Package: nichevol
Type: Package
Title: Tools for Ecological Niche Evolution Assessment Considering
        Uncertainty
Version: 0.1.20
Authors@R: c(
    person("Marlon E.", "Cobos", email = "manubio13@gmail.com", role = c("aut","cre")),
    person("Hannah L.", "Owens", email = "hannah.owens@gmail.com", role = "aut"),
    person("A. Townsend", "Peterson", email = "town@ku.edu", role = "aut"))
Author: Marlon E. Cobos [aut, cre], Hannah L. Owens [aut], A. Townsend
        Peterson [aut]
Maintainer: Marlon E. Cobos <manubio13@gmail.com>
Date: 2023-03-09
Description: A collection of tools that allow users to perform critical
        steps in the process of assessing ecological niche evolution
        over phylogenies, with uncertainty incorporated explicitly in
        reconstructions. The method proposed here for ancestral
        reconstruction of ecological niches characterizes species'
        niches using a bin-based approach that incorporates uncertainty
        in estimations. Compared to other existing methods, the
        approaches presented here reduce risk of overestimation of
        amounts and rates of ecological niche evolution. The main
        analyses include: initial exploration of environmental data in
        occurrence records and accessible areas, preparation of data
        for phylogenetic analyses, executing comparative phylogenetic
        analyses of ecological niches, and plotting for
        interpretations. Details on the theoretical background and
        methods used can be found in: Owens et al. (2020)
        <doi:10.1002/ece3.6359>, Peterson et al. (1999)
        <doi:10.1126/science.285.5431.1265>, Soberón and Peterson
        (2005) <doi:10.17161/bi.v2i0.4>, Peterson (2011)
        <doi:10.1111/j.1365-2699.2010.02456.x>, Barve et al. (2011)
        <doi:10.1111/ecog.02671>, Machado-Stredel et al. (2021)
        <doi:10.21425/F5FBG48814>, Owens et al. (2013)
        <doi:10.1016/j.ecolmodel.2013.04.011>, Saupe et al. (2018)
        <doi:10.1093/sysbio/syx084>, and Cobos et al. (2021)
        <doi:10.1111/jav.02868>.
URL: https://github.com/marlonecobos/nichevol
BugReports: https://github.com/marlonecobos/nichevol/issues
Imports: castor (>= 1.4), geiger (>= 2.0), graphics (>= 3.6), grDevices
        (>= 3.6), stringr (>= 1.4), stats (>= 3.6), terra (>= 1.6),
        utils (>= 3.6)
Suggests: knitr(>= 1.25), phytools (>= 0.6)
Depends: ape (>= 5.3), R (>= 3.5.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
Config/pak/sysreqs: libgdal-dev gdal-bin libgeos-dev libglpk-dev make
        libicu-dev libxml2-dev libproj-dev libsqlite3-dev
Repository: https://phylotastic.r-universe.dev
Date/Publication: 2023-03-10 19:02:37 UTC
RemoteUrl: https://github.com/marlonecobos/nichevol
RemoteRef: HEAD
RemoteSha: e3a1112b803b5ac38c5bc5b1422423f80e509b5a
NeedsCompilation: no
Packaged: 2026-06-03 07:29:57 UTC; root