Global Species Altitude and Latitude Range Limits

A Shiny web application that visualizes the latitudinal and altitudinal range limits of species from iNaturalist data. This is a proof-of-concept that extends Brian Buma's "Edges of (All) Life" to a global scale and adds altitude data.

Major Packages

• R Shiny - Web application framework
• DuckDB - High-performance columnar database engine
• Maplibre GL - Interactive web mapping
• sf - Spatial data handling

Data Processing Pipeline

The data-prep.R script performs a multi-stage data processing workflow:

Input Data:

• Raw GBIF database (.duckdb format) containing global biodiversity observations
• SRTM v3 digital elevation model (.tif format, 100+GB) providing global altitude data

Processing Steps:

1. Filter iNaturalist records - Extracts all iNaturalist observations from the complete GBIF dataset (January 2025 snapshot) with valid coordinates
2. Altitude extraction - Uses parallel processing to extract elevation values from 30m SRTM rasters for all iNaturalist observation points (~50 minutes runtime)
3. Range limit calculation - Groups data by species and identifies northernmost/southernmost latitudes and highest/lowest altitudes for each of ~390,000 species (~15 minutes runtime)

Output:

• data/shiny.duckdb - Optimized database (~500MB) containing species range limit points with:
  • Geographic coordinates (lat/lon)
  • Altitude values
  • Range limit flags (max/min latitude and altitude per species)
  • Database indexes for fast querying in the Shiny application

Local Setup Requirements: Note that you won't be able to run the data processing workflow of this application on your own machine without:

1. A local .duckdb version of the GBIF dataset
2. SRTM elevation data files (100+GB)
3. Significant computational resources for data processing (the workflow uses up to 300GB memory, and could use less but would take longer)