Ellipses: Groups' confidence ellipses

Description

Groups' confidence ellipses

Usage

Ellipses(pts, groups, match.color=TRUE, usecolors=NULL, centers=FALSE, c.pch=0, c.cex=3,
 level=0.95, coords=NULL, plot=TRUE, ...)

Arguments

pts

Data points to plot

groups

Grouping variable

level

Confidence level

match.color

Match colors

usecolors

Use colors (palette)

centers

Show centers?

c.pch

Color of center points

c.cex

Scale of center points

coords

List of coordinates: two-column matrices named as groups, does not need by default

plot

Plot?

...

Arguments to 'Confelli()' and finally to 'lines()'

Value

Invisibly returns the list in form similar to Hulls(), to use as 'coords' or with Overlap()

Details

Uses internal 'Confelli()' function which plots an ellipse with covariance matrix C, center b, and P-content level according to the F(2, df) distribution.

Examples

Run this code

# NOT RUN {
iris.p <- prcomp(iris[, 1:4], scale=TRUE)$x[, 1:2]
plot(iris.p, type="n", xlab="PC1", ylab="PC2")
text(iris.p, labels=abbreviate(iris[, 5], 1, method="both.sides"))
Ellipses(iris.p[, 1:2], iris[, 5], centers=TRUE)

library(MASS)
ch.lda <- lda(Species ~ ., data=chaetocnema[, -2])
ch.lda.pred <- predict(ch.lda, chaetocnema[, -(1:2)])
## ellipses here are by default bigger then plot so use workaround:
ee <- Ellipses(ch.lda.pred$x, chaetocnema$Species, plot=FALSE)
xx <- range(c(do.call(rbind, ee)[, 1], ch.lda.pred$x[, 1]))
yy <- range(c(do.call(rbind, ee)[, 2], ch.lda.pred$x[, 2]))
plot(ch.lda.pred$x, col=chaetocnema$Species, xlim=xx, ylim=yy)
Ellipses(ch.lda.pred$x, chaetocnema$Species, coords=ee)

## search for the maximal level which gives zero overlap
plot(x5 ~ x17, data=haltica, pch=as.numeric(haltica$Species))
for (i in (99:59)/100) {
cat(i, "\n")
ee <- Ellipses(haltica[, c("x17", "x5")], haltica$Species, level=i, plot=FALSE)
print(mean(Overlap(ee), na.rm=TRUE))
cat("\n")
}
Ellipses(haltica[, c("x17", "x5")], haltica$Species, level=.62)
# }