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OpenTreeChronograms: a database of phylogenetic trees with branch lengths proportional to time

Welcome to OpenTreeChronograms GitHub repository!

OpenTreeChronograms is an R package that hosts a chronogram database assembled with data from the Open Tree of Life phylogenetic database, the Phylesystem.

OpenTreeChronograms has been developed to work along with the datelife R package.

README topics:

Local installation of the OpenTreeChronograms R package

OpenTreeChronograms’s most recent stable version can be installed with:

install.packages("OpenTreeChronograms")

OpenTreeChronograms’s previous stable versions are available for installation from the CRAN repository. For example, to install version 2022.01.28, you can run:

devtools::install_version("OpenTreeChronograms", version="2022.01.28")

You can install OpenTreeChronograms’s development version from its GitHub repository with:

devtools::install_github("phylotastic/OpenTreeChronograms")

Loading the database

data("opentree_chronograms", package = "OpenTreeChronograms")
opentree_chronograms$version

[1] “2022.01.28”

opentree_chronograms$update

[1] “2022-01-28 15:24:53 PST”

Citing OpenTreeChronograms

If you use OpenTreeChronograms for a publication, please cite the Open Tree of Life database Phylesystem, the OpenTreeChronograms R package, the accompanying paper, and all chronograms used.

License

This package is free and open source software, licensed under GPL.

Funding

OpenTreeChronograms was developed and is maintained as part of the Datelife project, funded by the phylotastic and the Open Tree of Life projects.

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Version

Install

install.packages('OpenTreeChronograms')

Monthly Downloads

48

Version

2022.1.28

License

GPL (>= 2)

Maintainer

Luna L. Sanchez Reyes

Last Published

June 22nd, 2022

Functions in OpenTreeChronograms (2022.1.28)

check_ott_input

Check input for other functions
get_fossil_range

Get the ages for a taxon from PBDB
extract_ott_ids

Get OTT ids from a character vector containing species names and OTT ids.
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
.get_ott_lineage

Get the lineage of a set of taxa. .get_ott_lineage uses rotl::taxonomy_taxon_info() with include_lineage = TRUE.
get_opentree_chronograms

Get all chronograms from Open Tree of Life database
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.
classification_paths_from_taxonomy

Gets classification paths for a vector of taxa
clean_taxon_info_children

Identify, extract and clean taxonomic children names from a taxonomy_taxon_info() output.
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_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
make_overlap_table

Create an overlap table
make_otol_associations

Associate Open Tree of Life authors with studies
phylo_has_brlen

Check if a tree has branch lengths
make_treebase_associations

Associate TreeBase authors with studies
make_treebase_cache

Create a cache from TreeBase
is_phylo

Checks if phy is a phylo object and/or a chronogram.
date_with_pbdb

Date with Paleobiology Database and paleotree.
is_good_chronogram

Check if a tree is a valid chronogram.
update_all_cached

Update all data files as data objects for the package
update_datelife_cache

Create an updated OpenTree chronograms database object
phylo_tiplabel_space_to_underscore

Convert spaces to underscores in trees.
make_all_associations

Find all authors and where they have deposited their trees
map_nodes_ott

Add Open Tree of Life Taxonomy to tree nodes.
opentree_chronograms

Open Tree of Life Chronogram database in R
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.
phylo_tiplabel_underscore_to_space

Convert underscores to spaces in trees.
tnrs_match

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
make_contributor_cache

Create a cache from Open Tree of Life
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
get_valid_children

Extract valid children from given taxonomic name(s) or Open Tree of Life Taxonomic identifiers (OTT ids) from a taxonomic source.
summarize_fossil_range

Summarize taxon age from PBDB to just a single min and max age