Split Frequencies and Conversion Among Split Classes

Description

bitsplits returns the bipartitions (aka splits) for a single tree or a list of trees.

countBipartitions returns the frequencies of the bipartitions from a reference tree (phy) observed in a list of trees (X).

as.bitsplits and as.prop.part are generic functions for converting between the "bitsplits" and "prop.part" classes.

Usage

bitsplits(x)
countBipartitions(phy, X)
as.bitsplits(x)
## S3 method for class 'prop.part'
as.bitsplits(x)
## S3 method for class 'bitsplits'
print(x, ...)
as.prop.part(x)
## S3 method for class 'bitsplits'
as.prop.part(x)

Arguments

Details

These functions count bipartitions as defined by internal branches, so they do not work with rooted trees (see examples). The structure of the class "bitsplits" is described in a separate document on ape's web site.

Value

bitsplits and as.bitsplits return an object of class "bitsplits".

countBipartitions returns a vector of integers.

as.prop.part returns an object of class "prop.part".

Author(s)

Emmanuel Paradis

See Also

prop.part

Examples

tr <- rtree(20)
pp <- prop.part(tr)
as.bitsplits(pp)
## doesn't work for rooted trees...:
countBipartitions(rtree(10), rmtree(100, 10))
## ... but OK with unrooted trees:
countBipartitions(rtree(10, rooted = FALSE), rmtree(100, 10, rooted = FALSE))