notablyDistant: Find notably distant targets

Description

Notably distant targets are those with relatively large distances from the closest reference observation. A suitable threshold is used to detect large distances.

Usage

notablyDistant(object,kth=1,threshold=NULL,p=0.01)

Arguments

object

an object of class yai.

kth

the kth neighbor is used.

threshold

the thereshold distance that identifies notably large distances between observations.

the percentile point in the distribution of distances used to compute the threshold (only used when threshold is NULL).

Value

List of two data frames that contain 1) the references that are notably distant from other references, 2) the targets that are notably distant from the references, and 3) the threshold used.

Details

When threshold is NULL, the function computes one by assuming the distances follow the lognormal distribution, unless the method used to find neighbors is randomForest, in which case the distances are assumed to follow the beta distribution. A specified p value is used to compute the threshold.

Examples

Run this code

data(iris)

# form some test data
refs=sample(rownames(iris),50)
x <- iris[,1:3]      # Sepal.Length Sepal.Width Petal.Length
y <- iris[refs,4:5]  # Petal.Width Species

# build an msn run, first build dummy variables for species.

sp1 <- as.integer(iris$Species=="setosa")
sp2 <- as.integer(iris$Species=="versicolor")
y2 <- data.frame(cbind(iris[,4],sp1,sp2),row.names=rownames(iris))
y2 <- y2[refs,]

names(y2) <- c("Petal.Width","Sp1","Sp2")

msn <- yai(x=x,y=y2,method="msn")

notablyDistant(msn)