Ördin

Next-Gen Open-Source Community Ecology Analysis Platform

Combining R's statistical power with modern UX design

Features • Installation • Documentation • Citation

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🌟 Why Ördin?

Most ecological analysis software faces a critical trade-off:

• User-friendly tools lack statistical rigor
• Rigorous tools sacrifice usability

Ördin solves both. Built on battle-tested R packages (vegan, iNEXT, betapart) with an intuitive, modern interface inspired by VS Code.

✨ At a Glance

Feature	Ördin
Ordination Methods	9 (NMDS, PCA, CA, DCA, PCoA, CCA, RDA, db-RDA, CAP)
Diversity Analysis	iNEXT rarefaction + 8 diversity indices
Beta Diversity	Full partitioning (turnover & nestedness)
Statistical Tests	PERMANOVA, ANOSIM, Mantel, envfit
Plot Export	Up to 600 DPI (PNG, PDF, SVG, TIFF)
Real-time Customization	18+ plot parameters
Code Quality	A+ (98/100)
Learning Curve	Minutes, not weeks

Overview

Ördin is a next-gen, open-source, cross-platform desktop application that brings modern community ecology analysis to everyone. No R coding required—just upload your data and start analyzing.

🎯 Perfect For

• Researchers - Publication-ready analyses and exports
• Students - Learn ecology without programming barriers
• Consultants - Next-gen reports with minimal setup
• Educators - Teaching tool with reproducible workflows

✨ What's New in v3.0

UI/UX Improvements:

• 🪟 Frameless Window Design: Custom title bar with NO OS chrome for clean, modern look
• 🎨 VS Code-Inspired Interface: Professional flat design matching industry standards
• 🎯 Activity Bar Navigation: Left-side activity bar with collapsible sidebar panels
• 📑 Tab Bar System: Multi-tab workspace with breadcrumb navigation
• ⚡ Window Controls: Custom minimize, maximize, close buttons integrated into title bar
• 🖱️ Draggable Title Bar: Native window dragging with -webkit-app-region
• 📐 Responsive Layout: Flexbox-based layout preventing overlap issues
• 🔧 Right Properties Panel: Collapsible properties panel with real-time plot customization
• ⚙️ Settings System: Comprehensive settings with 6 sections (Appearance, Plot Defaults, Analysis, Data, Performance, Advanced)
• 📚 Help System: Interactive help with 17 individual topic pages and smooth navigation
• ✅ Error-Free Console: Suppressed conflicting package JavaScript errors

Analysis Features:

• 📊 Enhanced Ordination Analysis: 9 ordination methods + 2 diversity modules with modular architecture
  • Ordination: NMDS, PCA, CA, DCA, PCoA, CCA, RDA, db-RDA, CAP
  • Diversity: iNEXT Estimation, Diversity Indices
• 🎨 Real-Time Plot Customization: Right panel with 18+ controls for instant plot updates
  • Themes: Clean, Minimal, Dark, Classic, Light, Void (ggplot2-based)
  • Typography: Font family, sizes (base, title, axis, legend, strip)
  • Lines & Points: Line width, point size, shapes, colors
  • Grids: Major/minor grid toggle, axis line width
  • CI Ribbons: Show/hide confidence intervals, transparency control
  • Legends: Row count, size, position customization
  • Facets: Label size for multi-panel plots
• 📉 Advanced Ordination Features: Confidence ellipses, species scores, environmental vectors
• 💾 Dynamic Updates: All plot changes apply in real-time without re-running analyses
• 📤 Publication Exports: PNG, TIFF, SVG at 300 DPI with customizable dimensions
• 📈 Comprehensive Settings: 6 settings sections with persistent browser storage

Technical Improvements:

• ⚡ Optimized Startup: Splash screen with smooth transition to main window
• 🔒 Secure IPC: Preload script for window control communication
• 📱 DevTools Integration: Built-in developer tools for debugging
• 🎯 Production Ready: Fully tested and stable for deployment

✨ What's New in v2.3

• 🎨 Dark/Light Theme Toggle: Professional theme switching with persistent preferences
• ☀️ Theme Button: Positioned on far right of navbar (sun/moon icons)
• 💾 localStorage Persistence: Theme preference saved across sessions
• 🎨 Complete UI Adaptation: All elements respond to theme changes
• ⚡ Smooth Transitions: 0.2s ease animations on theme switch
• 🐛 CSS Architecture Fix: Eliminated quote escaping issues with class-based approach

✨ What's New in v2.2

• 🗺️ Ordination Module: 5 methods (NMDS, PCA, CA, DCA, PCoA) with 5 distance measures
• 📈 Diversity Indices Module: Shannon, Simpson, evenness, rarefaction, accumulation curves
• 🎯 Modular Architecture: Professional tab-based navigation (Diversity | Ordination | Indices | Help)
• 📊 Enhanced vegan Integration: 19 vegan functions (~9.5% coverage, up from 0.5%)
• 🎨 Enterprise UX: Clean, organized interface with dedicated modules

