Homework Review
- Extract the OTT id of a biological group using the function
tnrs_match_names(). - Get a subtree from the group using its OTT id.
- If you get an error, try with a different group until you get a subtree from Open Tree
- Plot your subtree
Working with non-monophyletic taxa
- Example: a subtree of the genus Canis
- Finding “broken” and “invalid” taxa with
is_in_tree() - Getting the MRCA of a taxon with
tol_node_info() - Getting a subtree using a node id instead of the taxon OTT id with
tol_subtree(node_id = MY NODE ID)
Getting an induced tree from Open Tree of Life
- Get an induced subtree for a set of taxa and plot it with
tol_induced_subtree() - Example: Get an induced tree for the 3 orders of amphibians
- For families:
amphibia_families <- datelife::get_ott_children(ott_ids = resolved_names["Amphibia",]$ott_id, ott_rank = "family")