Open Tree of Life Chronograms.
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.