CRAN/E | datelife

datelife

Scientific Data on Time of Lineage Divergence for Your Taxa

Installation

About

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 . 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).

Citation datelife citation info
github.com/phylotastic/datelife
phylotastic.org/datelife/
System requirements PATHd8

Key Metrics

Version 0.6.8
R ≥ 3.6.0
Published 2023-06-19 284 days ago
Needs compilation? no
License GPL-2
License GPL-3
CRAN checks datelife results

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Maintainer

Maintainer

Luna L. Sanchez Reyes

sanchez.reyes.luna@gmail.com

Authors

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

Material

README
NEWS
Reference manual
Package source

Vignettes

Getting started
Case study: the true finches
make_datelife_query
making_bold_trees

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

datelife archive

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
data.table
curl

Suggests

testthat
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