Includes functions to wrap most endpoints of the
    'PaleobioDB' API and to visualize and process the obtained fossil
    data. The API documentation for the Paleobiology Database can be
    found at <https://paleobiodb.org/data1.2/>.

Simulation of species diversification, fossil records, and phylogenies. While the literature on species birth-death simulators is extensive, including important software like 'paleotree' and 'APE', we concluded there were interesting gaps to be filled regarding possible diversification scenarios. Here we strove for flexibility over focus, implementing a large array of regimens for users to experiment with and combine. In this way, 'paleobuddy' can be used in complement to other simulators as a flexible jack of all trades, or, in the case of scenarios implemented only here, can allow for robust and easy simulations for novel situations. Environmental data modified from that in 'RPANDA': Morlon H. et al (2016) <doi:10.1111/2041-210X.12526>.

Contains various tools for conveniently downloading and editing taxon-specific datasets from the Paleobiology Database <https://paleobiodb.org>, extracting information on abundance, temporal distribution of subtaxa and taxonomic diversity through deep time, and visualizing these data in relation to phylogeny and stratigraphy.

Fill missing symmetrical data with mirroring, calculate Procrustes alignments with or without scaling, and compute standard or vector correlation and covariance matrices (congruence coefficients) of 3D landmarks. Tolerates missing data for all analyses.

This extension of the poems pattern-oriented modeling (POM) framework
    provides a collection of modules and functions customized for paleontological
    time-scales, and optimized for single-generation transitions and large populations,
    across multiple generations.

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.