SuccessiveApproximations: Tree search using successive approximations

In ms609/TreeSearch: Phylogenetic Analysis with Discrete Character Data

Tree search using successive approximations

Description

Searches for a tree that is optimal under the Successive Approximations criterion \insertCiteFarris1969TreeSearch.

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)

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.
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	Numeric specifying level of detail to display in console: larger numbers provide more verbose feedback to the user.
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.

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

References

\insertAllCited

See Also

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

ms609/TreeSearch documentation built on Sept. 8, 2024, 3:26 a.m.