Skip to contents

Hierarchical partition structure

Source: R/HPart.R
HPart.Rd

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.

Value

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

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