degradeTree: Randomly Collapse a Portion of Nodes on a Phylogeny

Description

degradeTree 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, nCollapse = NULL, node.depth = NA,
  leave.zlb = FALSE)

collapseNodes(tree, nodeID, collapseDir, leave.zlb = FALSE)

Arguments

tree

A phylogeny of class 'phylo'

prop_collapse

Proportion of nodes to collapse

nCollapse

Number of nodes to collapse, can be supplied as an alternative to prop_collapse

node.depth

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

leave.zlb

If FALSE, the default option, the original branch length distribution is destroyed and branches set to zero by this function will return polytomies. If TRUE, then the original edge lengths are kept for unmodified edges, and modified edges are changed t

nodeID

The node ID number(s) to be collapsed into a polytomy, as identified in the $edge matrix of the'phylo' object. Must be a vector of one or more ID numbers.

collapseDir

Whether to collapse the edge leading the listed node (if "forward"), or to collapse the child edges leading away from the node (if "backward"). Collapsing a node into a polytomy conceptually could be either and users should heed this option carefully.

Value

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

Details

The related function collapseNodes given a tree and a vector of nodes to collapse, removes those nodes from a tree, creating a polytomy. In the function degradeTree, the nodes are removed at random using the basic R 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. By default, branch lengths are removed from the input tree prior to degradation and entirely absent from the output tree. This is changed if argument leave.zlb is TRUE.

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)

#now with collapseNodes
tree <- rtree(10)
#collapse nodes backwards
   #let's collapse lucky node number 13!
tree1 <- collapseNodes(nodeID=13,tree=tree,collapseDir="backward")
#collapse nodes forwards
tree2 <- collapseNodes(nodeID=13,tree=tree,collapseDir="forward")

#let's compare
layout(1:3)
plot(tree,use.edge.length=FALSE,main="original")
plot(tree1,use.edge.length=FALSE,main="backward collapse")
plot(tree2,use.edge.length=FALSE,main="forward collapse")

layout(1)