SuccessiveApproximations: Tree search using successive approximations

In 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. 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

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()

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