xnicher-package: xnicher: Estimates Ecological Niche Models Using Ellipses

In xnicher: Estimates Ecological Niche Models Using Ellipses

xnicher: Estimates Ecological Niche Models Using Ellipses

Description

Ecological niche model estimation using ellipsoidal geometry under an M hypothesis. Fits nine likelihood families (presence-only, weighted, inverse-probability-weighted, skew-normal, skew-normal-weighted, skew-t, skew-t-weighted, ncst, and ncst-weighted) via multi-start optimisation with Sobol sequences. Methods for the optimisation of ellipses parameters are as described in Jimenez et al. (2022) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.ecolmodel.2021.109823")}.

Estimates ecological niche models by fitting multivariate distributions (Gaussian, skew-normal, skew-t, or non-central skew-t) to species occurrence data in environmental space.

Likelihood families

Nine likelihood formulations are available via [optimize_niche()]:

"presence_only"

Multivariate normal density estimated from presence records alone (Jimenez et al. 2019, Eq. 2).

"weighted"

Paper-faithful weighted-normal model with KDE weights accounting for the density of available environments in M (Jimenez & Soberon 2022, Eq. 5/8), plus a ridge prior on \log\sigma. Default and recommended.

"ip_weighted"

Inverse-probability-weighted (IPW) normal. Assumes the Jimenez et al. (2019) DGP (presences drawn from f restricted to M) and uses w = 1/\hat{g} (Horvitz–Thompson correction) to estimate the fundamental niche on uniform environmental space (Lebesgue measure), removing the distortion caused by non-uniform environmental density in M. See loglik_niche_math_ip_weighted for the full derivation, model comparison, and known limitations. Formerly "kde_bias_corrected".

"skew_normal"

Presence-only multivariate skew-normal (Azzalini & Capitanio 1999).

"skew_normal_weighted"

Weighted skew-normal (Eq. 8 with skew-normal density).

"skew_t"

Presence-only non-central skew-t (Branco & Dey 2001) via 32-node Gauss-Laguerre quadrature.

"skew_t_weighted"

Weighted skew-t (Eq. 8 with NCST density).

"ncst"

Presence-only non-central skew-t (Hasan & Chen 2025) with the location entering before chi-squared scaling.

"ncst_weighted"

Weighted non-central skew-t.

See the package website for the full mathematical specification of each model.

Author(s)

Maintainer: Angel Robles [e-mail]

Authors:

• Angel Robles [e-mail]

• Laura Jimenez [e-mail] (ORCID) [contributor]

References

Jimenez, L., Soberon, J., Christen, J. A., & Soto, D. (2019). On the problem of modeling a fundamental niche from occurrence data. Ecological Modelling, 397, 109823. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.ecolmodel.2019.01.009")}

Jimenez, L., & Soberon, J. (2022). Weighted-normal model for the fundamental niche. Ecological Modelling, 438, 109982.

Azzalini, A., & Capitanio, A. (1999). Statistical applications of the multivariate skew normal distribution. J. R. Stat. Soc. B, 61(3), 579–602.

Branco, M. D., & Dey, D. K. (2001). A general class of multivariate skew-elliptical distributions. J. Multivariate Anal., 79(1), 99–113.

See Also

Useful links:

• https://github.com/alrobles/xnicher

• Report bugs at https://github.com/alrobles/xnicher/issues

xnicher documentation built on Sept. 15, 2026, 5:08 p.m.