Man pages for treeducken
Nested Phylogenetic Tree Simulator
| 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 |
| calculate_expected_leaves_locustree | Calculate expected leaves of a locus tree |
| calculate_expected_leaves_sptree | Calculate expected leaves of a species tree |
| c.cophy | Combine cophylogenetic sets into a multiCophy object |
| 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... |
| convert_to_cophy | Converts an object into an object of type cophy |
| cophy_summary_stat | 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 |
| genetree_summary_stat | Calculate summary statistics for gene trees |
| get_ana_events | Internal function for plotting anagenetic events |
| get_loci | Separate a locus tree into loci |
| get_tip_labels_tree_list | Get all the tip labels of a 'multiPhylo' object |
| 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... |
| plot.cophy | Plot host and symbiont pair with current associations |
| print.cophy | Print a cophylogenetic set |
| retrieve_parent_genetrees | Retrieve all gene trees of the parent tree from a list... |
| sim_cophyBD | Simulates a host-symbiont system using a cophylogenetic... |
| sim_cophyBD_ana | Simulates a host-symbiont system using a cophylogenetic... |
| sim_ltBD | Simulates locus tree using constant rate birth-death-transfer... |
| 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... |
| sim_stBD_t | Simulates species tree using constant rate birth-death... |
| str.multiCophy | Retrieve the structure of a class multiCophy |
| summary.cophy | Summarize a cophylogenetic set |
| treeducken-package | treeducken: simulates cophylogenetic systems & nested... |
