TreeSearch (version 1.6.1)

SuccessiveApproximations: Tree search using successive approximations

Description

Searches for a tree that is optimal under the Successive Approximations criterion Farris1969TreeSearch.

Usage

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

Value

SuccessiveApproximations() returns a list of class multiPhylo

containing optimal (and slightly suboptimal, if suboptimal > 0) trees.

SuccessiveWeights() returns the score of a tree, given the weighting instructions specified in the attributes of the dataset.

Arguments

tree

A tree of class phylo.

dataset

A phylogenetic data matrix of phangorn class phyDat, whose names correspond to the labels of any accompanying tree. Perhaps load into R using ReadAsPhyDat. Additive (ordered) characters can be handled using Decompose.

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 specifying level of messaging; higher values give more detailed commentary on search progress. Set to 0 to run silently.

suboptimal

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

References

See Also

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