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
Config/pak/sysreqs: libglpk-dev make libpng-dev libxml2-dev
Repository: https://dwbapst.r-universe.dev
Date/Publication: 2024-07-09 05:08:05 UTC
RemoteUrl: https://github.com/dwbapst/paleotree
RemoteRef: HEAD
RemoteSha: 72ad91ba4ce2aa5edd07624291c1abc9df305e5c
NeedsCompilation: no
Packaged: 2026-07-03 17:34:32 UTC; root