collapseTips: Remove all tips smaller than min.length

In DomBennett/MoreTreeTools: Tools for manipulating phylogenetic trees

Description

Return a phylo object with tip edges less than min.length removed.

Usage

collapseTips(tree, min.length, iterative = TRUE)

Arguments

tree	phylogenetic tree (ape class)
min.length	smallest length for a tip edge
iterative	run until no tip edges less than min.length, default TRUE

Details

Tips are removed, but the tree age is preserved. Returned trees are therefore not the same phylogenetic tree as that given. The purpose of the function is to generate representations of trees with fewer tips for plotting purposes.

Set iterative as TRUE to keep removing all tip edges less than min.length.

References

No references yet! https://github.com/DomBennett/MoreTreeTools.

Examples

tree <- rtree (100)
par (mfrow = c (1,2))
plot (tree, show.tip.label=FALSE, main='Full tree')
tree.age <- getSize (tree, 'rtt')
ctree <- collapseTips (tree, min.length=tree.age*0.1)
plot (ctree, show.tip.label=FALSE, main='Collapsed tree')

DomBennett/MoreTreeTools documentation built on May 6, 2019, 2:51 p.m.