R: Collapse and Resolve Multichotomies

multi2di {ape} | R Documentation

## Collapse and Resolve Multichotomies

### Description

These two functions collapse or resolve multichotomies in phylogenetic trees.

### Usage

    multi2di(phy, ...)
    ## S3 method for class 'phylo'
    multi2di(phy, random = TRUE, ...)
    ## S3 method for class 'multiPhylo'
    multi2di(phy, random = TRUE, ...)
    di2multi(phy, ...)
    ## S3 method for class 'phylo'
    di2multi(phy, tol = 1e-08, ...)
    ## S3 method for class 'multiPhylo'
    di2multi(phy, tol = 1e-08, ...)

### Arguments

`phy` | an object of class `"phylo"` or `"multiPhylo"`.
`random` | a logical value specifying whether to resolve the multichotomies randomly (the default) or in the order they appear in the tree (if `random = FALSE`).
`tol` | a numeric value giving the tolerance to consider a branch length significantly greater than zero.
`...` | arguments passed among methods.

### Details

`multi2di` transforms all multichotomies into a series of dichotomies with one (or several) branch(es) of length zero.

`di2multi` deletes all branches smaller than `tol` and collapses the corresponding dichotomies into a multichotomy.

### Value

an object of the same class than the input.

### Author(s)

Emmanuel Paradis

### See Also

`is.binary`

### Examples

    data(bird.families)
    is.binary(bird.families)
    is.binary(multi2di(bird.families))
    all.equal(di2multi(multi2di(bird.families)), bird.families)
    ### To see the results of randomly resolving a trichotomy:
    tr <- read.tree(text = "(a:1,b:1,c:1);")
    layout(matrix(1:4, 2, 2))
    for (i in 1:4)
      plot(multi2di(tr), use.edge.length = FALSE, cex = 1.5)
    layout(1)

[Package ape version 5.4 Index]