Isolation Forest-Based Presence-Only Species Distribution Modeling


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Documentation for package ‘itsdm’ version 0.1.1

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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.