RearrangeEdges: Rearrange edges of a phylogenetic tree

In ms609/TreeSearch: Phylogenetic Analysis with Discrete Character Data

Rearrange edges of a phylogenetic tree

Description

RearrangeEdges() performs the specified edge rearrangement on a matrix that corresponds to the edges of a phylogenetic tree, returning the score of the new tree. Will generally be called from within a tree search function.

Usage

RearrangeEdges(
  parent,
  child,
  dataset,
  TreeScorer = MorphyLength,
  EdgeSwapper,
  scoreToBeat = TreeScorer(parent, child, dataset, ...),
  iter = "?",
  hits = 0L,
  verbosity = 0L,
  ...
)

Arguments

parent	Integer vector corresponding to the first column of the edge matrix of a tree of class phylo, i.e. tree$edge[, 1].
child	Integer vector corresponding to the second column of the edge matrix of a tree of class phylo, i.e. tree$edge[, 2].
dataset	Third argument to pass to TreeScorer.
TreeScorer	function to score a given tree. The function will be passed three parameters, corresponding to the parent and child entries of a tree's edge list, and a dataset.
EdgeSwapper	a function that rearranges a parent and child vector, and returns a list with modified vectors; for example SPRSwap().
scoreToBeat	Double giving score of input tree.
iter	iteration number of calling function, for reporting to user only.
hits	Integer giving number of times the input tree has already been hit.
verbosity	Numeric specifying level of detail to display in console: larger numbers provide more verbose feedback to the user.
...	further arguments to pass to TreeScorer(), e.g. ⁠dataset = ⁠.

Details

RearrangeTree() performs one tree rearrangement of a specified type, and returns the score of the tree (with the given dataset). It also reports the number of times that this score was hit in the current function call.

Value

This function returns a list with two to four elements, corresponding to a binary tree: - 1. Integer vector listing the parent node of each edge; - 2. Integer vector listing the child node of each edge; - 3. Score of the tree; - 4. Number of times that score has been hit.

Author(s)

Martin R. Smith

Examples

data("Lobo", package="TreeTools")
tree <- TreeTools::NJTree(Lobo.phy)
edge <- tree$edge
parent <- edge[, 1]
child <- edge[, 2]
dataset <- PhyDat2Morphy(Lobo.phy)
RearrangeEdges(parent, child, dataset, EdgeSwapper = RootedNNISwap)
# Remember to free memory:
dataset <- UnloadMorphy(dataset)

ms609/TreeSearch documentation built on April 7, 2024, 7:06 p.m.