as.star.tree {phyclust}

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 [e-mail]

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)