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.
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