TreeSearch: Search for most parsimonious trees
In TreeSearch: Phylogenetic Analysis with Discrete Character Data

EdgeListSearch

R Documentation

Search for most parsimonious trees

Description

Run standard search algorithms (NNI, SPR or TBR) to search for a more parsimonious tree.

For detailed documentation of the "TreeSearch" package, including full instructions for loading phylogenetic data into R and initiating and configuring tree search, see the package documentation.

Usage

EdgeListSearch(
  edgeList,
  dataset,
  TreeScorer = MorphyLength,
  EdgeSwapper = RootedTBRSwap,
  maxIter = 100,
  maxHits = 20,
  bestScore = NULL,
  stopAtScore = NULL,
  stopAtPeak = FALSE,
  stopAtPlateau = 0L,
  verbosity = 1L,
  ...
)

TreeSearch(
  tree,
  dataset,
  InitializeData = PhyDat2Morphy,
  CleanUpData = UnloadMorphy,
  TreeScorer = MorphyLength,
  EdgeSwapper = RootedTBRSwap,
  maxIter = 100L,
  maxHits = 20L,
  stopAtPeak = FALSE,
  stopAtPlateau = 0L,
  verbosity = 1L,
  ...
)

IWTreeSearch(...)

EmptyPhyDat(tree)

DoNothing(...)

Arguments

`edgeList`	a list containing the following: vector of integers corresponding to the parent of each edge in turn vector of integers corresponding to the child of each edge in turn (optionally) score of the tree (optionally, if score provided) number of times this score has been hit
`dataset`	Data in format required by `InitializeData`.
`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()`.
`maxIter`	Numeric specifying maximum number of iterations to perform before abandoning the search.
`maxHits`	Numeric specifying maximum times to hit the best pscore before abandoning the search.
`stopAtPeak`	Logical specifying whether to terminate search once a subsequent iteration recovers a sub-optimal score. Will be overridden if a passed function has an attribute `stopAtPeak` set by `attr(FunctionName, "stopAtPeak") <- TRUE`.
`stopAtPlateau`	Integer. If > 0, tree search will terminate if the score has not improved after `stopAtPlateau` iterations. Will be overridden if a passed function has an attribute `stopAtPlateau` set by `attr(FunctionName, "stopAtPlateau") <- TRUE`.
`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 = ⁠`.
`tree`	A fully-resolved starting tree in `phylo` format, with the desired outgroup. Edge lengths are not supported and will be removed.
`InitializeData`	Function that sets up data object to prepare for tree search. The function will be passed the `dataset` parameter. Its return value will be passed to `TreeScorer()` and `CleanUpData()`.
`CleanUpData`	Function to destroy data object on function exit. The function will be passed the value returned by `InitializeData()`.

Value

TreeSearch() returns a tree, with an attribute pscore conveying its parsimony score. #" Note that the parsimony score will be inherited from the tree"s attributes, which is only valid if it was generated using the same data that is passed here.

EmptyPhyDat() returns a phyDat object comprising a single null character, coded with state zero for every leaf in tree.

Functions

EdgeListSearch(): Tree search from edge lists

Author(s)

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

Examples

data("Lobo", package="TreeTools")
njtree <- TreeTools::NJTree(Lobo.phy)

## Only run examples in interactive R sessions
if (interactive()) {
  TreeSearch(njtree, Lobo.phy, maxIter = 20, EdgeSwapper = NNISwap)
  TreeSearch(njtree, Lobo.phy, maxIter = 20, EdgeSwapper = RootedSPRSwap)
  TreeSearch(njtree, Lobo.phy, maxIter = 20, EdgeSwapper = TBRSwap)
}

TreeSearch documentation built on April 11, 2025, 5:49 p.m.