Open Tree of Life Chronograms

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Documentation for package ‘OpenTreeChronograms’ version 2022.1.28

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.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