Martin Lysy, Ashley Stasko, Heidi Swanson
This R 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. 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.
The CRAN version (1.1.2) is available here.
For the GitHub development version, first install the R package devtools, then run
devtools::install_github("mlysy/nicheROVER", ref = "master")
A step-by-step walkthrough of a basic analysis is provided in the package vignette.
Find the basic niche.plot() and niche.par.plot() options a bit rigid? This blog post shows how to create equivalent plots from scratch using ggplot2, which can then be customized at will.