LIFE implementation#

This repository implements the LIFE extinction risk methodology as published in Eyres et al. The code will generate maps that cover the impact to extinction risk in an area under the two scenarios: conversion of the land to arable use, and coversion of the land to pre-human.

Running the code#

The methodology is explained in more detail in method.md. The pipeline is implemented as a Snakemake workflow in workflow/.

Prerequisites#

The following tools must be available on PATH:

• reclaimer — downloads inputs from Zenodo (quantifyearth/reclaimer)
• aoh-calc, aoh-habitat-process, aoh-collate-data, aoh-species-richness, aoh-endemism, aoh-validate-prevalence — from the aoh Python package
• gdalwarp — part of GDAL

The following environment variables must be set:

For GBIF occurrence validation (optional):

Running the pipeline#

# Full pipeline: delta P maps for all scenarios + model validation
snakemake --cores N all

# Delta P maps only, without validation
snakemake --cores N life

# Species richness and endemism maps (not included in 'all')
snakemake --cores N summaries

# Model validation only
snakemake --cores N validation

# GBIF occurrence validation (expensive — downloads gigabytes of data)
snakemake --cores N occurrence_validation

Other useful targets for incremental runs:

snakemake --cores N prepare       # Download and warp all base layers
snakemake --cores N species_data  # Extract species data from the database
snakemake --cores N aohs          # Generate all AOH rasters and collated CSVs

Precious layers#

The habitat and elevation layers are expensive to generate and are treated as precious: they will only be rebuilt if their output files are explicitly deleted, even if upstream inputs or code have changed. This applies to:

• habitat_layers/current/ — food-enhanced current habitat map at ~1.67km resolution
• habitat_layers/{scenario}/ — per-scenario fractional habitat maps
• habitat_layers/pnv/ — potential natural vegetation fractional maps
• elevation-max.tif, elevation-min.tif — warped elevation layers

To force a rebuild of any of these, delete the relevant .sentinel file (or the output file itself) before re-running.

Configuration#

Pipeline parameters are in config/config.yaml:

• taxa — taxonomic classes to process (default: AMPHIBIA, AVES, MAMMALIA, REPTILIA)
• scenarios — habitat change scenarios to evaluate (default: arable, restore)
• curve — extinction curve exponent for delta P (default: "0.25")
• pixel_scale — output raster resolution in degrees (default: ~5 arc-seconds)

Inspecting the pipeline graph#

The rule graph can be generated with:

snakemake --forceall --rulegraph 2>/dev/null | dot -Tsvg > graph.svg

Note that rules whose inputs are determined by the species-extraction checkpoint (generate_aoh, calculate_delta_p) will not appear in the static rule graph — this is a known snakemake limitation with checkpoint-based expansion. To see the complete job graph after species data has been extracted:

snakemake --forceall --dag 2>/dev/null | unflatten -f -l 5 | dot -Tsvg > dag.svg

Credits#

Originally derived from and using IUCN modlib and aoh lib by Daniele Baisero.