R: Coerce a Rooted Tree to a Star Tree in Class phylo

as.star.tree {phyclust} | R Documentation

## Coerce a Rooted Tree to a Star Tree in Class phylo

### Description

Coerce a rooted tree generating by `ms` to a star tree and maintain a bifurcation structure.

### Usage

    as.star.tree(rooted.tree, keep.bifurcation = TRUE)

### Arguments

`rooted.tree` | a rooted tree in `Class phylo`.
`keep.bifurcation` | keep a bifurcation structure.

### Details

A tree with a star shape means that all internal branches are 0 and all leaf branches are equal.

The `rooted.tree` should be in a `phylo` class of ape, and may be created by `ms`.

Basically, it is a list with an attribute that the class is phylo, and the other elements are:

- 'edge'edge ids.

- 'Nnode'number of internal nodes.

- 'tip.lab'number of tips (leaves).

- 'edge.length'length of edges.

If `keep.bifurcation` is TRUE, then internal branches are set to be 0 and leaves branches are set to the original tree height. Otherwise, the internal branches will be dropped from rooted.tree.

### Value

Return a rooted tree in `Class phylo` with a star shape.

### Author(s)

Wei-Chen Chen wccsnow@gmail.com

### References

Phylogenetic Clustering Website: https://snoweye.github.io/phyclust/

### See Also

`ms`, `read.tree`, `as.phylo`, `plot.phylo`.

### Examples

    ## Not run:
    library(phyclust, quiet = TRUE)

    set.seed(1234)
    ret.ms <- ms(5, 1, opts = paste("-T", sep = " "))
    tree.ms <- read.tree(text = ret.ms[3])
    str(tree.ms)
    (tree.star <- as.star.tree(tree.ms))

    # Plot results
    par(mfrow = c(1, 2))
    plot(tree.ms, type = "u", main = "original tree")
    plot(tree.star, type = "u", main = "as star tree")

    ## End(Not run)

[Package phyclust version 0.1-30 Index]