# Isolation Forest-Based Presence-Only Species Distribution Modeling

## 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.