#MoonBit Reef Connect

#Why it is useful

• Which reef patches export or receive the most larval flow?
• Which paths and stepping-stone nodes keep a network connected?
• How does a planned failure sequence change connectivity retention?
• Which MPA candidates balance protected area, retention, and portfolio score?

#Capabilities

• RK4 advection-diffusion particle simulation with larval PLD, mortality, competency, settlement, and out-of-bounds outcomes.
• Dense and sparse transition matrices, normalization, matrix powers, eigensystems, decompositions, Markov-chain helpers, and quality diagnostics.
• Directed reef graphs with centrality, community, flow, shortest paths, reachability, source/sink ranking, and ordered-failure robustness curves.
• Greedy, genetic, and simulated-annealing MPA optimizers with candidate normalization, Pareto-frontier extraction, and sensitivity analysis.
• Validation and statistics primitives, including confidence intervals, quantiles, flow-field checks, scenario grids, and risk/monitoring decisions.
• JSON, CSV, GeoJSON, Markdown, and HTML/SVG export paths.

#Repository layout

src/
├── types/       Geometry, reef nodes, larval traits, flow fields, and validation
├── simulation/  Particle lifecycle, settlement, ensembles, diagnostics, and replicates
├── matrix/      Dense/CSR matrices, decompositions, Markov analysis, and diagnostics
├── network/     Graph algorithms, centrality, paths, reachability, and robustness
├── mpa/         Portfolio constraints, optimizers, Pareto analysis, and stress tests
├── io/          JSON/CSV/GeoJSON/HTML exports and benchmark report formatting
├── cli/         Sample fixtures, analysis pipeline, and benchmark command
└── main.mbt     Command-line entry point

#Quick start

moon version --all

moon fmt --check
moon check --target all --deny-warn
moon test --target all --deny-warn

moon run src/main.mbt -- sim

moon run src/main.mbt -- json
moon run src/main.mbt -- geojson
moon run src/main.mbt -- csv
moon run src/main.mbt -- benchmark

#Library workflow

let diagnostics = @matrix.validate_transition_matrix(transition_matrix)
let graph = @network.ReefGraph::from_dispersal_matrix(reefs, transition_matrix)
let route = @network.compute_weighted_path(graph, source_idx, target_idx)
let summary = @simulation.SimulationDiagnostics::from_result(simulation_result)

#Continuous integration

#License