Man pages for OpenTreeChronograms
Open Tree of Life Chronograms
| check_ott_input | Check input for other functions |
| classification_paths_from_taxonomy | Gets classification paths for a vector of taxa |
| clean_ott_chronogram | Clean up some issues with Open Tree of Life chronograms For... |
| clean_taxon_info_children | Identify, extract and clean taxonomic children names from a... |
| clean_tnrs | Eliminates unmatched (NAs) and invalid taxa from a... |
| date_with_pbdb | Date with Paleobiology Database and paleotree. |
| dot-get_ott_lineage | Get the lineage of a set of taxa. '.get_ott_lineage' uses... |
| extract_ott_ids | Get OTT ids from a character vector containing species names... |
| get_fossil_range | Get the ages for a taxon from PBDB |
| get_opentree_chronograms | Get all chronograms from Open Tree of Life database |
| get_ott_children | Use this instead of 'rotl::tol_subtree()' when taxa are not... |
| get_ott_clade | Get the Open Tree of Life Taxonomic identifiers (OTT ids) and... |
| get_ott_lineage | Get the Open Tree of Life Taxonomic identifier (OTT id) and... |
| get_valid_children | Extract valid children from given taxonomic name(s) or Open... |
| is_good_chronogram | Check if a tree is a valid chronogram. |
| is_phylo | Checks if 'phy' is a 'phylo' object and/or a chronogram. |
| make_all_associations | Find all authors and where they have deposited their trees |
| make_contributor_cache | Create a cache from Open Tree of Life |
| make_otol_associations | Associate Open Tree of Life authors with studies |
| make_overlap_table | Create an overlap table |
| make_treebase_associations | Associate TreeBase authors with studies |
| make_treebase_cache | Create a cache from TreeBase |
| map_nodes_ott | Add Open Tree of Life Taxonomy to tree nodes. |
| opentree_chronograms | Open Tree of Life Chronogram database in R |
| phylo_has_brlen | Check if a tree has branch lengths |
| phylo_tiplabel_space_to_underscore | Convert spaces to underscores in trees. |
| phylo_tiplabel_underscore_to_space | Convert underscores to spaces in trees. |
| problematic_chronograms | Problematic chronograms from Open Tree of Life. |
| recover_mrcaott | Get an mrcaott tag from an OpenTree induced synthetic tree... |
| summarize_fossil_range | Summarize taxon age from PBDB to just a single min and max... |
| tnrs_match | Taxon name resolution service (tnrs) applied to a vector of... |
| tree_from_taxonomy | Gets a taxonomic tree from a vector of taxa |
| update_all_cached | Update all data files as data objects for the package |
| update_datelife_cache | Create an updated OpenTree chronograms database object |
