Packaged: 2021-04-23 06:02:06 UTC; Julia Pilowsky

person("Stuart", "Brown", email = "s.brown@adelaide.edu.au", role = c("aut"),
person("Damien", "Fordham", email = "damien.fordham@adelaide.edu.au", role = c("aut"),
Packaged: 2021-10-14 01:01:40 UTC; Julia Pilowsky
Julia Pilowsky [aut, cre] (<https://orcid.org/0000-0002-6376-2585>),

Packaged: 2022-10-05 23:24:37 UTC; Julia Pilowsky

Packaged: 2022-10-13 00:15:59 UTC; Julia Pilowsky

Title: Analyses for Paleontological Phylogenies
Description: Analyzes, time-scales and simulates phylogenies of
extinct/fossil lineages. Also plots diversity curves for
stratigraphic range data and phylogenies, including
combinations of the those two data types.

Title: Paleontological and Phylogenetic Analyses of Evolution

extinct/fossil lineages. Also calculates diversity curves for
stratigraphic range data and phylogenies.

extinct/fossil lineages, along with calculation of diversity
curves. Also fits likelihood models to estimate sampling rates

Description: Analyzes, time-scales and simulates phylogenies of extinct/fossil lineages, along with calculation of diversity curves. Also fits likelihood models to estimate sampling rates from stratigraphic ranges.

Maintainer: David W. Bapst <dwbapst@gmail.com>
Description: Analyzes, time-scales and simulates phylogenies of extinct/fossil
lineages, along with calculation of diversity curves. Also fits likelihood
models to estimate sampling rates from stratigraphic ranges.

Packaged: 2014-02-04 04:47:23 UTC; adminosaur

Packaged: 2014-08-16 06:59:30 UTC; adminosaur

Packaged: 2014-09-18 06:46:18 UTC; adminosaur

Packaged: 2015-01-16 16:17:06 UTC; adminosaur

Packaged: 2015-05-01 22:02:32 UTC; adminosaur

Imports: phangorn (>= 1.99.12), stats, phytools, graphics, grDevices,
Packaged: 2015-09-21 03:43:10 UTC; adminosaur

Package: paleotree
Type: Package
Version: 2.6
Title: Paleontological and Phylogenetic Analyses of Evolution
Date: 2015-12-01
Author: David W. Bapst
Depends: R (>= 3.0.0), ape (>= 3.2)
Imports: phangorn (>= 1.99.12), stats, phytools, graphics, grDevices,
methods, utils
ByteCompile: TRUE
Maintainer: David W. Bapst <dwbapst@gmail.com>
Description: Provides tools for transforming, time-scaling, and
modifying phylogenies containing extinct (i.e. fossil) lineages. In particular,
most users are interested in the functions timePaleoPhy, bin_timePaleoPhy,
cal3TimePaleoPhy and bin_cal3TimePaleoPhy, which time-scale cladograms of
fossil taxa into dated phylogenies. This package also contains a large number
of likelihood functions for estimating sampling and diversification rates from
different types of data available from the fossil record (e.g. range data,
occurrence data, etc). paleotree users can also simulate diversification and
sampling in the fossil record using the function simFossilRecord, which is a
detailed simulator for branching birth-death-sampling processes composed of
discrete taxonomic units arranged in ancestor-descendant relationships. Users
can use simFossilRecord to simulate diversification in incompletely sampled
fossil records, under various models of morphological differentiation (i.e.
the various patterns by which morphotaxa originate from one another), and
with time-dependent, longevity-dependent and/or diversity-dependent rates of
diversification, extinction and sampling. Additional functions allow users to
translate simulated ancestor-descendant data from simFossilRecord into standard
time-scaled phylogenies or unscaled cladograms that reflect the relationships
among taxon units.
License: CC0
URL: https://github.com/dwbapst/paleotree ,
http://webpages.sdsmt.edu/~dbapst/
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-12-02 19:04:15 UTC; adminosaur
Repository: CRAN
Date/Publication: 2015-12-03 00:21:42