This function makes a “clade tree”, where tips
represent clades. It is designed to make working with unresolved
clade information in make.bisse more straightforward.
clade.tree objects have their own plotting methods.
make.clade.tree(tree, clades)
clades.from.polytomies(tree)
clades.from.classification(tree, class, check=TRUE)
An ultrametric phylogenetic tree, in ape
“phylo” format.
A list, where the name of each element represents a tip
in tree and each element is a character vector containing the
names of species contained within that clade.
A vector along tree$tip.label, indicating the
class to which each tip belongs.
Logical, indicating whether a (potentially slow) check will be done to ensure that all resulting clades are reciprocally monophyletic within the tree.
Richard G. FitzJohn
The idea here is that make.bisse takes a tree and a named
character state vector. If the phylogenetic tree contains information
about the membership of clades, then the unresolved clade information
can be constructed automatically. The names chosen should therefore
reflect the names used in the state information.