HPart: Hierarchical partition structure

In TreeDist: Calculate and Map Distances Between Phylogenetic Trees

Hierarchical partition structure

Description

A structure of class HPart comprises a pointer to a C++ representation of hierarchical partitions, with the attribute tip.label recording the character labels of its leaves. HPart objects with identical tip labels can be compared using HierarchicalMutualInfo().

Usage

as.HPart(tree, tipLabels)

## S3 method for class 'HPart'
as.HPart(tree, tipLabels = NULL)

## Default S3 method:
as.HPart(tree, tipLabels = NULL)

## S3 method for class 'list'
as.HPart(tree, tipLabels = NULL)

## S3 method for class 'phylo'
as.HPart(tree, tipLabels = TipLabels(tree))

is.HPart(x)

## S3 method for class 'HPart'
print(x, ...)

## S3 method for class 'HPart'
as.phylo(x, ...)

## S3 method for class 'HPart'
plot(x, ...)

Arguments

tree	An object to convert to an HPart structure, in a supported format (see details).
tipLabels	Character vector specifying sequence in which to order tip labels.
x	HPart object to plot.
...	Additional arguments to plot.phylo.

Details

An HPart object may be created from various representations of hierarchical structures:

• a tree (possibly phylogenetic) of class phylo

• A hierarchical list of lists, in which elements are represented by integers 1 to n

• A vector, which will be interpreted as a flat structure in which all elements bearing the same label are assigned to the same cluster

Value

HPart() returns a structure containing a pointer to a C++ representation of a hierarchical partition structure.

TreeDist documentation built on Nov. 5, 2025, 6:04 p.m.