Niche Region and Niche Overlap Metrics for Multidimensional
Ecological Niches
c(person("Martin", "Lysy", role = c("aut", "cre"),
email = "mlysy@uwaterloo.ca"),
person("Ashley D.", "Stasko", role = "aut"),
person("Heidi K.", "Swanson", role = "aut"))
Implementation of a probabilistic method to calculate 'nicheROVER' (_niche_ _r_egion and niche _over_lap) metrics using multidimensional niche indicator data (e.g., stable isotopes, environmental variables, etc.). The niche region is defined as the joint probability density function of the multidimensional niche indicators at a user-defined probability alpha (e.g., 95%).  Uncertainty is accounted for in a Bayesian framework, and the method can be extended to three or more indicator dimensions.  It provides directional estimates of niche overlap, accounts for species-specific distributions in multivariate niche space, and produces unique and consistent bivariate projections of the multivariate niche region.  The article by Swanson et al. (Ecology, 2015) provides a detailed description of the methodology.  See the package vignette for a worked example using fish stable isotope data.
Martin Lysy [aut, cre],
Ashley D. Stasko [aut],
Heidi K. Swanson [aut]

Tools for Ecological Niche Evolution Assessment Considering
Uncertainty
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"))
Marlon E. Cobos [aut, cre],
Hannah L. Owens [aut],
A. Townsend Peterson [aut]
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: Peterson et al. (1999) <doi:10.1126/science.285.5431.1265>,
Soberon 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>,
Owens et al. (2013) <doi:10.1016/j.ecolmodel.2013.04.011>, and
Saupe et al. (2018) <doi:10.1093/sysbio/syx084>.