R: Clustering by a threshold

tclust

R Documentation

Clustering by a threshold

Description

Identifies clusters, excluding individuals greater than the threshold from any member.

Usage

tclust(distobj, threshold = 0.01)

Arguments

`distobj`	A distance object (usually from `dist.dna`).
`threshold`	Distance cutoff for clustering. Default of 0.01 (1%).

Details

If two individuals are more distant than threshold from each other, but both within threshold of a third, all three are contained in a single cluster.

Value

A list with each element giving the index of the individuals contained in each cluster.

Author(s)

Samuel Brown <s_d_j_brown@hotmail.com>

Examples



data(anoteropsis)
anoSpp <- sapply(strsplit(dimnames(anoteropsis)[[1]], split="_"), 
	function(x) paste(x[1], x[2], sep="_"))
anoDist <- ape::dist.dna(anoteropsis)

tclust(anoDist)

#Names of individuals
anoClust <- tclust(anoDist)
lapply(anoClust, function(x) anoSpp[x])