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nichevol: Tools for Ecological Niche Evolution Assessment Considering Uncertainty

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>, SoberĂ³n 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>.

Version: 0.1.20
Depends: ape (≥ 5.3), R (≥ 3.5.0)
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)
Published: 2023-03-10
DOI: 10.32614/CRAN.package.nichevol
Author: Marlon E. Cobos [aut, cre], Hannah L. Owens [aut], A. Townsend Peterson [aut]
Maintainer: Marlon E. Cobos <manubio13 at gmail.com>
BugReports: https://github.com/marlonecobos/nichevol/issues
License: GPL-3
URL: https://github.com/marlonecobos/nichevol
NeedsCompilation: no
Citation: nichevol citation info
Materials: README NEWS
CRAN checks: nichevol results

Documentation:

Reference manual: nichevol.pdf

Downloads:

Package source: nichevol_0.1.20.tar.gz
Windows binaries: r-devel: nichevol_0.1.20.zip, r-release: nichevol_0.1.20.zip, r-oldrel: nichevol_0.1.20.zip
macOS binaries: r-release (arm64): nichevol_0.1.20.tgz, r-oldrel (arm64): nichevol_0.1.20.tgz, r-release (x86_64): nichevol_0.1.20.tgz, r-oldrel (x86_64): nichevol_0.1.20.tgz
Old sources: nichevol archive

Linking:

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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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