paleotree: Paleontological and Phylogenetic Analyses of Evolution

paleotree is an R library for analyzing, time-scaling and simulating phylogenies of extinct/fossil lineages. In particular, most users are interested in the functions timePaleoPhy, bin_timePaleoPhy, cal3TimePaleoPhy and bin_cal3TimePaleoPhy, which time-scales cladograms of fossil taxa into dated phylogenies.

This package also contains a large number of functions associated with simulating diversification in incompletely sampled fossil records, under various models of morphological differentiation, and translating such simulated fossil records into their respective phylogenies. There are also likelihood functions offered for estimating sampling rates from different types of observables available from fossil record data.

This code is authored by David Bapst and offered under GPL >2.0.


