 1, specifying the color of the lines.

c.select

integer vector of maximum length of columns of x, selects the columns of the resulting data matrix that should be used for plotting. E.g. if x has 5 columns, then c.select = c(1, 2, 5) will sel

fill.select

integer vector, select pairwise the columns of the resulting data matrix that should form one polygon with a certain background color specified in argument col. E.g. x has three columns, or is specified wit

col.polygons

specify the background color for the upper and lower confidence bands, e.g. col = c("green", "red").

data

if x is a formula, a data.frame or list. By default the variables are taken from environment(x): typically the environment from which plotblock is called.

...

graphical parameters, please see the details.

Details

Function plotblock draws for every factor or group the effect as a "block" in one graphic, i.e. similar to boxplots, estimated fitted effects, e.g. containing quantiles for MCMC estimated models, are drawn as one block, where the upper lines represent upper quantiles, the middle line the mean or median, and lower lines lower quantiles, also see the examples. The following graphical parameters may be supplied additionally:

• cex: specify the size of partial residuals,
• lty: the line type for each column that is plotted, e.g.lty = c(1, 2),
• lwd: the line width for each column that is plotted, e.g.lwd = c(1, 2),
• poly.lty: the line type to be used for the polygons,
• poly.lwd: the line width to be used for the polygons,
• densityangle,border: seepolygon,
• ...: other graphical parameters, see functionplot.

See Also

plot.bayesx, bayesx, read.bayesx.output, fitted.bayesx.

Examples

## generate some data
set.seed(111)
n <- 500

## regressors
dat <- data.frame(fac = factor(rep(1:10, n/10)))

## response
dat$y <- with(dat, 1.5 + c(2.67, 5, 6, 3, 4, 2, 6, 7, 9, 7.5)[fac] + 
  rnorm(n, sd = 0.6))

## estimate model
b <- bayesx(y ~ fac, data = dat)
summary(b)

## plot factor term effects
plot(b, term = "f(fac)")

## extract fitted effects
f <- fitted(b, term = "f(fac)")

## now use plotblock
plotblock(f)

## some variations
plotblock(f, col.poly = c(2, 3))
plotblock(f, col.poly = NA, lwd = c(2, 1, 1, 1, 1))
plotblock(f, col.poly = NA, lwd = 3, range = c(0.5,0.5))
plotblock(f, col.poly = NA, lwd = 3, col.lines = 1:5, lty = 1)
plotblock(f, col.poly = NA, lwd = 3, col.lines = 1:5, 
  lty = c(3, 1, 2, 2, 1))
plotblock(f, resid = TRUE)
plotblock(f, resid = TRUE, cex = 0.1)
plotblock(f, resid = TRUE, cex = 0.1, col.resid = 2)
plotblock(f, resid = TRUE, cex = 2, col.resid = 3, pch = 3)
plotblock(f, lty = 0, poly.lty = 1, density = c(5, 20))
plotblock(f, lty = 0, poly.lty = 1, density = c(5, 20), 
  poly.lwd = c(1, 2))
plotblock(f, lty = 0, poly.lty = c(1, 2), density = c(5, 20))
plotblock(f, lty = 0, poly.lty = c(1, 2), density = c(5, 20), 
  border = c("red", "green3"))
plotblock(f, lty = 0, poly.lty = c(1, 2), density = c(5, 20), 
  border = c("red", "green3"), col.poly = c("blue", "yellow"))
plotblock(f, lty = c(1,0,0,0,0), poly.lty = c(1, 2), 
  density = c(5, 20), border = c("red", "green3"), 
  col.poly = c("blue", "yellow"))
plotblock(f, lty = c(1,0,0,0,0), poly.lty = c(1, 2), 
  density = c(20, 20), border = c("red", "green3"), 
  col.poly = c("blue", "yellow"), angle = c(10, 75))

## another example
plotblock(y ~ fac, data = dat, range = c(0.45, 0.45))

dat <- data.frame(fac = factor(rep(1:10, n/10)))
dat$y <- with(dat, c(2.67, 5, 6, 3, 4, 2, 6, 7, 9, 7.5)[fac])
plotblock(y ~ fac, data = dat)
plotblock(cbind(y - 0.1, y + 0.1) ~ fac, data = dat)
plotblock(cbind(y - 0.1, y + 0.1) ~ fac, data = dat, 
  fill.select = c(0, 1, 1))
plotblock(cbind(y - 0.1, y + 0.1) ~ fac, data = dat, 
  fill.select = c(0, 1, 1), poly.lty = 2, lty = 1, 
  border = "grey5")