a phylogenetic tree of class 'phylo' ('multiPhylo' in phylo.clades)
taxonomy
a linkage table (of class matrix) between tips of the phylogeny and clades represented in the tree; rownames of 'taxonomy' should be tips found in the phylogeny
clades
a named list of clade definitions (i.e., spanning taxa; see Examples); spanning taxa may invoke other definitions found within the clades list
unplaced
whether to use 'unplaced' taxa if given as an element in clades
subtrees
a list of trees to be grafted into phy; each subtrees element must either be a 'phylo' or 'multiPhylo' object with branch lengths in the same units as phy (see Examples)
strict
whether to enforce strict labeling of nodes or allow
liberal estimates of the best location of a given nodelabel
ncores
the maximum number of cores to be used
Details
nodelabel.phylo provides a function (as part of the phylo object returned) to resolve the hash key and node identifier for a label found in taxonomy.
This function is the FUN element of the returned object. If the taxonomic label cannot be properly placed in the tree (i.e., no subtree is found that is absolutely
consistent with the supplied taxonomy, the nearest matching node(s) will be returned when invoking FUN).
phylo.lookup converts a taxonomy into a phylogenetic tree.
lookup.phylo converts a phylogenetic tree (phy) into a linkage table based on nodelabels associated with phy, which can be supplemented with a taxonomy and (or)
clades object.
phylo.clades returns a series of phylogenetic subtrees based on clade definitions found in the clades object. Definitions can be handles that are recursive (see Examples).