tcdist {treeClust}

Compute treeClust dissimilarities

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