build.edgelist          For a sample, produce the transmission tree as
                        a 'igraph' object
draw.fully.sampled      For a sample with no unsampled hosts, draw the
                        annotated phylogeny using 'ggtree'
draw.incompletely.sampled
                        For a sample with or without unsampled hosts,
                        draw the annotated phylogeny using 'ggtree'
grouping.map            A vector assigning the tips of
                        'stratus.example.tree' to groups (in the order
                        they appear in
                        'stratus.example.tree$tip.label'), as an
                        example of multiple sampling.
sample.partial.tt       Resample the subtree rooted at any tree node,
                        keeping the annotations for the rest of the
                        tree fixed
sample.tt               Sample one or more transmission trees uniformly
stratus.example.tree    An unexceptional phylogeny generated with
                        'rtree' from 'ape'
tt.generator            Enumerate transmission trees for the given
                        pathogen phylogeny, and provide a uniform
                        sample generator
