TreeSearch (version 0.4.0)

SuccessiveApproximations: Tree Search using Successive Approximations

Description

Searches for a tree that is optimal under the Successive Approximations criterion.

Usage

SuccessiveApproximations(tree, dataset, outgroup = NULL, k = 3,
  maxSuccIter = 20, ratchetHits = 100, searchHits = 50,
  searchIter = 500, ratchetIter = 5000, verbosity = 0,
  suboptimal = 0.1)

Arguments

tree

A tree of class phylo.

dataset

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

outgroup

if not NULL, taxa on which the tree should be rooted

k

Constant for successive approximations, see Farris 1969 p. 379

maxSuccIter

maximum iterations of successive approximation

ratchetHits

maximum hits for parsimony ratchet

searchHits

maximum hits in tree search

searchIter

maximum iterations in tree search

ratchetIter

maximum iterations of parsimony ratchet

verbosity

integer (default 0) specifying how much detail to print to stdout

suboptimal

retain trees that are this proportion less optimal than the optimal tree

Value

SuccessiveApproximations() returns a list of class multiPhylo containing optimal (and slightly suboptimal, if suboptimal > 0) trees.