Protocols and Software

The Peterson Lab group has a long tradition of conceptualizing and developing protocols and software for diverse analyses in distributional ecology and related topics. Links to publications or sources of the software or protocols are provided with the name of the protocol or package.

KUENM

KUENM represents a shell built around the very popular Maxent algorithm, which allows a unique, three-way filtering of candidate models, based on statistical significance, predictive performance, and model complexity. Github.

GRINNELL

One long-term challenge in distributional ecology has been that of delimiting calibration areas for modeling. GRINNELL is a simulation-based solution to this problem, which takes into account ecological niche, dispersal, and real-world landscapes in geographic and environmental spaces. Github.

BIOSURVEY

Biodiversity surveys are often planned in geographic spaces (e.g., random points, grids, transects), but have not generally been extended over the Hutchinsonian Duality (i.e., linked geographic and environmental spaces). BIOSURVEY performs a variety of optimizations of surveys that take into account both of these spaces for any defined region. Github.

NICHEVOL

The nichevol R package helps users to perform critical steps in the process of assessment of species’ ecological niche evolution, with uncertainty incorporated explicitly in phylogenetic reconstructions. Code. Guide.

The protocols presented here help to detect signals of species’ ecological niches in results of studies with defined sampling protocols. Code includes an example application to pathogen niches. Code.

NICHE SIGNAL

ELLIPSENM

The ellipsenm R package implements multiple tools to help in using ellipsoid envelopes to model ecological niches of species, with options for calibrating and selecting models, producing models with replicates and projections, and assessing niche overlap. Code.