Package index • spesim

All functions

calculate_distance_decay(): Distance-Decay Data

calculate_occupancy_abundance(): Occupancy-Abundance Table

calculate_quadrat_environment(): Summarise mean environmental conditions per quadrat

calculate_rank_abundance(): Rank-Abundance Data

calculate_rarefaction(): Rarefaction Curves Data

calculate_species_area(): Species-Area (Accumulation) Data

create_abundance_matrix(): Build a site-by-species abundance matrix from point–polygon overlaps

create_environmental_gradients(): Create synthetic environmental gradients over a spatial domain

create_sampling_domain(): Create an irregular sampling domain polygon

generate_advanced_panel(): Advanced Analysis Panel (rank/occupancy/SAR/decay/rarefaction + optional PPC)

generate_fisher_log_series(): Generate Fisher's log-series abundances with a dominant species

generate_heterogeneous_distribution(): Generate a heterogeneous community (point process + environment + interactions)

load_config(): Load Simulation Configuration (with defaults & validation)

load_interactions(): Load interspecific interaction settings (radius + matrix)

load_interactions_inline(): Parse inline interaction rules from the init file

place_quadrats(): Random Non‑Overlapping Quadrat Placement

place_quadrats_systematic(): Systematic Grid Quadrat Placement

place_quadrats_tiled(): Tiled (Systematic Cell) Quadrat Placement

place_quadrats_transect(): Parallel‑Transect Quadrat Placement

place_quadrats_voronoi(): Voronoi‑based Quadrat Placement

plot_distance_decay(): Plot Distance-Decay Relationship

plot_occupancy_abundance(): Plot Occupancy-Abundance Relationship

plot_rank_abundance(): Plot Rank-Abundance Curve

plot_rarefaction(): Plot Rarefaction Curves

plot_spatial_sampling(): Plot the spatial sampling simulation (domain, individuals, quadrats, optional gradient)

plot_species_area(): Plot Species-Area Relationship (SAR)

print_interactions(): Pretty-print a compact interaction matrix summary

read_latest_report(): Read the most recent simulation report from an output directory

rthomas_fast(): Fast Thomas Process (Rcpp-backed) in an arbitrary polygon

run_spatial_simulation(): Run the full spatial sampling simulation

simulate_points_geyer_fast(): Fast Geyer saturation simulator (bbox Metropolis–Hastings)

simulate_points_strauss_fast(): Fast Strauss simulator (Rcpp backend) returning an sf point layer

validate_interactions(): Validate an interaction specification