What is datelife?
datelife is an R package that allows researchers and the general audience to obtain open scientific data on the age of any organism they are interested in, by retrieving organism ages from a database of dated phylogenetic trees (aka chronograms), that have been peer-reviewed and published as part of a scientific research article, in an indexed journal (Open Tree of Life’s tree store). As such, organism ages retrieved by datelife constitute state-of-the-art, peer-reviewed, public scientific knowledge, that can be accessed and reused by experts and non-experts in the field alike.
How can you use datelife?
You can install the datelife R package on your own computer and use it locally. You can find instructions for a local installation below.
If you do not want/have time to deal with installation and R code, you can use DateLife’s interactive website application. Note that the website is not live at the moment, apologies.
Local installation of the datelife R package
datelife’s most recent stable version can be installed with:
install.packages("datelife")datelife’s previous stable versions are available for installation from the CRAN repository. For example, to install version 0.6.1, you can run:
devtools::install_version("datelife", version="0.6.1")You can install datelife’s development version from its GitHub repository with:
devtools::install_github("phylotastic/datelife")Citing datelife
If you use datelife for a publication, please cite the R package and the accompanying paper:
O’Meara B, Sanchez-Reyes L, Eastman J, Heath T, Wright A, Schliep K, Chamberlain S, Midford P, Harmon L, Brown J, Pennell M, Alfaro M (2023). datelife: Scientific Data on Time of Lineage Divergence for Your Taxa. R package version 0.6.7, https://doi.org/10.5281/zenodo.593938.
Sanchez-Reyes L, O’Meara B (2019). “datelife: Leveraging databases and analytical tools to reveal the dated Tree of Life.” bioRxiv, 782094. https://doi.org/10.1101/782094.
You can get these citations and the bibtex entry with:
Acknowledgements
datelife has been developed as part of the phylotastic (NSF-funded) project, and is still under development.