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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>.
| 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 |
| Reference manual: | nichevol.pdf |
| 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 |
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