SuccessiveApproximations {TreeSearch} | R Documentation |
Tree search using successive approximations
Description
Searches for a tree that is optimal under the Successive Approximations criterion (Farris 1969).
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 |
dataset |
A phylogenetic data matrix of phangorn class
|
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
Farris JS (1969). “A successive approximations approach to character weighting.” Systematic Biology, 18(4), 374–385. doi:10.2307/2412182.
See Also
Other custom search functions:
EdgeListSearch()
,
Jackknife()
,
MorphyBootstrap()