# Nested Phylogenetic Tree Simulator

## Documentation for package ‘treeducken’ version 1.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

treeducken-package | treeducken: simulates cophylogenetic systems & nested phylogenies
add_events | Add events from sim_cophyBD to plot.cophy
add_scalebar | Add scale bar to cophylo plot
association_mat | Print a cophylogenetic set
association_mat.cophy | Print a cophylogenetic set
association_mat.multiCophy | Print a cophylogenetic set
ave_tips_lt | Calculate expected leaves of a locus tree
ave_tips_st | Calculate expected leaves of a species tree
build_historical_association_matrix | Reconstruct historical association matrix
c.cophy | Combine cophylogenetic sets into a multiCophy object
c.multiCophy | 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_clade | Collapse a clade into a single tip
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 | Calculates summary statistics for cophylogenetic objects
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
event_history.cophy | Summarize a cophylogenetic set
event_history.multiCophy | Print a cophylogenetic set
genetree_summary_stat | Calculate summary statistics for gene trees
get_assoc | Reconstruct historical association matrix
get_child_gts | Retrieve all gene trees of the parent tree from a list generated from sim_mlc
get_loci | Separate a locus tree into loci
get_parent_gts | Retrieve all gene trees of the parent tree from a list generated from sim_mlc
get_tipnames | Get all the tip labels of a 'multiPhylo' object
get_tip_labels_tree_list | Get all the tip labels of a 'multiPhylo' object
host_tree | Print a cophylogenetic set
host_tree.cophy | Print a cophylogenetic set
host_tree.multiCophy | Print a cophylogenetic set
is.cophy | Test for the cophygenetic set object
is.multiCophylo | Test for the cophygenetic set object
is_extinct | Identify extinct tips from tree
make_mat | Convert a table with host and symbiont associations to a matrix
make_textbox | Internal tree plot function
node_heights | Calculate expected time to branching point of a species tree
parafit_stat | Calculate the ParafitGlobal statistic on 2 trees and their association matrix
parafit_test | Calculate the ParafitGlobal statistic on 2 trees and their association matrix
plot.cophy | Plot host and symbiont pair with current associations
plot.multiCophy | Plot host and symbiont pair with current associations
print.cophy | Print a cophylogenetic set
print.multiCophy | Print a cophylogenetic set
retrieve_child_genetrees | Retrieve all gene trees of the parent tree from a list generated from sim_mlc
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_cophylo_bdp | Simulates a host-symbiont system using a cophylogenetic birth-death process
sim_cophylo_bdp_ana | Simulates a host-symbiont system using a cophylogenetic birth-death process
sim_locustree_bdp | Simulates locus tree using constant rate birth-death-transfer process
sim_ltBD | Simulates locus tree using constant rate birth-death-transfer process
sim_mlc | Simulates multi-locus coalescent on a given locus tree
sim_msc | Simulate multispecies coalescent on a species tree
sim_multilocus_coal | Simulates multi-locus coalescent on a given locus tree
sim_multispecies_coal | Simulate multispecies coalescent on a species tree
sim_sptree_bdp | Simulates species trees using constant rate birth-death process
sim_sptree_bdp_time | Simulates species tree using constant rate birth-death process to a time
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
summarize_1cophy | Calculates summary statistics for cophylogenetic objects
summarize_cophy | Calculates summary statistics for cophylogenetic objects
summarize_gt | Calculate summary statistics for gene trees
summary.cophy | Summarize a cophylogenetic set
symb_tree | Print a cophylogenetic set
symb_tree.cophy | Print a cophylogenetic set
symb_tree.multiCophy | Print a cophylogenetic set
to_cophy | Converts an object into an object of type cophy
treeducken | treeducken: simulates cophylogenetic systems & nested phylogenies