Package index • itsdm

All functions

cmcc_bioclim(): Download historic Bioclimatic indicators (BIOs) named CMCC-BioClimInd.

convert_to_pa(): Convert predicted suitability to presence-absence map.

detect_envi_change(): Detect areas influenced by a changing environment variable.

dim_reduce(): Remove environmental variables that have high correlation with others.

evaluate_po(): Evaluate the model based on presence-only data.

format_observation(): Format the occurrence dataset for usage in itsdm

future_cmcc_bioclim(): Download future Bioclimatic indicators (BIOs) named CMCC-BioClimInd.

future_worldclim2(): A function to parse the future climate from worldclim version 2.1.

independent_response(): Calculate independent responses of each variables.

isotree_po(): Build Isolation forest species distribution model and explain the the model and outputs.

itsdm-package itsdm: Isolation forest-based presence-only species distribution modeling

mainland_africa: Boundary of mainland Africa

marginal_response(): Calculate marginal responses of each variables.

occ_virtual_species: Occurrence dataset of a virtual species

plot(<EnviChange>): Display the figure and map of the EnviChange object.

plot(<EnvironmentalOutlier>): Exhibit suspicious outliers in an observation dataset.

plot(<IndependentResponse>): Show independent response curves.

plot(<MarginalResponse>): Show marginal response curves.

plot(<PAConversion>): Display results of conversion to presence-absence (PA).

plot(<POEvaluation>): Show model evaluation.

plot(<SHAPSpatial>): Display Shapley values-based spatial variable dependence maps.

plot(<ShapDependence>): Show variable dependence plots and variable interaction plots obtained from Shapley values.

plot(<SpatialResponse>): Display spatial variable dependence maps.

plot(<VariableAnalysis>): Display variable importance.

plot(<VariableContribution>): Exhibit variable contribution for target observations.

print(<EnviChange>): Print summary information from EnviChange object.

print(<EnvironmentalOutlier>): Print summary information from EnvironmentalOutlier object.

print(<FormatOccurrence>): Print summary information from FormatOccurrence object.

print(<PAConversion>): Print summary information from PAConversion object.

print(<POEvaluation>): Print summary information from model evaluation object (POEvaluation).

print(<POIsotree>): Print summary information from POIsotree object.

print(<ReducedImageStack>): Print summary information from ReducedImageStack object.

print(<VariableAnalysis>): Print summary information from variable importance object (VariableAnalysis).

probability(): Estimate suitability on stars object using trained isolation.forest model.

shap_dependence(): Calculate Shapley value-based variable dependence.

shap_spatial_response(): Calculate shapley values-based spatial response.

spatial_response(): Calculate spatial response or dependence figures.

suspicious_env_outliers(): Function to detect suspicious outliers based on environmental variables.

variable_analysis(): Function to evaluate relative importance of each variable.

variable_contrib(): Evaluate variable contributions for targeted observations.

worldclim2(): Download environmental variables made by worldclim version 2.1.