tcdist: Compute treeClust dissimilarities

In treeClust: Cluster Distances Through Trees

Description

Given a treeClust object, or the necessary components, compute all pairwise dissimilarities for input to a clustering algorithm

Usage

tcdist(obj, d.num = 1, tbl, mat, trees, verbose=0)

Arguments

obj	Object of class treeClust
d.num	Method of dissimilarities computation. See "Details".
tbl	Two-column of information about trees. Always included in a treeClust object, but may be supplied separately. Required if d.num = 2 or 4.
mat	Matrix of leaf-membership factors, if not supplied in "obj".
trees	List of trees, if not supplied in obj.
verbose	If > 0, print some information useful for debugging.

Details

There are four ways to compute inter-point dissimilarities from a treeClust object. If d.num = 1, two points differ by the number of trees in which they land in different leaves. "Mat" is required. If d.num = 2, the computation for d.num = 1 is used, but each tree gets a different weight. "Mat" and "tbl" are required.tbl" are required.

The computation for d.num = 3 requires that the set of trees be supplied. With this approach two observations differ, on a particular tree, according to how far apart they are on that tree. For d.num = 4, both tree and "tbl" are required; this is a weighted version of the d.num = 3 dissimilarity.

Value

Object of class "dist" giving pairwise distances for the original data used to build the treeClust object.

Author(s)

Sam Buttrey

See Also

treeClust

treeClust documentation built on May 1, 2019, 7:59 p.m.