DESCRIPTION

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