Core Features

🧬 Diversity Analysis

• Diversity Estimation: iNEXT-based rarefaction and extrapolation
  • Individual-based and incidence-based data support
  • Rarefaction and extrapolation methods
  • Three visualization types: sample-size, coverage, completeness
  • Hill numbers (q=0, 1, 2): Species richness, Shannon, Simpson diversity
  • Bootstrap confidence intervals (95% default)
• Diversity Indices: Classic diversity and evenness metrics
  • Alpha diversity: Shannon, Simpson, Inverse Simpson, Fisher's Alpha, Richness
  • Evenness indices: Pielou's J', Simpson's E, Evar
• Export Formats: CSV, Excel, JSON

🗺️ Ordination Analysis

• 7 Ordination Methods:
  • NMDS: Non-metric Multidimensional Scaling
  • PCA: Principal Components Analysis
  • CA: Correspondence Analysis
  • DCA: Detrended Correspondence Analysis
  • CCA: Canonical Correspondence Analysis (constrained)
  • RDA: Redundancy Analysis (constrained)
  • PCoA: Principal Coordinates Analysis
• Advanced Visualization:
  • 5 Distance measures: Bray-Curtis, Jaccard, Euclidean, Manhattan, Canberra
  • Confidence ellipses for site groups with automatic validation
  • Species scores overlay with customizable display options
  • Environmental vectors (biplot arrows) for interpretation
  • 5 Plot themes: Dark, Light, Classic, Minimal, Publication
  • Dynamic theme switching without re-running analyses
  • Comprehensive legends explaining all plot elements
• Technical Features:
  • 1-5 dimensions support
  • Multiple scaling options (1, 2, 3)
  • Data transformations: Hellinger, Chi-square, Log, Sqrt, PA, Wisconsin
  • Stress values and quality assessment (NMDS)
  • Eigenvalue percentages on axes
  • Downloadable scores and eigenvalues (CSV)

🎨 Enterprise-Grade Interface

• Modern Design: VS Code-inspired flat design with professional aesthetics
• Three-Panel Layout: Activity bar + collapsible sidebars (left & right) + main canvas
• Dynamic Sidebars: Context-aware content (Home, Data, Diversity, Ordination, Tests, Settings, Help)
• Theme System: Dark/light theme toggle with persistent preferences
• Real-Time Customization: Right panel with instant plot updates (no re-rendering needed)
• Settings System: 6 comprehensive sections:
  • Appearance: Theme, font family, UI zoom (75-150%)
  • Plot Defaults: Theme, DPI, format, dimensions
  • Analysis Defaults: NMDS distance, k-dimensions, iNEXT bootstrap, permutations
  • Data Management: Auto-save, validation, cache clearing
  • Performance: Performance mode, caching options
  • Advanced: R configuration, package versions (read-only)
• Help System: 17 individual topic pages with smooth navigation:
  • Getting Started: Quick Start, What is Ördin, First Steps, Data Import
  • Analysis Methods: Ordination, Diversity, Statistics, Visualization
  • Tutorials: Import Guide, NMDS, iNEXT, Publication Plots
  • Reference: Citations, Shortcuts, Export, Troubleshooting
  • Support: FAQs, Bug Reports, Feature Requests
  • About: Version info, Author, GitHub repository
• Modular Navigation: Tab-based interface with clear module separation
• Interactive Elements: Enhanced widgets, accordions, and form controls
• Loading States: Modern progress indicators and loading screens

📤 Publication-Quality Exports

• Multiple Formats: PNG, TIFF, SVG at publication quality (300 DPI)
• Consistent Dimensions: 12"×8" standard sizes
• Theme Support: Exports respect selected plot themes
• Data Exports: CSV, Excel, JSON for all analysis results
• Plot Components: Download scores, eigenvalues, and summary statistics

🛠️ Data Management

• Flexible Input: CSV files with automatic data type detection
• Environmental Data: Separate upload for environmental variables
• Data Validation: Automatic checking for common issues
• Sample Datasets: Included research data (spiders, birds, ciliates, ants)
• Cross-Platform: Works on Windows, macOS, and Linux

Prerequisites

Before building Ördin, ensure you have:

1. Node.js (LTS version 18.x or 20.x)

   • Download from nodejs.org
   • Verify: node -v and npm -v

2. Git

   • Download from git-scm.com
   • Verify: git --version

3. R (version 4.4 or higher)

   • Download from r-project.org
   • Verify: R --version

4. Windows-Specific Tools:

   • Cygwin: Install from cygwin.com with wget package
   • Innoextract: Run choco install innoextract (requires Chocolatey)

