addtree: Additive Tree Distances

Description

Objects representing additive tree distances.

Usage

as.cl_addtree(x)

Arguments

an R object representing additive tree distances.

Value

An object of class "cl_addtree" containing the additive tree distances.

Details

Additive tree distances are object dissimilarities $d$ satisfying the so-called additive tree conditions, also known as four-point conditions $d_{i j} + d_{k l} \leq max (d_{i k} + d_{j l}, d_{i l} + d_{j k})$ for all quadruples $i, j, k, l$ . Equivalently, for each such quadruple, the largest two values of the sums $d_{i j} + d_{k l}$ , $d_{i k} + d_{j l}$ , and $d_{i l} + d_{j k}$ must be equal. Centroid distances are additive tree distances where the inequalities in the four-point conditions are strengthened to equalities (such that all three sums are equal), and can be represented as $d_{i j} = g_{i} + g_{j}$ , i.e., as sums of distances from a “centroid”. See, e.g., Barth<U+00E9>l<U+00E9>my and Gu<U+00E9>noche (1991) for more details on additive tree distances.

as.cl_addtree is a generic function. Its default method can handle objects representing ultrametric distances and raw additive distance matrices. In addition, there is a method for coercing objects of class "phylo" from package ape.

Functions ls_fit_addtree and ls_fit_centroid can be used to find the additive tree distance or centroid distance minimizing least squares distance (Euclidean dissimilarity) to a given dissimilarity object.

There is a plot method for additive tree distances.

References