Searches for a tree that is optimal under the Successive Approximations criterion
SuccessiveApproximations(tree, dataset, outgroup = NULL, k = 3,
maxSuccIter = 20, ratchetHits = 100, searchHits = 50,
searchIter = 500, ratchetIter = 5000, verbosity = 0,
suboptimal = 0.1)A tree of class phylo.
A phylogenetic data matrix of class phyDat, whose names
correspond to the labels of any accompanying tree.
if not NULL, taxa on which the tree should be rooted
Constant for successive approximations, see Farris 1969 p. 379
maximum iterations of successive approximation
maximum hits for parsimony ratchet
maximum hits in tree search
maximum iterations in tree search
maximum iterations of parsimony ratchet
integer (default 0) specifying how much detail to print to stdout
retain trees that are this proportion less optimal than the optimal tree
list of optimal (and slightly suboptimal, if suboptimal > 0) trees