Isolation Forest-Based Presence-Only Species Distribution Modeling

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Documentation for package ‘itsdm’ version 0.2.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

itsdm-package	Isolation forest-based presence-only species distribution modeling
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	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.ShapDependence	Show variable dependence plots and variable interaction plots obtained from Shapley values.
plot.SHAPSpatial	Display Shapley values-based spatial variable dependence maps.
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.