Estimates Ecological Niche Models Using Ellipses

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Documentation for package ‘xnicher’ version 1.0.0

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AIC.xnicher Akaike information criterion for a xnicher fit
assess Assess acceptance criteria for an optimization result
assess.xnicher Assess acceptance criteria for a xnicher result
BIC.xnicher Bayesian information criterion for a xnicher fit
compare_xnicher Compare xnicher fits side-by-side via AIC and BIC
cvine_cholesky Build Cholesky factor of a correlation matrix from C‑vine partial correlations
cv_xnicher k-fold (or leave-one-out) cross-validation for a xnicher fit
example_env_m_2d Samples of environmental data from M hypothesis to estimate negative log likelihood from Abeillia abeillei presence points. This is a hummingbird example. A dataset with two variables containing points contains 2 bioclimatic variables
example_env_m_3d Samples points from M hypothesis to estimate negative log likelihood from Abeillia abeillei presence points. This is a hummingbird example. A dataset with three columns containing extracted information from 3 bioclimatic variables
example_env_occ_2d Species occurrence points to estimate negative log likelihood from Abeillia abeillei presence points. This is a hummingbird example. A dataset with two variables containing points contains 2 bioclimatic variables
example_env_occ_3d Species occurrence points to estimate negative log likelihood from Abeillia abeillei presence points. This is a hummingbird example. A dataset with three variables containing points contains 3 bioclimatic variables
example_mu_vec Example of a vector of the center of an ellipsoid from two environmental variables. vector of length 2 corresponding to the centroid of an ellipsoid
example_occ_df Species occurrence points from Abeillia abeillei presence points after download and clean from GBIF. This is a hummingbird example. A dataset with three variables. Contains scientific name, longitude and latitude.
example_s_mat Example of a covariance matrix of an ellipsoid from two environmental variables. The 2 x 2 matrix corresponded to a positive semi-definite matrix. In two dimensions encodes the rotation (orientation) and scaling of an ellipse.
example_vicugna Samples of environmental data from M hypothesis to estimate negative log likelihood from Vicugna vicugna.
geom_xnicher_background Background environment layer
geom_xnicher_ellipse Niche-ellipse layer derived from a fitted 'xnicher' model
geom_xnicher_isosuitability Iso-suitability contour layer derived from a fitted 'xnicher' model
geom_xnicher_occ Occurrence-points layer
get_ellipsoid_pars Get ellipsoid parameters. A function to compute average and the inverse of covariance matrix from environmental data
habitat_suitability Tiled habitat-suitability map from an environmental 'terra' stack
kde_gaussian Multivariate Gaussian KDE with fixed Scott bandwidth
logLik.xnicher Log-likelihood of a fitted xnicher model
loglik_niche Negative log likelihood of an ellipsoid corrected with environmental combinations which come from the area of study (M)
loglik_niche_math_cpp Negative log-likelihood (M-restricted, math scale, Cholesky version)
loglik_niche_math_ip_weighted Negative log-likelihood (inverse-probability-weighted normal, math scale)
loglik_niche_math_ip_weighted_integrated Negative log-likelihood (inverse-probability-weighted normal, integrated C++)
loglik_niche_math_presence_only Negative log-likelihood (presence-only, math scale)
niche_ip_weighted Fit inverse-probability-weighted (IPW) normal niche model
niche_presence_only Fit presence-only Gaussian niche model
nobs.xnicher Number of observations used to fit a xnicher model
optimize_niche Optimize niche model log-likelihood with multi-start Sobol design
optimize_niche_xptr Optimize niche model using a compiled XPtr backend
predict.xnicher Habitat-suitability raster from a fitted 'xnicher' object
print.xnicher Print a xnicher object
rhipicephalus Rhipicephalus microplus occurrence and background environment data
rhipicephalus_occ Rhipicephalus microplus occurrence coordinates
start_theta Starting values for niche model on math scale
start_theta_multiple Generate multiple starting points for niche model optimization