DoTreeSearch: DoTreeSearch

In ms609/inapplicable: Inapplicable data in parsimony analysis

Description

Performs a tree search

Usage

DoTreeSearch(tree, morphyObj, Rearrange, maxIter = 100, maxHits = 20,
  forestSize = 1, cluster = NULL, verbosity = 1, ...)

Arguments

tree	A tree of class phylo, with tip labels in the order generated by RenumberTips, i.e. corresponding to the sequence of taxa in the corresponding Morphy object.
morphyObj	A morphy object created with LoadMorphy.
Rearrange	Function to use to rearrange trees; example: TreeSearch::RootedTBR.
maxIter	maximum iterations to conduct.
maxHits	stop search after this many hits.
forestSize	how many trees to hold.
cluster	a cluster, prepared with codelinkPrepareCluster, to accelerate searches on multicore machines. #TODO not tested. #TODO restore code link
verbosity	Level of detail to display in console: larger numbers provides more verbose feedback to the user.
...	additional variables to pass to MorphyRearrangeTree.

Details

Does the hard work of searching for a most parsimonious tree. End-users are expected to access this function through its wrapper, TreeSearch It is also called directly by RatchetSearch and Sectorial functions

Author(s)

Martin R. Smith

ms609/inapplicable documentation built on May 23, 2019, 7:49 a.m.