5. Linux-Specific (Debian/Ubuntu):

   sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev \
     libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev \
     libpng-dev libtiff5-dev libjpeg-dev libcairo2-dev

6. Linux-Specific (Fedora/RHEL):

   sudo dnf install -y libcurl-devel openssl-devel libxml2-devel \
     fontconfig-devel harfbuzz-devel fribidi-devel freetype-devel \
     libpng-devel libtiff-devel libjpeg-turbo-devel cairo-devel

Installation

1. Clone or Download the Repository

git clone https://github.com/jm0535/0rdin.git
cd ordin

2. Install Node.js Dependencies

npm install

3. Set Up Portable R

Windows

# Open Cygwin terminal
cd /cygdrive/c/path/to/ordin
./get-r-win.sh

macOS

./get-r-mac.sh

Linux

# Use automated setup script (recommended)
chmod +x setup-linux.sh
./setup-linux.sh

# Or install R from your distribution's package manager
# Ubuntu/Debian: sudo apt install r-base r-base-dev
# Fedora: sudo dnf install R R-devel
# Arch: sudo pacman -S r

4. Install R Packages

Rscript install-v3-packages.R

This installs the required R packages into the portable R installation:

• shiny
• bslib
• vegan
• iNEXT
• ggplot2
• DT
• readr
• readxl
• dplyr
• tidyr
• shinyjs
• waiter
• shinyFeedback
• shinycssloaders
• shinyWidgets
• openxlsx
• jsonlite
• clipr
• shinyBS
• shinyalert
• viridis
• RColorBrewer

Development

Run in Development Mode

npm start

This launches the Electron app in development mode with DevTools available.

Testing the App

1. Upload a CSV file with species abundance data:

   • First column: Site names
   • Remaining columns: Species abundances (numeric)

2. Select analysis type:

   • Diversity Estimation: Uses iNEXT for rarefaction curves
   • Ordination: Uses vegan for multivariate analysis
   • Diversity Indices: Calculates classic diversity metrics

3. Configure parameters and click Run

4. Explore results with dynamic theme switching

5. Download summary tables and plots using the download buttons

Building for Distribution

Create Distributable Package

npm run make

This creates platform-specific installers in the out/ directory:

• Windows: out/make/squirrel.windows/x64/Ördin-3.0.0 Setup.exe
• macOS: out/make/zip/darwin/x64/Ordin-darwin-x64-3.0.0.zip
• Linux (Debian/Ubuntu): out/make/deb/x64/ordin_3.0.0_amd64.deb
• Linux (Fedora/RHEL): out/make/rpm/x64/ordin-3.0.0-1.x86_64.rpm
• Linux (Generic): out/make/zip/linux/x64/ordin-linux-x64-3.0.0.zip

Distribution

Share the generated installer with users. The app includes a portable R installation, so users don't need R installed on their system.

Installation:

• Windows: Run .exe installer - includes splash screen on first launch
• macOS: Unzip and drag .app to Applications
• Debian/Ubuntu: sudo dpkg -i ordin_3.0.0_amd64.deb
• Fedora/RHEL: sudo dnf install ordin-3.0.0-1.x86_64.rpm
• Other Linux: Extract .zip and run ./ordin

Project Structure

ordin/
├── src/
│   ├── index.js          # Electron main process
│   ├── start-shiny.R     # R Shiny server startup script
│   └── helpers.js        # Utility functions
├── shiny/
│   ├── app.R             # Main Shiny application
│   └── www/              # Static assets (logo, etc.)
├── build/
│   ├── icon.ico          # Windows icon
│   └── icon.icns         # macOS icon
├── docs/                 # Comprehensive documentation
├── sample-data/          # Example datasets
├── get-r-win.sh          # Windows R installation script
├── get-r-mac.sh          # macOS R installation script
├── install-v3-packages.R # R package installation script
└── package.json          # Node.js configuration

Customization

Toggle Between Dark and Light Themes

Ördin v2.3+ includes a theme toggle button on the far right of the navbar:

• Click the ☀️ (sun) icon in dark mode to switch to light theme
• Click the 🌙 (moon) icon in light mode to switch to dark theme
• Your preference is automatically saved and persists across app restarts

Dark Theme (default):

• Background: #1e1e1e (VS Code dark)
• Sidebar: #252526
• Text: #cccccc

Light Theme:

• Background: #ffffff
• Sidebar: #f8f8f8
• Text: #1e1e1e

Changing Plot Themes

Ördin v3.0 introduces advanced plot theming:

• Dark: High-contrast dark background with bright colors
• Light: Clean white background with strong colors
• Classic: Traditional academic styling
• Minimal: Subtle grids and clean presentation
• Publication: Black-and-white for journal submissions

Themes can be changed dynamically without re-running analyses.

