API for treeducken
Nested Phylogenetic Tree Simulator
| Global functions | |
|---|---|
| .c_cophy_single | Source code |
| .makeMultiCophyFromObj | Source code |
| .uncompressSetTipLabel | Source code |
| `$.multiCophy` | Source code |
| `$<-.multiCophy` | Source code |
| `[<-.multiCophy` | Source code |
| `[[<-.multiCophy` | Source code |
| add_events | Man page Source code |
| add_scalebar | Man page Source code |
| association_mat | Man page Source code |
| association_mat.cophy | Man page Source code |
| association_mat.multiCophy | Man page Source code |
| ave_tips_lt | Man page Source code |
| ave_tips_st | Man page Source code |
| build_historical_association_matrix | Man page Source code |
| c.cophy | Man page Source code |
| c.multiCophy | Man page Source code |
| calculate_expected_leaves_locustree | Man page Source code |
| calculate_expected_leaves_sptree | Man page Source code |
| collapse_clade | Man page Source code |
| collapse_locus_subtree | Man page Source code |
| convert_assoc_table_to_matrix | Man page Source code |
| convert_to_cophy | Man page Source code |
| cophy_summary_stat | Man page Source code |
| cophy_summary_stat_by_indx | Man page Source code |
| count_cherries | Man page Source code |
| draw_cophy | Man page Source code |
| draw_curve | Man page Source code |
| drop_extinct | Man page Source code |
| estimate_node_heights | Man page Source code |
| event_history | Man page Source code |
| event_history.cophy | Man page Source code |
| event_history.multiCophy | Man page Source code |
| genetree_summary_stat | Man page Source code |
| get_ana_events | Man page Source code |
| get_assoc | Man page Source code |
| get_child_gts | Man page Source code |
| get_loci | Man page Source code |
| get_parent_gts | Man page Source code |
| get_tip_labels_tree_list | Man page Source code |
| get_tipnames | Man page Source code |
| host_tree | Man page Source code |
| host_tree.cophy | Man page Source code |
| host_tree.multiCophy | Man page Source code |
| is.cophy | Man page Source code |
| is.multiCophylo | Man page Source code |
| is_extinct | Man page |
| make_mat | Man page Source code |
| make_textbox | Man page Source code |
| node_heights | Man page Source code |
| parafit_stat | Man page Source code |
| parafit_test | Man page Source code |
| plot.cophy | Man page Source code |
| plot.multiCophy | Man page Source code |
| print.cophy | Man page Source code |
| print.multiCophy | Man page Source code |
| retrieve_child_genetrees | Man page Source code |
| retrieve_parent_genetrees | Man page Source code |
| sim_cophyBD | Man page Source code |
| sim_cophyBD_ana | Man page Source code |
| sim_cophylo_bdp | Man page Source code |
| sim_cophylo_bdp_ana | Man page Source code |
| sim_locustree_bdp | Man page Source code |
| sim_ltBD | Man page Source code |
| sim_mlc | Man page Source code |
| sim_msc | Man page Source code |
| sim_multilocus_coal | Man page Source code |
| sim_multispecies_coal | Man page Source code |
| sim_sptree_bdp | Man page Source code |
| sim_sptree_bdp_time | Man page Source code |
| sim_stBD | Man page Source code |
| sim_stBD_t | Man page Source code |
| str.multiCophy | Man page Source code |
| summarize_1cophy | Man page Source code |
| summarize_cophy | Man page Source code |
| summarize_gt | Man page Source code |
| summary.cophy | Man page Source code |
| symb_tree | Man page Source code |
| symb_tree.cophy | Man page Source code |
| symb_tree.multiCophy | Man page Source code |
| to_cophy | Man page Source code |
| treeducken | Man page |
| treeducken-package | Man page |
