Package: xnicher 1.0.0

xnicher: Estimates Ecological Niche Models Using Ellipses

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) <doi:10.1016/j.ecolmodel.2021.109823>.

Authors:Angel Robles [aut, cre], Laura Jimenez [aut, ctb]

xnicher_1.0.0.tar.gz
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xnicher_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
xnicher/json (API)

# Install 'xnicher' in R:
install.packages('xnicher', repos = c('https://alrobles.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/alrobles/xnicher/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • 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.
  • rhipicephalus - Rhipicephalus microplus occurrence and background environment data
  • rhipicephalus_occ - Rhipicephalus microplus occurrence coordinates

On CRAN:

Conda:

cpp

3.18 score 9 scripts 22 exports 7 dependencies

Last updated from:ba5f206f67. Checks:15 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK208
linux-devel-x86_64OK211
source / vignettesOK247
linux-release-arm64OK208
linux-release-x86_64OK203
macos-release-arm64OK420
macos-release-x86_64OK376
macos-oldrel-arm64OK147
macos-oldrel-x86_64OK315
windows-devel-arm64OK260
windows-devel-x86_64OK301
windows-release-arm64OK277
windows-release-x86_64OK298
windows-oldrel-x86_64OK243
wasm-releaseOK169

Exports:assesscompare_xnichercv_xnichercvine_choleskygeom_xnicher_backgroundgeom_xnicher_ellipsegeom_xnicher_isosuitabilitygeom_xnicher_occget_ellipsoid_parshabitat_suitabilitykde_gaussianloglik_nicheloglik_niche_math_cpploglik_niche_math_ip_weightedloglik_niche_math_ip_weighted_integratedloglik_niche_math_presence_onlyniche_ip_weightedniche_presence_onlyoptimize_nicheoptimize_niche_xptrstart_thetastart_theta_multiple

Dependencies:backportscheckmateRcppRcppEigenRcppParallelterraucminfcpp

Readme and manuals

Help Manual

Help pageTopics
Akaike information criterion for a xnicher fitAIC.xnicher
Assess acceptance criteria for an optimization resultassess
Assess acceptance criteria for a xnicher resultassess.xnicher
Bayesian information criterion for a xnicher fitBIC.xnicher
Compare xnicher fits side-by-side via AIC and BICcompare_xnicher
k-fold (or leave-one-out) cross-validation for a xnicher fitcv_xnicher
Build Cholesky factor of a correlation matrix from C‑vine partial correlationscvine_cholesky
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 variablesexample_env_m_2d
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 variablesexample_env_m_3d
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 variablesexample_env_occ_2d
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 variablesexample_env_occ_3d
Example of a vector of the center of an ellipsoid from two environmental variables. vector of length 2 corresponding to the centroid of an ellipsoidexample_mu_vec
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_occ_df
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_s_mat
Samples of environmental data from M hypothesis to estimate negative log likelihood from Vicugna vicugna.example_vicugna
Background environment layergeom_xnicher_background
Niche-ellipse layer derived from a fitted 'xnicher' modelgeom_xnicher_ellipse
Iso-suitability contour layer derived from a fitted 'xnicher' modelgeom_xnicher_isosuitability
Occurrence-points layergeom_xnicher_occ
Get ellipsoid parameters. A function to compute average and the inverse of covariance matrix from environmental dataget_ellipsoid_pars
Tiled habitat-suitability map from an environmental 'terra' stackhabitat_suitability
Multivariate Gaussian KDE with fixed Scott bandwidthkde_gaussian
Negative log likelihood of an ellipsoid corrected with environmental combinations which come from the area of study (M)loglik_niche
Negative log-likelihood (M-restricted, math scale, Cholesky version)loglik_niche_math_cpp
Negative log-likelihood (inverse-probability-weighted normal, math scale)loglik_niche_math_ip_weighted
Negative log-likelihood (inverse-probability-weighted normal, integrated C++)loglik_niche_math_ip_weighted_integrated
Negative log-likelihood (presence-only, math scale)loglik_niche_math_presence_only
Log-likelihood of a fitted xnicher modellogLik.xnicher
Fit inverse-probability-weighted (IPW) normal niche modelniche_ip_weighted
Fit presence-only Gaussian niche modelniche_presence_only
Number of observations used to fit a xnicher modelnobs.xnicher
Optimize niche model log-likelihood with multi-start Sobol designoptimize_niche
Optimize niche model using a compiled XPtr backendoptimize_niche_xptr
Habitat-suitability raster from a fitted 'xnicher' objectpredict.xnicher
Print a xnicher objectprint.xnicher
Rhipicephalus microplus occurrence and background environment datarhipicephalus
Rhipicephalus microplus occurrence coordinatesrhipicephalus_occ
Starting values for niche model on math scalestart_theta
Generate multiple starting points for niche model optimizationstart_theta_multiple