R: Split Frequencies and Conversion Among Split Classes

as.bitsplits {ape} | R Documentation

## 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, ...)
    ## S3 method for class 'bitsplits'
    sort(x, decreasing = FALSE, ...)
    as.prop.part(x, ...)
    ## S3 method for class 'bitsplits'
    as.prop.part(x, include.trivial = FALSE, ...)

### Arguments

`x` | an object of the appropriate class.
`phy` | an object of class `"phylo"`.
`X` | an object of class `"multiPhylo"`.
`decreasing` | a logical value to sort the bipartitions in increasing (the default) or decreasing order of their frequency.
`include.trivial` | a logical value specifying whether to include the trivial split with all tips in the returned object.
`...` | further arguments passed to or from other methods.

### 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`, `as.bitsplits`, and `sort` 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`, `is.compatible`

### 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))

[Package ape version 5.4 Index]