# Isolation Forest-Based Presence-Only Species Distribution Modeling

## Documentation for package ‘itsdm’ version 0.1.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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.
dim_reduce | Reduce dimensions using auto-correlation between numeric raster layers.
evaluate_po | Evaluate the model based on presence-only data.
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 | Function to run extended isolation forest as SDM.
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.EnvironmentalOutlier | Function to plot suspicious outliers in an observation dataset.
plot.IndependentResponse | Function to plot independent response curves.
plot.MarginalResponse | Function to plot marginal response curves.
plot.PAConversion | Function to plot results of conversion to PA.
plot.POEvaluation | Function to plot presence-only evaluation.
plot.ShapDependence | Function to plot variable dependence obtained from SHAP test.
plot.SpatialResponse | Function to plot spatial variable dependence maps.
plot.VariableAnalysis | Function to plot variable importance.
plot.VariableContribution | Function to plot variable contribution for target observations.
print.EnvironmentalOutlier | Print summary information from PAConversion object.
print.PAConversion | Print summary information from PAConversion object.
print.POEvaluation | Print summary information from presence-only evaluation object.
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.
probability | Estimate suitability on stars object using trained 'isolation.forest' model.
shap_dependence | Calculate Shapley value based variable dependence.
spatial_response | Calculate spatial response or dependence plot.
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.