Package index • spesim

Getting started

spesim_demo(): Run a compact spesim demonstration workflow
spesim_method_test(): Run a method-testing bundle (simulate + audit + standard outputs)
spesim_run(): Run a complete spesim simulation (recommended)
load_config(): Load Simulation Configuration (with defaults & validation)
validate_config(): Validate a spesim configuration (without running the simulation)
list_examples(): List shipped example configuration files
spesim_use_example(): Copy a shipped example init file into your working directory
spesim_open_docs(): Open spesim documentation pages in your browser

run_spatial_simulation(): Run the full spatial sampling simulation (legacy wrapper)
generate_heterogeneous_distribution(): Generate a heterogeneous community (point process + environment + interactions)
create_sampling_domain(): Create a random sampling domain polygon
create_environmental_gradients(): Create synthetic environmental gradients over a spatial domain
create_abundance_matrix(): Build a site-by-species abundance matrix from point–polygon overlaps
calculate_quadrat_environment(): Summarise mean environmental conditions per quadrat

place_quadrats(): Random Non‑Overlapping Quadrat Placement
place_quadrats_route(): Route-Based Quadrat Placement for Linearized Domains
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_quadrats(): Plot a sampling domain with quadrats
plot_spatial_sampling(): Plot the spatial sampling simulation (domain, individuals, quadrats, optional gradient)
plot_filtering_response(): Plot environmental filtering responses (sanity check)
theme_spesim(): A consistent ggplot2 theme for spesim teaching plots

generate_advanced_panel(): Advanced Analysis Panel (rank/occupancy/SAR/decay/rarefaction + optional PPC)
generate_full_report(): (Advanced) Build a human-readable multi-section report
calculate_rank_abundance(): Rank-Abundance Data
plot_rank_abundance(): Plot Rank-Abundance Curve
calculate_occupancy_abundance(): Occupancy-Abundance Table
plot_occupancy_abundance(): Plot Occupancy-Abundance Relationship
calculate_species_area(): Species-Area (Accumulation) Data
plot_species_area(): Plot Species-Area Relationship (SAR)
calculate_distance_decay(): Distance-Decay Data
plot_distance_decay(): Plot Distance-Decay Relationship
calculate_rarefaction(): Rarefaction Curves Data
plot_rarefaction(): Plot Rarefaction Curves

load_interactions(): Load interspecific interaction settings (radius + matrix)
load_interactions_inline(): Parse inline interaction rules from the init file
validate_interactions(): Validate an interaction specification
print_interactions(): Pretty-print a compact interaction matrix summary

rthomas_fast(): Fast Thomas Process (Rcpp-backed) in an arbitrary polygon
simulate_points_strauss_fast(): Fast Strauss simulator (Rcpp backend) returning an sf point layer
simulate_points_geyer_fast(): Fast Geyer saturation simulator (Rcpp backend; polygon-clipped)

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

spesim_from_observed(): Build a spesim_result directly from observed data
build_network_edges(): Build network edges from ordered sites
simulate_between_observed(): Simulate unsampled sites between observed sites
place_quadrats_route(): Route-Based Quadrat Placement for Linearized Domains

spesim_audit(): Audit whether a spesim run matches the intended qualitative regime
spesim_regime(): Classify whether a spesim run matches the intended qualitative regime
audit_spatial_structure(): Audit spatial structure via nearest-neighbour distances
audit_environmental_filtering(): Audit environmental filtering (optima/tolerances vs realised abundances)
audit_sampling_scheme(): Audit quadrat placement: boundary exclusion and rejection metrics
spesim_spatstat_diagnostics(): Spatstat diagnostics for one or more species

sad_generators: Species abundance distribution (SAD) generators
generate_sad(): Generate a species abundance distribution (SAD)
generate_fisher_log_series(): Generate Fisher's log-series abundances with a dominant species
generate_geometric_probabilities(): Geometric-series (niche pre-emption) SAD probabilities
generate_brokenstick_probabilities(): Broken-stick SAD probabilities
generate_zipf_probabilities(): Zipf / Zipf–Mandelbrot SAD probabilities
generate_lognormal_probabilities(): Lognormal SAD probabilities (weights)

spesim_result spesim_quadrats summary_spesim_result: spesim_result objects