TreeSearch (version 1.0.1)

AdditionTree: Addition tree

Description

Generates a starting tree by adding each taxon in turn to the most parsimonious location.

Usage

AdditionTree(dataset, concavity = Inf, constraint, sequence)

Arguments

dataset

A phylogenetic data matrix of class phyDat, whose names correspond to the labels of any accompanying tree.

concavity

Numeric specifying concavity constant for implied step weighting; set as Inf for equal step weights (which is a bad idea; see Smith2019;textualTreeSearch).

constraint

An object of class phyDat; returned trees will be perfectly compatible with each character in constraint. See ImposeConstraint() and vignette for further examples.

sequence

Character or numeric vector listing sequence in which to add taxa. Randomized if not provided.

Value

AdditionTree() returns a tree of class phylo, rooted on sequence[1].

See Also

Other tree generation functions: RandomMorphyTree()

Examples

# NOT RUN {
data('Lobo', package = 'TreeTools')
AdditionTree(Lobo.phy, concavity = 10)
# }