paleotree (version 1.0)

degradeTree: Randomly collapse nodes on a phylogeny

Description

This function removes a proportion of the total nodes in a tree, chosen randomly, collapsing the nodes such that it causes the tree to be more unresolved.

Usage

degradeTree(tree, prop_collapse, node.depth = NA)

Arguments

tree

A tree of class phylo

prop_collapse

Proportion of nodes to collapse

node.depth

Conditions depth of nodes removed. Default is NA (no conditioning).

Value

• Returns the modified tree as an object of class phylo

Details

This function can be conditioned to remove nodes of a particular depth with greater probability by setting node.depth to some value between zero (deep nodes close to the root) or one (shallow nodes far from the root).

See Also

di2multi

Examples

set.seed(444)
tree<-rtree(100)
tree1<-degradeTree(tree,0.5)
layout(matrix(1:2,,2))
plot(tree,show.tip.label=FALSE,use.edge.length=FALSE)
plot(tree1,show.tip.label=FALSE,use.edge.length=FALSE)