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>,
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 |
Documentation:
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