nicheROVER: (Niche) (R)egion and Niche (Over)lap Metrics for Multidimensional Ecological Niches

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This package uses a probabilistic method to calculate niche regions and pairwise niche overlap 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. A forthcoming article by Swanson et al. (Ecology, 2014) provides a detailed description of the methodology. See the package vignette for a worked example using fish stable isotope data.

Author
Martin Lysy [aut, cre], Ashley D. Stasko [aut, ctb], Heidi K. Swanson [aut, ctb]
Date of publication
2014-07-25 21:15:59
Maintainer
Martin Lysy <mlysy@uwaterloo.ca>
License
GPL-2
Version
1.0

View on CRAN

Man pages

ellipse
Point coordinates for a 2-D ellipse.
fish
Fish stable isotope dataset.
niche.par.plot
Plot for niche parameters
niche.plot
Plot for 2-d projection of niche regions
nicheROVER
(Niche) (R)egion and Niche (Over)lap Metrics for...
niiw.post
Random draws from the posterior distribution with...
niw.coeffs
Posterior coefficients of the Normal-Inverse-Wishart...
niw.mom
Mean and variance of the Normal-Inverse-Wishart distribution.
niw.post
Random draws from the posterior distribution with...
overlap
Monte Carlo calculation of niche region overlap metrics
overlap.plot
Plot the overlap metric
rniw
Random draws from a Normal-Inverse-Wishart distribution.
rwish
Random draws from a Wishart (or Inverse-Wishart)...

Files in this package

nicheROVER
nicheROVER/inst
nicheROVER/inst/doc
nicheROVER/inst/doc/ecol-vignette.html
nicheROVER/inst/doc/ecol-vignette.R
nicheROVER/inst/doc/ecol-vignette.Rmd
nicheROVER/NAMESPACE
nicheROVER/data
nicheROVER/data/fish.rda
nicheROVER/R
nicheROVER/R/niw.coeffs.R
nicheROVER/R/niche.par.plot.R
nicheROVER/R/ellipse.R
nicheROVER/R/niw.mom.R
nicheROVER/R/rniw.R
nicheROVER/R/nicheROVER-package.R
nicheROVER/R/niiw.post.R
nicheROVER/R/overlap.R
nicheROVER/R/niche.plot.R
nicheROVER/R/rwish.R
nicheROVER/R/ecol-package2.R
nicheROVER/R/overlap.plot.R
nicheROVER/R/niw.post.R
nicheROVER/vignettes
nicheROVER/vignettes/ecol-vignette.Rmd
nicheROVER/MD5
nicheROVER/build
nicheROVER/build/vignette.rds
nicheROVER/DESCRIPTION
nicheROVER/man
nicheROVER/man/nicheROVER.Rd
nicheROVER/man/niw.post.Rd
nicheROVER/man/niw.coeffs.Rd
nicheROVER/man/ellipse.Rd
nicheROVER/man/niche.plot.Rd
nicheROVER/man/overlap.Rd
nicheROVER/man/overlap.plot.Rd
nicheROVER/man/rniw.Rd
nicheROVER/man/fish.Rd
nicheROVER/man/niche.par.plot.Rd
nicheROVER/man/niw.mom.Rd
nicheROVER/man/niiw.post.Rd
nicheROVER/man/rwish.Rd