TreeTools: SplitFrequency – R documentation

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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. May be used to calculate edge ("node") support for majority consensus or bootstrap trees.

Usage

SplitFrequency(reference, forest)

SplitNumber(tips, tree, tipIndex, powersOf2)

ForestSplits(forest, powersOf2)

TreeSplits(tree)

Arguments

`reference`	A tree of class `phylo`, a `Splits` object.
`forest`	a list of trees of class `phylo`, or a `multiPhylo` object; or a `Splits` object. See vignette for possible methods of loading trees into R.
`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.

Details

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

Value

SplitFrequency() returns the 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 as.Splits instead.

Author(s)

Martin R. Smith (martin.smith@durham.ac.uk)

Examples

# An example forest of 100 trees, some identical
forest <- as.phylo(c(1, rep(10, 79), rep(100, 15), rep(1000, 5)), nTip = 9)

# Generate an 80% consensus tree
cons <- ape::consensus(forest, p = 0.8)
plot(cons)

splitFreqs <- SplitFrequency(cons, forest)
LabelSplits(cons, splitFreqs, unit = '%',
            col = SupportColor(splitFreqs / 100),
            frame = 'none', pos = 3L)

TreeTools

Create, Modify and Analyse Phylogenetic Trees

v1.4.4

GPL (>= 3)

Authors

Martin R. Smith [aut, cre, cph] (<https://orcid.org/0000-0001-5660-1727>), Emmanuel Paradis [cph] (<https://orcid.org/0000-0003-3092-2199>)

Initial release