tclust: Clustering by a threshold

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/tclust.R

Description

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

Usage

1
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 <[email protected]>

See Also

dist.dna, localMinima.

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
data(anoteropsis)
anoSpp <- sapply(strsplit(dimnames(anoteropsis)[[1]], split="_"), 
	function(x) paste(x[1], x[2], sep="_"))
anoDist <- dist.dna(anoteropsis)

tclust(anoDist)

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

spider documentation built on May 31, 2017, 2:59 a.m.