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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "datelife" in publications use:'
type: software
title: 'datelife: Scientific Data on Time of Lineage Divergence for Your Taxa'
version: 0.6.9
identifiers:
- type: doi
  value: 10.32614/CRAN.package.datelife
abstract: 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) <https://doi.org/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) <https://doi.org/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) <https://doi.org/10.1371/journal.pone.0148228>).
  To obtain and apply secondary calibrations, the package implements the congruification
  method described in Eastman et al. (2013) <https://doi.org/10.1111/2041-210X.12051>.
  Tree dating can be performed with different methods including BLADJ (Webb et al.
  (2008) <https://doi.org/10.1093/bioinformatics/btn358>), PATHd8 (Britton et al.
  (2007) <https://doi.org/10.1080/10635150701613783>), mrBayes (Huelsenbeck and Ronquist
  (2001) <https://doi.org/10.1093/bioinformatics/17.8.754>), and treePL (Smith and
  O'Meara (2012) <https://doi.org/10.1093/bioinformatics/bts492>).
authors:
- family-names: O'Meara
  given-names: Brian
  email: bomeara@gmail.com
- family-names: Eastman
  given-names: Jonathan
- family-names: Heath
  given-names: Tracy
- family-names: Wright
  given-names: April
- family-names: Schliep
  given-names: Klaus
- family-names: Chamberlain
  given-names: Scott
- family-names: Midford
  given-names: Peter
- family-names: Harmon
  given-names: Luke
- family-names: Brown
  given-names: Joseph
- family-names: Pennell
  given-names: Matt
- family-names: Alfaro
  given-names: Mike
- family-names: Sanchez Reyes
  given-names: Luna L.
  email: sanchez.reyes.luna@gmail.com
preferred-citation:
  type: manual
  title: 'datelife: Scientific Data on Time of Lineage Divergence for Your Taxa'
  authors:
  - family-names: O'Meara
    given-names: Brian
    email: omeara.brian@gmail.com
  - family-names: Sanchez-Reyes
    given-names: Luna L.
    email: sanchez.reyes.luna@gmail.com
  - family-names: Eastman
    given-names: Jonathan
  - family-names: Heath
    given-names: Tracy
  - family-names: Wright
    given-names: April
  - family-names: Schliep
    given-names: Klaus
  - family-names: Chamberlain
    given-names: Scott
  - family-names: Midford
    given-names: Peter
  - family-names: Harmon
    given-names: Luke
  - family-names: Brown
    given-names: Joseph
  - family-names: Pennell
    given-names: Matt
  - family-names: Alfaro
    given-names: Mike
  - family-names: McTavish
    given-names: Emily Jane
  year: '2024'
  notes: R package version 0.6.9
  url: https://doi.org/10.5281/zenodo.593938
repository: https://phylotastic.r-universe.dev
repository-code: https://github.com/phylotastic/datelife
commit: 0311e7ce8dff63bac3c1521892c96f0be20fade6
url: http://phylotastic.org/datelife/
contact:
- family-names: Sanchez Reyes
  given-names: Luna L.
  email: sanchez.reyes.luna@gmail.com
references:
- type: article
  title: 'datelife: Leveraging databases and analytical tools to reveal the dated
    Tree of Life'
  authors:
  - family-names: Sanchez-Reyes
    given-names: Luna L.
    email: sanchez.reyes.luna@gmail.com
  - family-names: McTavish
    given-names: Emily Jane
    email: ejmctavish@ucmerced.edu
  - family-names: O'Meara
    given-names: Brian
    email: omeara.brian@gmail.com
  journal: bioRxiv
  year: '2022'
  volume: '782094'
  url: https://doi.org/10.1101/782094