treeducken-package	treeducken-package
add_events	add_events
add_scalebar	add_scalebar
association_mat	print.cophy
association_mat.cophy	print.cophy
association_mat.multiCophy	print.cophy
ave_tips_lt	calculate_expected_leaves_locustree
ave_tips_st	calculate_expected_leaves_sptree
build_historical_association_matrix	build_historical_association_matrix
c.cophy	c.cophy
c.multiCophy	c.cophy
calculate_expected_leaves_locustree	calculate_expected_leaves_locustree
calculate_expected_leaves_sptree	calculate_expected_leaves_sptree
collapse_clade	collapse_locus_subtree
collapse_locus_subtree	collapse_locus_subtree
convert_assoc_table_to_matrix	convert_assoc_table_to_matrix
convert_to_cophy	convert_to_cophy
cophy_summary_stat	cophy_summary_stat
cophy_summary_stat_by_indx	cophy_summary_stat
count_cherries	count_cherries
draw_cophy	draw_cophy
draw_curve	draw_curve
drop_extinct	drop_extinct
estimate_node_heights	estimate_node_heights
event_history	summary.cophy
event_history.cophy	summary.cophy
event_history.multiCophy	print.cophy
genetree_summary_stat	genetree_summary_stat
get_ana_events	get_ana_events
get_assoc	build_historical_association_matrix
get_child_gts	retrieve_parent_genetrees
get_loci	get_loci
get_parent_gts	retrieve_parent_genetrees
get_tipnames	get_tip_labels_tree_list
get_tip_labels_tree_list	get_tip_labels_tree_list
host_tree	print.cophy
host_tree.cophy	print.cophy
host_tree.multiCophy	print.cophy
is.cophy	is.cophy
is.multiCophylo	is.cophy
is_extinct	is_extinct
make_mat	convert_assoc_table_to_matrix
make_textbox	make_textbox
node_heights	estimate_node_heights
parafit_stat	parafit_stat
parafit_test	parafit_stat
plot.cophy	plot.cophy
plot.multiCophy	plot.cophy
print.cophy	print.cophy
print.multiCophy	print.cophy
retrieve_child_genetrees	retrieve_parent_genetrees
retrieve_parent_genetrees	retrieve_parent_genetrees
sim_cophyBD	sim_cophyBD
sim_cophyBD_ana	sim_cophyBD_ana
sim_cophylo_bdp	sim_cophyBD
sim_cophylo_bdp_ana	sim_cophyBD_ana
sim_locustree_bdp	sim_ltBD
sim_ltBD	sim_ltBD
sim_mlc	sim_multilocus_coal
sim_msc	sim_msc
sim_multilocus_coal	sim_multilocus_coal
sim_multispecies_coal	sim_msc
sim_sptree_bdp	sim_stBD
sim_sptree_bdp_time	sim_stBD_t
sim_stBD	sim_stBD
sim_stBD_t	sim_stBD_t
str.multiCophy	str.multiCophy
summarize_1cophy	cophy_summary_stat
summarize_cophy	cophy_summary_stat
summarize_gt	genetree_summary_stat
summary.cophy	summary.cophy
symb_tree	print.cophy
symb_tree.cophy	print.cophy
symb_tree.multiCophy	print.cophy
to_cophy	convert_to_cophy
treeducken	treeducken-package
