species-distribution-guide

Species Distribution Modeling Guide

A skill for building and evaluating species distribution models (SDMs), covering occurrence data acquisition from biodiversity databases, environmental predictor preparation, model fitting with MaxEnt and ensemble methods, model evaluation, and projection under climate change scenarios.

Occurrence Data

Accessing GBIF Data

The Global Biodiversity Information Facility (GBIF) is the primary source of species occurrence records:

from pygbif import occurrences, species

def download_occurrences(species_name: str, country: str = None,
                          limit: int = 5000,
                          has_coordinate: bool = True) -> dict:
    """
    Download species occurrence records from GBIF.
    species_name: scientific name (e.g., 'Panthera tigris')
    Returns cleaned occurrence records with coordinates.
    """
    # Get GBIF species key
    name_result = species.name_backbone(name=species_name)
    if "usageKey" not in name_result:
        return {"error": f"Species not found: {species_name}"}

    species_key = name_result["usageKey"]

    # Search occurrences
    params = {
        "taxonKey": species_key,
        "hasCoordinate": has_coordinate,
        "hasGeospatialIssue": False,
        "limit": limit,
    }
    if country:
        params["country"] = country

    results = occurrences.search(**params)

    # Clean records
    records = []
    seen_coords = set()
    for rec in results.get("results", []):
        lat = rec.get("decimalLatitude")
        lon = rec.get("decimalLongitude")
        if lat is None or lon is None:
            continue

        # Remove exact duplicates
        coord_key = (round(lat, 4), round(lon, 4))
        if coord_key in seen_coords:
            continue
        seen_coords.add(coord_key)

        records.append({
            "species": rec.get("species", species_name),
            "latitude": lat,
            "longitude": lon,
            "year": rec.get("year"),
            "basis_of_record": rec.get("basisOfRecord"),
            "institution": rec.get("institutionCode"),
            "country": rec.get("country"),
        })

    return {
        "species": species_name,
        "gbif_key": species_key,
        "n_records": len(records),
        "records": records,
    }