# Open Tree of Life Chronograms

## Documentation for package ‘OpenTreeChronograms’ version 2022.1.28

- DESCRIPTION file.
- Package NEWS.

## Help Pages

.get_ott_lineage | Get the lineage of a set of taxa. '.get_ott_lineage' uses 'rotl::taxonomy_taxon_info()' with 'include_lineage = TRUE'.
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 now it 1) checks unmapped taxa and maps them with tnrs_match.phylo, 2) roots the chronogram if unrooted
clean_taxon_info_children | Identify, extract and clean taxonomic children names from a 'taxonomy_taxon_info()' output.
clean_tnrs | Eliminates unmatched (NAs) and invalid taxa from a 'rotl::tnrs_match_names()' or 'tnrs_match()' output. Useful to get ott ids to retrieve an induced synthetic Open Tree of Life. Needed because using 'include_suppressed = FALSE' in 'rotl::tnrs_match_names()' does not drop all invalid taxa.
date_with_pbdb | Date with Paleobiology Database and paleotree.
extract_ott_ids | Get OTT ids from a character vector containing species names and OTT ids.
extract_ott_ids.default | Get OTT ids from a character vector containing species names and OTT ids.
get_fossil_range | Get the ages for a taxon from PBDB
get_opentree_chronograms | Get all chronograms from Open Tree of Life database
get_otol_chronograms | Get all chronograms from Open Tree of Life database
get_ott_children | Use this instead of 'rotl::tol_subtree()' when taxa are not in synthesis tree and you still need to get all species or an induced OpenTree subtree
get_ott_clade | Get the Open Tree of Life Taxonomic identifiers (OTT ids) and name of one or several given taxonomic ranks from one or more input taxa.
get_ott_lineage | Get the Open Tree of Life Taxonomic identifier (OTT id) and name of all lineages from one or more input taxa.
get_valid_children | Extract valid children from given taxonomic name(s) or Open Tree of Life Taxonomic identifiers (OTT ids) from a taxonomic source.
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 and get its name and ott id
summarize_fossil_range | Summarize taxon age from PBDB to just a single min and max age
tnrs_match | Taxon name resolution service (tnrs) applied to a vector of names by batches
tnrs_match.default | Taxon name resolution service (tnrs) applied to a vector of names by batches
tnrs_match.phylo | Taxon name resolution service (tnrs) applied to a vector of names by batches
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