paleotree: Paleontological and Phylogenetic Analyses of Evolution

Provides tools for transforming, a posteriori 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 a posteriori 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.

Version: 2.7
Depends: R (≥ 3.0.0), ape (≥ 3.2)
Imports: phangorn (≥ 1.99.12), stats, phytools, graphics, grDevices, methods, utils
Published: 2016-04-13
Author: David W. Bapst
Maintainer: David W. Bapst <dwbapst at gmail.com>
BugReports: NA
License: CC0
URL: https://github.com/dwbapst/paleotree , http://webpages.sdsmt.edu/~dbapst/
NeedsCompilation: no
Citation: paleotree citation info
Materials: README ChangeLog
In views: Phylogenetics
CRAN checks: paleotree results

Downloads:

Reference manual: paleotree.pdf
Package source: paleotree_2.7.tar.gz
Windows binaries: r-devel: paleotree_2.7.zip, r-release: paleotree_2.7.zip, r-oldrel: paleotree_2.7.zip
OS X Mavericks binaries: r-release: paleotree_2.7.tgz, r-oldrel: paleotree_2.7.tgz
Old sources: paleotree archive

Reverse dependencies:

Reverse imports: OUwie