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 to produce a less-resolved tree.

Usage

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

Arguments

tree

A tree of class phylo

prop_collapse

Proportion of nodes to collapse

node.depth

A number between 0 to 1, which conditions the depth of nodes removed. If NA, no conditioning (this is the default).

Value

Returns the modified tree as an object of class phylo, with no edge lengths.

Details

The nodes are removed at random using the basic function sample. degradeTree can be conditioned to remove nodes of a particular depth with greater probability/frequency by setting node.depth to a value between zero (favoring the removal of deep nodes close to the root) or one (shallow nodes far from the root). Depth is evaluated based on the number of descendant tips. If node.depth is not NA, the relative proportion of descendants from each node is calculated, summed to 1 and the node.depth value subtracted from this proportion. These values are then squared, normalized again to equal to 1 and then used as the probabilities for sampling nodes for removal. Branch lengths are removed from the input tree prior to degradation and entirely absent from the output tree.

Examples

Run this code

set.seed(444)
tree <- rtree(100)
tree1 <- degradeTree(tree,0.5)

#let's compare the input and output
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)

layout(1)