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R package containing datelife's core functionality
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README.md

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datelife

Get a phylogenetic tree with branch lengths proportional to geologic time (aka a chronogram) of any two or more lineages of interest to you: use this R package or go to www.datelife.org to make a query of chronograms available for your lineages in the Open Tree of Life’s tree store.

You can also date a phylogenetic tree of your own making (or choosing one from the literature), using node ages from chronograms queried with datelife and the congruification method (Eastman et al. 2013) implemented with geiger (Harmon et al. 2008).

datelife has been developed as part of the phylotastic (NSF-funded) project, and is still under rapid development.

Installation

Get the stable version from CRAN:

install.packages("datelife")

Or, install the development version from the GitHub repository:

devtools::install_github("phylotastic/datelife")

Quick intro

You can update the cached objects with the update_all_cached() function

Citation

If you use datelife for a publication, please cite the R package and the accompanying paper:

#> Warning in citation("datelife"): no date field in DESCRIPTION file of package
#> 'datelife'

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 (2019). datelife: Underlying Code for DateLife Web Service. https://github.com/phylotastic/datelife, http://www.datelife.org.

You can get these citations and the bibtex entry with:

citation("datelife")
toBibtex(citation("datelife"))

Feedback

All comments, ideas and questions about datelife are encouraged. You are welcome to post an issue here, or to make a pull request if you want to contribute with code directly.

License

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

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