Package: datelife
Title: Scientific Data on Time of Lineage Divergence for Your Taxa
Version: 0.6.9
Maintainer: Luna L. Sanchez Reyes <sanchez.reyes.luna@gmail.com>
Authors@R: c(
  person("Brian", "O'Meara", email = "bomeara@gmail.com", role=c("aut")),
  person("Jonathan", "Eastman", role=c("aut")),
  person("Tracy", "Heath", role=c("aut")),
  person("April", "Wright", role=c("aut")),
  person("Klaus", "Schliep", role=c("aut")),
  person("Scott", "Chamberlain", role=c("aut")),
  person("Peter", "Midford", role=c("aut")),
  person("Luke", "Harmon", role=c("aut")),
  person("Joseph", "Brown", role=c("aut")),
  person("Matt", "Pennell", role=c("aut")),
  person("Mike", "Alfaro", role=c("aut")),
  person("Luna L.", "Sanchez Reyes", email = "sanchez.reyes.luna@gmail.com", role=c("aut", "cre")),
  person("Emily Jane", "McTavish", role=c("ctb")))
Description: 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
        <https://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>).
Depends: R (>= 3.6.0)
biocViews: Software
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, knitr, rmarkdown, usethis, devtools, covr, msa,
        Biostrings, spelling
LazyDataCompression: xz
SystemRequirements: PATHd8
URL: https://github.com/phylotastic/datelife,
        http://phylotastic.org/datelife/
License: GPL (>=2)
LazyData: true
RoxygenNote: 7.2.3
Roxygen: list(markdown = TRUE)
Encoding: UTF-8
VignetteBuilder: knitr
Language: en-US
Config/pak/sysreqs: libglpk-dev make libicu-dev libpng-dev libxml2-dev
        libssl-dev
Repository: https://phylotastic.r-universe.dev
Date/Publication: 2025-11-02 17:40:04 UTC
RemoteUrl: https://github.com/phylotastic/datelife
RemoteRef: HEAD
RemoteSha: e1ff3e41f4e41ad79b060cdfc974dd893eee9ff3
NeedsCompilation: no
Packaged: 2026-06-24 10:32:37 UTC; root
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]