add_events              Add events from sim_cophyBD to plot.cophy
add_scalebar            Add scale bar to cophylo plot
build_historical_association_matrix
                        Reconstruct historical association matrix
c.cophy                 Combine cophylogenetic sets into a multiCophy
                        object
calculate_expected_leaves_locustree
                        Calculate expected leaves of a locus tree
calculate_expected_leaves_sptree
                        Calculate expected leaves of a species tree
collapse_locus_subtree
                        Collapse a clade into a single tip
convert_assoc_table_to_matrix
                        Convert a table with host and symbiont
                        associations to a matrix
convert_to_cophy        Converts an object into an object of type cophy
cophy_summary_stat_by_indx
                        Calculates summary statistics for
                        cophylogenetic objects
count_cherries          Calculate cherry statistic for gene-trees
draw_cophy              Internal tree plot function
draw_curve              Curve draw function
drop_extinct            Drops extinct tips from tree
estimate_node_heights   Calculate expected time to branching point of a
                        species tree
event_history           Summarize a cophylogenetic set
genetree_summary_stat   Calculate summary statistics for gene trees
get_loci                Separate a locus tree into loci
get_tip_labels_tree_list
                        Get all the tip labels of a 'multiPhylo' object
host_tree               Print a cophylogenetic set
is.cophy                Test for the cophygenetic set object
is_extinct              Identify extinct tips from tree
make_textbox            Internal tree plot function
parafit_stat            Calculate the ParafitGlobal statistic on 2
                        trees and their association matrix
plot.cophy              Plot host and symbiont pair with current
                        associations
retrieve_parent_genetrees
                        Retrieve all gene trees of the parent tree from
                        a list generated from sim_mlc
sim_cophyBD             Simulates a host-symbiont system using a
                        cophylogenetic birth-death process
sim_cophyBD_ana         Simulates a host-symbiont system using a
                        cophylogenetic birth-death process
sim_ltBD                Simulates locus tree using constant rate
                        birth-death-transfer process
sim_msc                 Simulate multispecies coalescent on a species
                        tree
sim_multilocus_coal     Simulates multi-locus coalescent on a given
                        locus tree
sim_stBD                Simulates species trees using constant rate
                        birth-death process
sim_stBD_t              Simulates species tree using constant rate
                        birth-death process to a time
str.multiCophy          Retrieve the structure of a class multiCophy
treeducken-package      treeducken: simulates cophylogenetic systems &
                        nested phylogenies
