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using a Gibbs sampling (heat-bath algorithm)", "Formatting the dataset", "Inputs", "Key preprocessing options", "Normalization (normalize)", "Occurrence binarization (the “0/1 threshold”)", "Species filtering by prevalence (min/max occurrence thresholds)", "Parameter fitting", "Extended maximum pairwise entropy model", "Parameter fitting algorithm", "Hyperparameter search for fitting", "What Findbp does", "Fitting results can be visualized by plotSAtest.", "Fitting the extended maximum pairwise entropy model", "Constructing the energy landscape", "ELA output", "What ELA does", "Pruning stable states", "Output and interpretation", "Basin depth and pruning criterion", "Relative depth pruning", "bootstrap samples pruning", "Visualization", "Disconnectivity graph", "How to interpret the graph", "Optional checking bootstrap resampling", "Pruning with bootstrap resampling", "Species interaction graph", "Environmental gradient analysis", "Concept of GradELA", "Output", "Visualization of 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