c(
person("Nathan", "Constantine-Cooke", , "nathan.constantine-cooke@ed.ac.uk", role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-4437-8713")),
person("Jonathan", "Kitt", , "jonathan.kitt@protonmail.com", role = c("ctb", "trl")),
person("Antonio J.", "Pérez-Luque", ,"ajpelu@gmail.com", role = c("ctb", "trl"),
comment = c(ORCID = "0000-0002-1747-0469")),
person("Daniel", "Possenriede", ,"possenriede+r@gmail.com", role = c("ctb", "trl"),
comment = c(ORCID = "0000-0002-6738-9845")),
person("Kaique dos S.", "Alves", , "kaiquedsalves@gmail.com", role = "rev",
comment = c(ORCID = "0000-0001-9187-0252")),
person("Al-Ahmadgaid B.", "Asaad", , "alahmadgaid@gmail.com", role = "rev",
comment = c(ORCID = "0000-0003-3784-8593"))
)
DT, htmltools, knitr, readxl, rmarkdown, shiny, shinytest,
spelling, testthat (>= 3.0.0), withr, parsedate, readr
Nathan Constantine-Cooke [aut, cre]
(<https://orcid.org/0000-0002-4437-8713>),
Jonathan Kitt [ctb, trl],
Antonio J. Pérez-Luque [ctb, trl]
(<https://orcid.org/0000-0002-1747-0469>),
Daniel Possenriede [ctb, trl] (<https://orcid.org/0000-0002-6738-9845>),
Kaique dos S. Alves [rev] (<https://orcid.org/0000-0001-9187-0252>),
Al-Ahmadgaid B. Asaad [rev] (<https://orcid.org/0000-0003-3784-8593>)

Scientific Data on Time of Lineage Divergence for Your Taxa
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")))
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 <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>).
ape, abind, bold, phangorn, phytools, ips, cluster, compare,
geiger, stats, stringr, rotl, paleotree, knitcitations,
phylobase, taxize, treebase, utils, httr, plyr, phylocomr
testthat, knitr, rmarkdown, usethis, devtools, covr, msa,
Biostrings
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]