Package: ELAplus 1.0.2

Overview | Example: Basic Energy Landscape Analysis | Input dataset | (Optional) Data generation 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 gradient ELA results | 3D plot of gradient ELA results | Appendix