Ördin 4

Next-Gen Open-Source Community Ecology Workbench

Real R statistics (vegan · iNEXT · betapart) running in the browser and on the desktop — no R installation required

Features • Quick start • Architecture • Documentation • Citation

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🌟 Why Ördin?

Most ecological analysis software forces a trade-off: friendly tools lack statistical rigour, rigorous tools lack usability. Ördin 4 keeps the rigour (the same vegan/iNEXT code a reviewer would expect) and drops the friction — it runs R in WebAssembly via webR, so there is nothing to install on a user's machine.

At a glance

	Ördin 4
Runtime	webR (R 4.4 compiled to WASM) + DuckDB-WASM for data
Delivery	Web app (ordin.in4metrix.dev), Tauri desktop bundle, installable PWA
Panels	Dashboard, Data, Diversity, Ordination, Tests, Beta, Classification, Traits, Settings, Help
Ordination	NMDS, PCA, CA, DCA, PCoA, CCA, RDA, db-RDA, CAP (+ varpart, forward selection)
Diversity	iNEXT rarefaction/extrapolation (Hill q=0/1/2, types 1–3) + classic indices
Beta diversity	Baselga turnover/nestedness partitioning, LCBD/SCBD
Tests	PERMANOVA, PERMDISP, ANOSIM, Mantel, envfit, anova.cca
Projects	.ordin bundle = data + analyses + provenance, portable across web/desktop
Offline	Desktop bundles webR + packages; web caches them after first load

Provenance first. Every result is labelled with how it was produced (REAL … via webR vs. mock preview data), so you always know whether a number came from R.

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✨ Key features

📊 Analysis panels

• Data (1) — CSV/Excel/Parquet import into DuckDB-WASM, virtualised grid preview, decostand transforms (Hellinger, chord, log, Wisconsin, presence/absence) with live preview, SQL inspector.
• Diversity (2) — iNEXT rarefaction & extrapolation: q = 0/1/2, abundance / incidence-raw / incidence-freq, sample-size (type 1), coverage (type 3) and completeness (type 2) curves, bootstrap CIs.
• Beta (3) — vegdist dissimilarities, Baselga partitioning (beta.pair, beta.multi), beta.div.comp replacement/richness-difference components.
• Ordination (4) — unconstrained (PCA, CA, DCA, PCoA, NMDS) and constrained (RDA, CCA, db-RDA, CAP, partial models) with DCA gradient-length adviser, varpart and ordiR2step.
• Tests (5) — adonis2, betadisper, anosim, mantel/mantel.partial, envfit, restricted permutation designs.
• Classification — hierarchical clustering (Ward D2, average, complete), k-means, cophenetic correlation and silhouette diagnostics (JS fast path, R verification).
• Traits — community-weighted means, RLQ / fourth-corner, functional diversity hooks (FD, picante).

🎨 Interface

• VS Code-inspired shell: activity bar, collapsible sidebar, right inspector, status bar, workflow footer.
• Command palette (Ctrl/Cmd + K), sidebar toggle (Ctrl/Cmd + B), inspector toggle (Ctrl/Cmd + I).
• Plot customisation panel (themes, typography, points/lines, grids, CI ribbons, legends, facets) applied without re-running analyses.
• Optional MapLibre + deck.gl site map for datasets with lon/lat columns — statistics first, maps only when useful.
• Plugin marketplace scaffold for optional analysis modules.

📤 Export

• Publication-quality figures (SVG/PNG, configurable DPI and dimensions).
• Tabular exports (CSV, JSON, Parquet) and reproducible R snippets per panel.
• .ordin project files bundling data, results and provenance.

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🚀 Quick start

Use it online

Open https://ordin.in4metrix.dev — no install. The first load fetches webR and the R package bundle, then caches them for offline use.

Run from source

git clone https://github.com/jm0535/0rdin.git
cd 0rdin
npm install          # Node.js >= 22
npm run dev          # Vite dev server on http://localhost:9054

Other workspace scripts:

Command	What it does
npm run dev	Dev server for apps/ordin-desktop (port 9054, bound to 0.0.0.0)
npm run build	Type-check + production build to apps/ordin-desktop/dist
npm run preview	Serve the production build locally
npm run tauri:dev	Run the desktop shell in dev mode
npm run typecheck	tsc --noEmit across all workspaces
npm run lint	ESLint over apps, packages, workers, tests
npm test	Workspace test suites
npm run test:frontend	Node test runner over tests/*.test.ts

Cross-origin isolation. Real R execution needs SharedArrayBuffer, which requires the COOP/COEP headers already configured in vercel.json and the Vite dev server. Sandboxed iframe previews without those headers fall back to mock results, clearly labelled in the UI.

