contour: Contour functions

Description

Contour levels and sizes.

Usage

contourLevels(x, ...)
# S3 method for kde
contourLevels (x, prob, cont, approx=TRUE, ...)
# S3 method for kda
contourLevels (x, prob, cont, approx=TRUE, ...)
# S3 method for kdde
contourLevels(x, prob, cont, approx=TRUE, which.deriv.ind=1, ...) 
contourSizes(x, abs.cont, cont=c(25,50,75), approx=TRUE)
contourProbs(x, abs.cont, cont=c(25,50,75), approx=TRUE)
contourBreaks(x, n=3, cont=c(25,50,75), type="density")

Value

--For contourLevels/contourBreaks, for kde objects, returns a vector of heights. For kda objects, returns a list of vectors, one for each training group. For kdde objects, returns a matrix, one row for each partial derivative.

--For contourSizes, returns an approximation of the Lebesgue measure of the level set, i.e. length (d=1), area (d=2), volume (d=3), hyper-volume (d>4).

--For contourProbs, returns an approximation of the probability measure of the level set.

Arguments

x: object of class kde, kdde or kda
prob: vector of probabilities corresponding to highest density regions
cont: vector of percentages which correspond to the complement of prob
abs.cont: vector of absolute contour levels
approx: flag to compute approximate contour levels. Default is TRUE.
which.deriv.ind: partial derivative index. Default is 1.
...: other parameters
type: type of contour levels: one of "density", "length", "quantile", "natural". Default is "density".
n: number of contour levels for type="length", "natural". Default is 3.

Details

--For contourLevels, the most straightforward is to specify prob. The heights of the corresponding highest density region with probability prob are computed. The cont parameter here is consistent with cont parameter from plot.kde, plot.kdde, and plot.kda i.e. cont=(1-prob)*100%. If both prob and cont are missing then a pretty set of nlevels contours are computed. From ks \(\geq\) 1.15.0, nlevels=5 always.

--For contourSizes, the length, area, volume etc. and for contourProbs, the probability, are approximated by Riemann sums. These are rough approximations and depend highly on resolution of the estimation grid, and so should be interpreted carefully.

If approx=FALSE, then the exact KDE is computed. Otherwise it is interpolated from an existing KDE grid: this can dramatically reduce computation time for large data sets.

--For contourBreaks, different contour level selection methods are available, including equal length ("length"), quantile ("quantile") and natural breaks/Jenks ("natural") for density estimates only. The default contourBreaks(type="density") is equivalent to contourLevels.

Examples

Run this code

set.seed(8192)
x <- rmvnorm.mixt(n=1000, mus=c(0,0), Sigmas=diag(2), props=1)
fhat <- kde(x=x, binned=TRUE)
contourLevels(fhat, cont=c(25,50,75))
contourProbs(fhat, abs.cont=contourLevels(fhat, cont=50))
## compare approx prob with target prob=0.5
contourSizes(fhat, cont=25, approx=TRUE) 
## compare to approx circle of radius=0.75 with area=1.77
contourBreaks(fhat, n=3, type="natural")
## natural or Jenks contour levels