Ratchet bootstrapper
MorphyBootstrap(edgeList, morphyObj, EdgeSwapper = NNISwap, maxIter, maxHits,
verbosity = 1L, ...)ProfileBootstrap(edgeList, dataset, EdgeSwapper = NNISwap, maxIter, maxHits,
verbosity = 1L, ...)
IWBootstrap(edgeList, dataset, concavity = 4L, EdgeSwapper = NNISwap,
maxIter, maxHits, verbosity = 1L, ...)
a list containing the following: - vector of integers corresponding to the parent of each edge in turn - vector of integers corresponding to the child of each edge in turn - (optionally) score of the tree - (optionally, if score provided) number of times this score has been hit
A morphy object, perhaps created with PhyDat2Morphy.
a function that rearranges a parent and child vector,
and returns a list with modified vectors; for example
SPRSwap.
maximum number of iterations to perform in tree search
maximum number of hits to accomplish in tree search
Level of detail to display in console: larger numbers provide more verbose feedback to the user.
further parameters to send to TreeScorer
A phylogenetic data matrix of class phyDat, whose names
correspond to the labels of any accompanying tree.
A numeric value to use as the concavity constant (`k`) in implied weighting.
A tree that is optimal under a random sampling of the original characters
ProfileBootstrap: Bootstrapper for Profile Parsimony
IWBootstrap: Bootstrapper for Implied weighting