Objects representing additive tree distances.
as.cl_addtree(x)An object of class "cl_addtree" containing the additive
tree distances.
an R object representing additive tree distances.
Additive tree distances are object dissimilarities \(d\) satisfying the so-called additive tree conditions, also known as four-point conditions \(d_{ij} + d_{kl} \le \max(d_{ik} + d_{jl}, d_{il} + d_{jk})\) for all quadruples \(i, j, k, l\). Equivalently, for each such quadruple, the largest two values of the sums \(d_{ij} + d_{kl}\), \(d_{ik} + d_{jl}\), and \(d_{il} + d_{jk}\) 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 \(d_{ij} = g_i + g_j\), i.e., as sums of distances from a “centroid”. See, e.g., Barthélémy and Guénoche (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.
J.-P. Barthélémy and A. Guénoche (1991). Trees and proximity representations. Chichester: John Wiley & Sons. ISBN 0-471-92263-3.