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 date
cladograms of fossil taxa using stratigraphic data. 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.
