Package: datelife
Title: Scientific Data on Time of Lineage Divergence for Your Taxa
Version: 0.6.8
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
LazyDataCompression: xz
SystemRequirements: PATHd8
URL: https://github.com/phylotastic/datelife,
        http://phylotastic.org/datelife/
License: GPL (>= 2)
LazyData: true
RoxygenNote: 7.2.3
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-06-19 22:49:25 UTC; luna
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]
Repository: CRAN
Date/Publication: 2023-06-19 23:20:02 UTC
Built: R 4.2.3; ; 2024-04-24 03:39:46 UTC; windows
