Function reference • ntbox

Launch the GUI Graphical User Interface
`run_ntbox()`	Function to run NicheToolBox shinyApp
Setting & getting environmental data Find an appropiate source of E-data and read it in R.
`get_bio_oracle()`	get_bio_oracle: Get environmental layers from Bio-Oracle.
`get_chelsa()`	get_chelsa: Get bioclimatic layers from CHELSA
`get_envirem_clim()`	get_envirem_clim: Get bioclimatic data from envirem
`get_envirem_elev()`	get_envirem_elev: Get elevation data from envirem
`rlayers_ntb()`	Function to read raster layers with the same extent and resolution in all `raster` acepted formats
Geographic data Look for GBIF data (https://www.gbif.org/), curate from spatial duplictes estimate a bias layer.
`searh_gbif_data()`	Function to search and download gbif data
`occs_history()`	Function to visualize GIBIF data using googleVis
`clean_dup()`	Function to clean duplicated longitude and latitude data
`biaslayer()`	biaslayer: Function to create a bias layer
Niche space (exploration and filtering)
`correlation_finder()`	Function to find out strong correlations in a correlation matrix
`ellipsoid_cluster_plot_3d()`	Function to plot clusters in 3-dimensions.
`inEllipsoid()`	inEllipsoid: Determine if a point is inside or outside an ellipsoid
`sample_envbg()`	Generate random environmental background data
Ecological Niche Modeling Ellispoid modeling functions and MaxEnt calls
`cov_center()`	Function to compute the Minimum Volume covariance Matrix of an ellipsoid niche model.
`ellipsoidfit()`	Function fit an ellipsoid model
`ellipsoid_selection()`	ellipsoid_selection: Performs variable selection for ellipsoid models
`maxent_call()`	maxent_call: Call maxent from R
`swd_format()`	swd_format: Prepare data in Maxents swd format.
SDM performance Model evaluation and thresholding
`bin_model()`	bin_model: Binarize a model using a threshold
`binomial_test()`	Binomial significance test for ecological niche models.
`confu_mat_optim()`	Function to find the cut-off threshold that optimizes the confusion matrix
`ellipsoid_omr()`	ellipsoid_omr
`omission_rate()`	Compute omission rate of a model
`pROC()`	Partial ROC calculation for Niche Models
Extrapolation risk assessment Tools to explore extrapolation risk in ENM
`exdet_univar()`	Exdet univariate: NT1 metric, univariate extrapolation risk analysis for model transfer
`exdet_multvar()`	Exdet multivariate: NT2 metric, multivariate extrapolation risk analysis for model transfer
`mop()`	MOP: Extrapolation risk analysis for model transfer
`ntb_mess()`	ntb_mess: Multivariate Environmental Similarity Surfaces (MESS)
GIS tools Transform into Principal Componets you E-layers
`spca()`	spca: Principal Component Analysis for Spatial Data
Helper functions Functions that perform calculations inside other functions
`nc()`	nc: Function to check the number of available cores
`plot_out()`	Detection of environmental values outside the calibration area of a model
`trapozoid_roc()`	Trapezoidal integration for Partial ROC curve

Reference

Launch the GUI

Setting & getting environmental data

Geographic data

Niche space (exploration and filtering)

Ecological Niche Modeling

SDM performance

Extrapolation risk assessment

GIS tools

Helper functions