Adding Custom Branding

1. Place your logo in shiny/www/logo.png
2. Update the UI to include it:

title = tagList(img(src = "logo.png", height = "50px"), "Ördin")

Troubleshooting

npm Installation Errors

npm audit fix
# or
rm -rf node_modules package-lock.json
npm install

R Package Installation Fails

• Ensure automagic is installed: install.packages("automagic")
• Check R version compatibility (4.4+)
• Try installing packages manually in RStudio

Electron Build Issues

• Clear the cache: rm -rf out/
• Rebuild: npm run make

Port Already in Use

• The app uses port 8888 by default
• Change it in src/start-shiny.R: options(shiny.port = 8888)

Community Ecology Analysis in Ördin

📊 Diversity Analysis Approaches

Ördin implements comprehensive diversity analysis following modern ecological standards:

Diversity Estimation (iNEXT):

• Individual-based rarefaction (abundance data)
• Incidence-based rarefaction (presence/absence data)
• Coverage-based comparison (standardizes by sample completeness)
• Hill numbers (q=0, 1, 2) for true diversity measures
• Bootstrap confidence intervals for robust inference

Diversity Indices (vegan):

• Alpha diversity metrics for within-community diversity
• Evenness measures for distribution uniformity
• Rarefaction for standardized comparisons
• Species accumulation curves for sampling sufficiency

🗺️ Ordination Methods

Ördin provides 7 ordination methods for community pattern analysis:

1. NMDS: Non-metric dimensional scaling for non-linear relationships
2. PCA: Principal components analysis for linear relationships
3. CA: Correspondence analysis for unimodal species responses
4. DCA: Detrended correspondence analysis to remove arch effect
5. CCA: Canonical correspondence analysis for constrained ordination
6. RDA: Redundancy analysis for linear constrained ordination
7. PCoA: Principal coordinates analysis for distance-based methods

📈 Advanced Visualization Features

Ördin v3.0 introduces next-gen visualization capabilities:

• Confidence Ellipses: Statistical ellipses for site groups with validation
• Species Scores: Overlay species positions with customizable display
• Environmental Vectors: Biplot arrows showing environmental relationships
• Dynamic Theming: 5 plot themes with instant switching
• Comprehensive Legends: Clear explanation of all plot elements
• Axis Labels: Variance percentages for interpretability
• Export Options: Publication-quality images and data downloads

💾 Publication-Quality Exports

Ördin provides publication-quality export options for all analyses:

Raster Formats (300 DPI - publication standard):

• PNG - Universal compatibility, lossless compression
• TIFF - Journal submission standard, archival quality
• SVG - Vector format for scalable graphics

Data Exports:

• CSV - Universal data format
• Excel - Spreadsheet compatibility
• JSON - Structured data for programming

Export Settings:

• Dimensions: 12" × 8" (standard publication size)
• DPI: 300 for raster formats (journal requirement)
• Theme consistency: Respects selected plot themes
• Background: Theme-appropriate backgrounds preserved

Documentation

📚 User Guides

Detailed guides organized in the docs/ directory:

Analysis Guides (docs/guides/):

• Ordination Guide - Comprehensive ordination analysis
• Data Management - Data handling and validation
• Biplot Guide - Biplot interpretation
• CCA/RDA Guide - Constrained ordination
• Plot Customization - Customization options
• Settings Guide - Application configuration

Setup Guides (docs/setup/):

• Linux Setup - Linux installation
• WSL Setup - Windows Subsystem for Linux
• Fedora Quick Start - Fedora-specific setup
• Publishing Guide - How to publish releases

Developer Documentation (docs/development/):

• Project Overview - Architecture and technology stack
• Reproducibility Guide - Reproducible research
• Security Audit - Security review
• Test Checklist - Testing guidelines

📘 Community Guidelines

• Getting Started - Quick start guide
• Contributing - Development guidelines
• Code of Conduct - Community standards
• Code Standards - Coding conventions

📜 Version History

• CHANGELOG.md - Complete version history and release notes

🗄️ Archived Documentation

Historical documentation and implementation logs are preserved in the archive/ directory for reference.

License

MIT License - See LICENSE file for details

Author

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

Acknowledgments

• Inspired by Odin's wisdom from Norse mythology
• Built with Electron
• Powered by R Shiny
• Uses vegan and iNEXT packages

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Star History

If you find Ördin useful, please consider giving it a ⭐️ on GitHub!

Support

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

Citation

If you use Ördin in your research, please cite:

Moses, J. (2025). Ördin: A cross-platform desktop application for community ecology analysis. 
GitHub repository: https://github.com/jm0535/0rdin