isoniche: abundance-independent habitat niche breadth

Estimates the habitat niche breadth of species from counts in several habitats, corrected for abundance with isodars (Granot, Dubiner & Belmaker 2026). For each species it reports density-independent (DI) niche breadth, how widely the species uses habitats when rare; density-dependent (DD) niche breadth, how widely it uses them when abundant; and the curve of niche breadth against abundance between the two.

A typical analysis

1. Put the data in long format, one row per species x site x habitat (community_to_long() converts a community matrix).

2. Check sampling coverage with check_coverage(); group nearby sites with group_sites() if sites are small or incomplete.

3. Estimate niche breadth with niche_breadth() and check the diagnostics with summary().

4. Plot niche breadth against abundance with iai_curve() and plot.iai_curve().

Start with vignette("isoniche"); see also vignette("data-preparation"), vignette("diagnostics") and vignette("method").

Lower-level functions

fit_isodars() fits pairwise or n-dimensional isodars; iai() computes niche breadth from fitted isodars at given total abundances; isoderr() bootstraps it for one species; pairwise_niche() gives indices from the isodar parameters; simulate_isodars() simulates data from known isodars.

References

Granot, I., Dubiner, S. & Belmaker, J. (2026). Why abundance-based indices of niche breadth are biased, and what can be done to improve them. Ecology Letters (in revision).

See also

Useful links:

• https://itai811.github.io/isoniche/

• https://github.com/itai811/isoniche

• Report bugs at https://github.com/itai811/isoniche/issues

Author

Maintainer: Itai Granot itai811@gmail.com (Contributed equally with Shahar Dubiner)

Authors:

• Shahar Dubiner dubiner@mail.tau.ac.il (ORCID) (Contributed equally with Itai Granot)

• Jonathan Belmaker (ORCID)