Searches for a tree that is optimal under the Successive Approximations criterion Farris1969TreeSearch.
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)
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.
A tree of class phylo
.
A phylogenetic data matrix of phangorn 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
Numeric specifying level of detail to display in console: larger numbers provide more verbose feedback to the user.
retain trees that are this proportion less optimal than the optimal tree
Other custom search functions:
EdgeListSearch()
,
Jackknife()
,
MorphyBootstrap()