Build the desktop app

npm run tauri:build -w ordin-desktop

Requires the Tauri prerequisites for your platform (Rust toolchain, plus WebKitGTK on Linux). Bundles land in the Tauri target/release/bundle directory and ship webR offline — end users never install R.

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🧱 Architecture

0rdin/
├── apps/
│   └── ordin-desktop/        # Vite + React 18 app (also the Tauri front end)
│       └── src/
│           ├── components/layout/   # ActivityBar, Sidebar, RightInspector, CommandPalette, …
│           ├── components/panels/   # Dashboard, Data, Diversity, Ordination, Tests, Beta, …
│           └── components/map/      # optional MapLibre + deck.gl view
├── packages/
│   ├── core/                 # Zustand store, OrdinProject schema (zod), panel types
│   ├── processing/           # webR bridge + JS fast paths (distances, hclust, k-means, CWM)
│   ├── ui/                   # shared primitives (Button, Card, Badge, Dialog, Sheet, …)
│   └── map/                  # MapLibre helpers
├── docs/                     # documentation + GitHub Pages site
├── sample-data/              # example datasets
├── scripts/ · tools/ · ci/   # build helpers, linters, R CI bootstrap
├── shiny/ · src/             # legacy v3 Shiny + Electron app (maintenance only)
└── vercel.json               # COOP/COEP headers for SharedArrayBuffer

Data flows file → DuckDB-WASM → typed store (@ordin/core) → analysis call (@ordin/processing) → panel render. Analyses run in webR when cross-origin isolation is available; lightweight JS implementations provide instant previews and a deterministic fallback.

Details: docs/ARCHITECTURE.md · docs/DEVELOPMENT.md · docs/API.md · docs/ORDIN_STACK_AUDIT_2026-09-26.md.

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📚 Documentation

Start at the documentation index.

Core

• Quick start — install, first analysis
• Architecture — stack, data flow, webR bridge
• Development guide — monorepo workflow, testing, releases
• API reference — @ordin/core, @ordin/processing, @ordin/ui, @ordin/map
• Workflow · Features overview

Analysis guides (docs/guides/)

• Ordination · CCA/RDA · Biplots
• Data structure · Data management
• Incidence vs abundance · Estimates & rarefaction types
• Plot customisation · Export features

Setup & publishing (docs/setup/) — Linux · WSL · Fedora · Publishing · GitHub Pages

Development (docs/development/) — Project overview · Reproducibility · Security audit · Test checklist

Community — Contributing · Code of Conduct · Code standards · Security policy · Changelog

Documents describing the v3 Shiny/Electron application are marked with a legacy banner at the top. They remain accurate for the shiny/ tree, which is kept for reference and maintenance only.

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🧪 Data format

A species matrix is a table with sites in rows and taxa in columns:

Site	Species_A	Species_B	Species_C
Site1	12	0	3
Site2	5	7	0

Environmental tables share the same site column and hold numeric or factor variables; trait tables are taxa × traits. Incidence-raw data uses one matrix per assemblage; incidence-frequency data uses the number of sampling units in the first cell. See docs/guides/DATA-STRUCTURE-GUIDE.md.

Sample datasets live in sample-data/ and dune, varespec and BCI can be loaded directly from the Data panel.

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🔁 Migrating from Ördin 3

v3 (Shiny + Electron)	v4 (React + webR)
Requires local/portable R install	R ships as WASM, zero install
npm start (Electron + Shiny server on port 9054)	npm run dev (Vite on port 9054)
Analyses in the R process	Analyses in webR worker, JS fast paths for previews
Results tied to the session	.ordin project files with provenance
Legacy code in shiny/, src/	Active code in apps/, packages/

The legacy app is still runnable — see docs/DEVELOPMENT.md.

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🤝 Contributing

Issues and pull requests are welcome. Please read .github/CONTRIBUTING.md and run npm run lint && npm run typecheck && npm test before opening a PR.

License

MIT — see LICENSE.

Author

Jimmy Moses (jimmy.moses@pnguot.ac.pg)

Acknowledgments

• Built with Tauri, React, Vite, Zustand, DuckDB-WASM and deck.gl
• R in the browser thanks to webR
• Statistics powered by vegan, iNEXT, betapart and adespatial
• Design inspiration from CANOCO 5 and VS Code

Support

• Issues: GitHub Issues
• Discussions: GitHub Discussions
• Email: jimmy.moses@pnguot.ac.pg

Citation

Moses, J. (2026). Ördin 4: A browser-native and desktop workbench for community ecology analysis.
GitHub repository: https://github.com/jm0535/0rdin