landscape-connectivity - SKILL.md Agent Skill

name: landscape-connectivity description: "Analyzes landscape connectivity using graph theory, resistance surfaces, and corridor identification for conservation planning. Use this skill when the user mentions habitat connectivity, wildlife corridors, Circuitscape, least-cost paths, resistance surfaces, IIC/dPC connectivity metrics, stepping stones, patch importance ranking, betweenness centrality, fragmentation analysis, landscape graphs, or pinchpoint identification." skill_version: 1.0.0

Skill: landscape-connectivity

Domain: Landscape connectivity · Graph theory · Circuitscape · Corridor · Resistance surface

Purpose

Guides the agent through quantifying structural and functional landscape connectivity, identifying wildlife corridors, and calculating the contribution of individual habitat patches to overall network connectivity. Covers resistance surface construction, graph-based connectivity indices (IIC, PC, dPC), Circuitscape current mapping, and least-cost path analysis for corridor delineation.

When to Invoke

Invoke this skill when:

The user asks about habitat connectivity, wildlife corridors, or dispersal pathways
Patches of habitat must be ranked by their importance to overall connectivity
A resistance surface is needed for Circuitscape or least-cost path modelling
The impact of habitat loss or fragmentation on connectivity must be quantified
Gene flow, dispersal barriers, or landscape permeability are the focus

trigger_keywords: habitat connectivity, wildlife corridor, dispersal, gene flow, landscape graph, resistance surface, least-cost path, circuit theory, Circuitscape, IIC, PC, dPC, corridor width, patch importance, landscape permeability

Inputs

Input	Format	Required
Habitat/land cover raster	GeoTIFF	Required
Study area polygon	SHP or GPKG	Required
Dispersal distance or dispersal kernel parameters	CSV or text	Required
Resistance value table (land cover class → resistance)	CSV	Recommended
Existing protected areas or focal nodes	SHP or GPKG	Optional
Habitat class codes	Integer codes or CSV lookup	Optional

Outputs

Output	Description
`patch_metrics.csv`	Area, perimeter, IIC, PC, dIIC, dPC per patch
`connectivity_summary.csv`	Global IIC, PC, and top-10 patches by dPC
`top_patches_map.tif`	Raster with dPC value per patch
`connectivity_graph.png`	Habitat patch network diagram
`resistance_surface.tif`	Resistance surface for Circuitscape input
`patch_betweenness.csv`	Betweenness centrality per patch (graph metric)
`least_cost_paths.gpkg`	Least-cost path lines between patch pairs

Steps

Prepare habitat patches Load land cover raster and mask to study area using geoprocessing-for-ecology. Reclassify to binary habitat/non-habitat. Extract discrete habitat patches with terra::patches() or landscapemetrics::get_patches(). Filter patches below minimum area threshold (document threshold in decision_log.md).
Build resistance surface (invoke resistance_surface.R) Reclassify land cover using the resistance table. Apply optional focal smoothing to avoid hard edges. Validate: all land cover classes must have an assigned resistance value. Output: resistance_surface.tif.
Calculate distance matrix between patches Compute pairwise Euclidean or least-cost distances between patch centroids. If dispersal distance threshold is unknown, use 3 values for sensitivity analysis: conservative (25th percentile), medium (median), optimistic (75th percentile).
Compute connectivity indices (invoke connectivity_metrics.R) Calculate IIC and PC for each dispersal distance scenario. Compute dIIC and dPC (patch removal importance) for all patches. Rank patches by dPC to identify conservation priorities.
Run Circuitscape for corridor mapping (optional, requires Circuitscape installed) Export focal nodes (top-N patches by dPC) and resistance surface. Run in all-to-one mode to produce cumulative current density map. Interpret high-current corridors as priority dispersal pathways.
Delineate least-cost paths (invoke connectivity_analysis.py) Use scikit-image.graph.route_through_array() for least-cost paths. Output vector lines between top-priority patch pairs.
Validate outputs and record decisions Check dPC values sum approximately to the global PC. Record dispersal distance scenario, resistance table source, and minimum patch area in decision_log.md.

Decision Points

Condition	Diagnosis	Recommended Action
Dispersal distance unknown	Sensitivity of results to this parameter is high	Run analysis at 3 distances (conservative, medium, optimistic); report range of outcomes
Landscape < 10 patches	Graph metrics statistically unstable	Use fragmentation metrics from ecological-impact-assessment skill instead
IIC or PC < 0.01	Extremely low connectivity	Prioritise restoration before corridor analysis; identify bottleneck patches
dPC > 0.8 for a patch already deforested	High-priority patch lost	Escalate to restoration planning; include in gap analysis
All patches isolated (no edges at chosen distance)	Threshold too restrictive	Increase dispersal distance or use resistance-based (cost) distance threshold

Key Decisions to Document

Record the following in decision_log.md after running this skill:

Dispersal distance(s) used and their biological justification
Source of resistance values (literature, telemetry, expert opinion)
Minimum patch area threshold applied and rationale
Whether Circuitscape was run; mode used (pairwise, all-to-one, one-to-all)
Top-N patches selected for focal node analysis

Tools and Libraries

suppressPackageStartupMessages(library(terra))              # raster operations
suppressPackageStartupMessages(library(sf))                 # vector operations
suppressPackageStartupMessages(library(landscapemetrics))   # patch extraction and metrics
suppressPackageStartupMessages(library(igraph))             # graph theory (IIC, PC, betweenness)
suppressPackageStartupMessages(library(dplyr))              # data manipulation
suppressPackageStartupMessages(library(ggplot2))            # plotting

Python

import networkx as nx           # graph metrics (betweenness centrality)
from skimage.graph import route_through_array  # least-cost path
import geopandas as gpd         # vector operations
import rasterio                 # raster reading
import numpy as np              # numerical operations
from pathlib import Path        # file system

CLI

# Circuitscape (optional, must be installed)
circuitscape_4_0 <config_file.ini>
# or Julia-based CS4
julia -e "using Circuitscape; compute(<config_file.ini>)"

Resources

skills/landscape-connectivity/resources/graph-theory-for-ecology.md — IIC, PC, dPC formulas, interpretation, and dispersal threshold definition
skills/landscape-connectivity/resources/resistance-surface-guide.md — Resistance value assignment by taxon, calibration methods, and Circuitscape export
skills/landscape-connectivity/resources/circuitscape-parameter-guide.md — Circuitscape modes, focal nodes, solver selection, and output interpretation

Notes

IIC and PC are scale-dependent: Both indices depend on the total landscape area (A). Always report the landscape extent used in calculation to enable comparison across studies.
Euclidean distance ≠ functional connectivity: Distance-based IIC/PC ignores landscape resistance. Use cost-distance for species sensitive to habitat matrix quality (e.g., forest-dependent species crossing agricultural land).
Circuitscape can be slow for large landscapes: For rasters > 10 million cells, use the Julia implementation (Circuitscape.jl) which is 10–50× faster than the Python version.
Betweenness centrality is a proxy, not a measure of flow: High betweenness patches are on many shortest paths but may not have high actual dispersal if resistance is high elsewhere.
Patch size confounds dPC: Large patches tend to have high dPC because their removal drastically reduces total habitat area. Always report patch area alongside dPC to distinguish area effect from connectivity effect.