datelife: Scientific Data on Time of Lineage Divergence for Your Taxa

Methods and workflows to get chronograms (i.e., phylogenetic trees with branch lengths proportional to time), using open, peer-reviewed, state-of-the-art scientific data on time of lineage divergence. This package constitutes the main underlying code of the DateLife web service at <www.datelife.org>. To obtain a single summary chronogram from a group of relevant chronograms, we implement the Super Distance Matrix (SDM) method described in Criscuolo et al. (2006) <doi:10.1080/10635150600969872>. To find the grove of chronograms with a sufficiently overlapping set of taxa for summarizing, we implement theorem 1.1. from Ané et al. (2009) <doi:10.1007/s00026-009-0017-x>. A given phylogenetic tree can be dated using time of lineage divergence data as secondary calibrations (with caution, see Schenk (2016) <doi:10.1371/journal.pone.0148228>). To obtain and apply secondary calibrations, the package implements the congruification method described in Eastman et al. (2013) <doi:10.1111/2041-210X.12051>. Tree dating can be performed with different methods including BLADJ (Webb et al. (2008) <doi:10.1093/bioinformatics/btn358>), PATHd8 (Britton et al. (2007) <doi:10.1080/10635150701613783>), mrBayes (Huelsenbeck and Ronquist (2001) <doi:10.1093/bioinformatics/17.8.754>), and treePL (Smith and O'Meara (2012) <doi:10.1093/bioinformatics/bts492>).

Version: 0.6.1
Depends: R (≥ 3.6.0)
Imports: ape, abind, bold, phangorn, phytools, ips, cluster, compare, geiger, stats, stringr, rotl, paleotree, knitcitations, phylobase, taxize, treebase, utils, httr, plyr, phylocomr, BiocManager
Suggests: testthat, knitr, rmarkdown, usethis, devtools, covr, msa, Biostrings
Published: 2022-01-31
Author: Brian O'Meara [aut], Jonathan Eastman [aut], Tracy Heath [aut], April Wright [aut], Klaus Schliep [aut], Scott Chamberlain [aut], Peter Midford [aut], Luke Harmon [aut], Joseph Brown [aut], Matt Pennell [aut], Mike Alfaro [aut], Luna L. Sanchez Reyes [aut, cre], Emily Jane McTavish [ctb]
Maintainer: Luna L. Sanchez Reyes <sanchez.reyes.luna at gmail.com>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL: https://github.com/phylotastic/datelife
NeedsCompilation: no
SystemRequirements: PATHd8
Citation: datelife citation info
Materials: README NEWS
CRAN checks: datelife results

Documentation:

Reference manual: datelife.pdf
Vignettes: Getting started
Case study: the Fringillidae

Downloads:

Package source: datelife_0.6.1.tar.gz
Windows binaries: r-devel: datelife_0.6.1.zip, r-release: datelife_0.6.1.zip, r-oldrel: datelife_0.6.1.zip
macOS binaries: r-release (arm64): datelife_0.6.1.tgz, r-release (x86_64): datelife_0.6.1.tgz, r-oldrel: datelife_0.6.1.tgz
Old sources: datelife archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=datelife to link to this page.