TreeSearch (version 0.3.2)

SplitFrequency: Frequency of splits

Description

SplitFrequency provides a simple way to count the number of times that bipartition splits, as defined by a reference tree, occur in a forest of trees.

Usage

SplitFrequency(reference, forest)
SplitNumber(tips, tree, tipIndex, powersOf2)
ForestSplits(forest, powersOf2)
TreeSplits(tree)

Arguments

reference

A tree of class phylo, or a character vector specifying its splits (as obtained through Tree2Splits)

forest

a list of trees of class phylo, or a multiPhylo object; or a list of their constituent splits (as obtained through Tree2Splits)

tips

Integer vector specifying the tips of the tree within the chosen split

tree

A tree of class phylo.

tipIndex

Character vector of tip names, in a fixed order

powersOf2

Integer vector of same length as tipIndex, specifying a power of 2 to be associated with each tip in turn

Value

Number of trees in forest that contain each split in reference. if reference is a tree of class phylo, then the sequence will correspond to the order of nodes (use `ape::nodelabels to view). Note that the three nodes at the root of the tree correspond to a single split; see the example for how these might be plotted on a tree.

Functions

• SplitNumber: Assign a unique integer to each split

• ForestSplits: Frequency of splits in a given forest of trees

• TreeSplits: Deprecated. Listed the splits in a given tree. Use Quartet::Tree2Splits instead.

Details

If multiple calculations are required, some time can be saved by using the constituent functions (see examples)

Examples

# NOT RUN {
{
  library(ape) # for functions rtree & nodelabels
  set.seed(0) # Set seed so random trees are reproducable
  tree1 <- rtree(7)
  tree2 <- rtree(7)
  tree3 <- rtree(7)
  forest <- list(tree1, tree2, tree2, tree3, rtree(7))
  
  # Simple, but means counting each split in the forest twice:
  tree1Freqs <- SplitFrequency(tree1, forest)
  SplitFrequency(tree2, forest)
  
  plot(tree1)
  nodelabels(tree1Freqs, node=as.integer(names(tree1Freqs)))
}

# }