Package: paleotree
Type: Package
Version: 3.4.7
Title: Paleontological and Phylogenetic Analyses of Evolution
Date: 2024-07-06
Author: David W. Bapst, Peter J. Wagner
Depends: R (>= 4.1.0), ape (>= 4.1)
Imports: phangorn (>= 2.6.3), stats, phytools (>= 0.6-00), jsonlite,
        graphics, grDevices, methods, png, RCurl, utils
Suggests: spelling, testthat, curl
Language: en-US
ByteCompile: TRUE
Encoding: UTF-8
Maintainer: David W. Bapst <dwbapst@gmail.com>
BugReports: https://github.com/dwbapst/paleotree/issues
Description: 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.
License: CC0
URL: https://github.com/dwbapst/paleotree
RoxygenNote: 7.3.2
NeedsCompilation: no
Packaged: 2024-07-06 19:17:17 UTC; dwbapst
Repository: CRAN
Date/Publication: 2024-07-06 20:20:02 UTC
Built: R 4.4.3; ; 2025-11-12 04:01:40 UTC; windows
