Search for most parsimonious trees

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

A phylogenetic data matrix of phangorn class phyDat, whose names correspond to the labels of any accompanying tree.

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

See also

• Fitch, calculates parsimony score;

• RootedNNI, conducts tree rearrangements;

• Ratchet, alternative heuristic, useful to escape local optima.

Other custom search functions: Jackknife(), MorphyBootstrap(), SuccessiveApproximations()

Author

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)
}