treeAnalysis: Tree Analysis Functions

Description

A collection of functions to provide summary characteristics of phylogenetic trees. There are other functions which do this included in other documentation files (links below).

Usage

splitTop(tree,dist)
sackin(tree)
widths(tree)
avgLadder(tree)
nLadders(tree)
colless(tree,normalize=TRUE)
nodeFrac(tree,func,threshold)
topSumm(tree,topList)
cherries(tree)
pitchforks(tree)
maxheight(tree)
stairs(tree)
ILnumber(tree)

Arguments

tree

An object of class phylo4

dist

An integer specifying the distance at which to do the splitting

normalize

A boolean specifying whether to normalize the Colless Imbalance

func

A function with input being a phylogenetic tree and output being a number.

threshold

A number.

topList

This is a list of functions. Each function in the list acts on an object of class phylo4 and returns a number - which is intended to be a topological property of the tree.

Value

splitTopAn integer vector of length equal to the number of nodes of the tree of the given distance - it is their number of tip children. Note that taking split topologies at every level is a very descriptive topological property and is useful for testing if trees with many nodes have the same topology.
sackinA numeric vector of length one giving the sum of the distance of each of the tips from the root.
widthsAn integer vector of length equal to the largest distance of a tip to the root.
avgLadderA number.
nLaddersA number.
collessA number.
nodeFracA number.
topSummA numeric vector of the same length as topList.
cherriesA number.
pitchforksA number.
maxheightA number.
stairsA vector whose first element is the average, over all internal nodes, of the absolute difference between the numbers of tips on the two edges descending from the node. The second element is the average of (number of tips in the smaller descending subtree)/(number of tips in the larger descending subtree).
ILnumberA number.

Details

splitTop gives the number of tip children of each of the nodes at the given distance from the node. Note that, in phylobase, Depth is how far the node is from the root taking edge length into account. I have stuck with this convention so Dist is the number of steps required to go to that node from the root. Returns an error if there are no nodes of the given distance. Note that it has been ordered to make it a topological porperty; if there is no order then trees with the same topology can give different results. sackin gives the sum of the distance of each of the tips from the root. This is a form of Sackin Imbalance. You may need to check that the definition you are using is the same as the one given here. widths gives the number of nodes at each distance from the root. Note that the elements of the returned vector give the lenths of the splitTop vectors for each distance. It uses dists. avgLadder gives the average length of all the ladders in the tree. Uses internal function laddItr. nLadders gives the number of distict ladders in the tree. Also uses laddItr. colless returns the normalised Colless Imblanace. That is the sum of all the node imbalances divided by 2/((n-1)(n-2)) where n is the number of tips. See nodeImb for the calculation of the imblalance for particular nodes. There is also an option to return the unnormalized Colless Imbalance. nodeFrac returns the fraction of nodes for which func(subtree)>=threshold where subtree is the subtree descending from that node. topSumm returns the result of each of the functions in topList on the specified tree. Similar functions (mostly applied to many trees or a model for generating trees) can be found in modelSummary.

cherries returns the number of cherries in the tree. A cherry is a node with two tip descendants.

pitchforks returns the number of pitchforks in the tree. A pitchfork is a node with one cherry descendant and one tip descendant.

maxheight returns the maximum height (discrete steps from the root, not taking branch length into account, or equivalently with branch lengths equal to 1) of any tip in the tree.

stairs returns a vector containing two measures of "staircase-ness" suggested by Norstrom et al (2012) in Evol. Bioinf. Online. See also the PhyloTempo package.

ILnumber returns the number of nodes with a single tip descendant in the tree.

Examples

Run this code

## Creates a random tree of class phylo4 and plots it with nodes labelled by ID
tree <- rtree4(50)
tree <- idNodeLabel(tree)
plot(tree,show.tip.label=FALSE,show.node.label=TRUE)
## Finds the split topology of the fourth level
splitTop(tree,4)

## Finds the Sackin Imbalance
sackin(tree)

## Finds the width topology of the tree
widths(tree)

## Finds the average ladder length
avgLadder(tree)

## Finds the number of distinct ladders in the tree
nLadders(tree)

## Finds the Colless Imbalance (normalized)
colless(tree)

## Finds the fraction of nodes for which colless(subtree of node) >= 0.25
nodeFrac(tree,colless,0.25)

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