AdditionTree() returns a tree of class phylo, rooted on
sequence[1].
Arguments
dataset
A phylogenetic data matrix of phangorn class
phyDat, whose names correspond to the labels of any accompanying tree.
concavity
Numeric specifying concavity constant for implied step
weighting.
The most appropriate value will depend on the dataset, but values around
10--15 often perform well Goloboff2018,Smith2019TreeSearch.
The character string "profile" employs an approximation of profile parsimony
Faith2001TreeSearch.
Set as Inf for equal step weights, which underperforms step weighting
approaches
Goloboff2008,Goloboff2018,Goloboff2019,Smith2019TreeSearch.
constraint
Either an object of class phyDat, in which case
returned trees will be perfectly compatible with each character in
constraint; or a tree of class phylo, all of whose nodes will occur
in any output tree.
See ImposeConstraint() and
vignette
for further examples.
sequence
Character or numeric vector listing sequence in which to add
taxa. Randomized if not provided.