GCN-HSI — User Guide

Great Crested Newt Habitat Suitability Index calculator for QGIS · based on Oldham et al. (2000)

Overview

GCN-HSI is a semi-automated calculator for the Great Crested Newt Habitat Suitability Index. It scores up to 10 candidate ponds per run and outputs a polygon layer with per-pond HSI scores and traffic-light symbology.

Important: This tool assists qualified ecologists — it does not replace a site survey or professional ecological assessment. Remote Assessment results alone are not sufficient to characterise a site's suitability for GCN or to inform planning decisions, but are a valuable rapid screening tool.

The two tools

The plugin provides two separate Processing tools, found in the Processing Toolbox under GCN-HSI → Ecology Tools. Choose the tool that matches the data you have — there is no mode dropdown to set.

Tool	Variables scored	Inputs shown	Site visit
GCN HSI (Remote Assessment)	7 / 10 (SI1–SI7)	The 7 remotely-derivable inputs only	Not required
GCN HSI (Full Assessment)	Up to 10 / 10 (SI1–SI10)	All inputs, including the 4 site-visit inputs	Required

Both tools share identical scoring logic, outputs and symbology. The Remote Assessment tool hides the 3 site-visit inputs (Fish, Water Quality, Macrophyte) and uses an automated NBN Atlas lookup for Waterfowl.

Step-by-step workflow

Open the Processing Toolbox (Ctrl+Alt+T).
Expand GCN-HSI → Ecology Tools and double-click either tool.
Set the Candidate Pond(s) layer (1–10 polygons).
Set the Existing Ponds and Terrestrial Habitats layers and the Habitat Type Field.
Leave GCN Risk Zone, Pond Permanence and, for Remote Assessment, Waterfowl Presence on (auto-detect), or set them manually.
(Full Assessment only) Enter the site-visit variables where available.
Choose an output location and click Run.
Review the Processing Log for any warnings, then inspect the symbolised output layer.

An internet connection is required so the automated variables can be retrieved.

Inputs & which variables are automated

Which variables are automated

Automatically determined (when left on (auto-detect)): GCN Risk Zone (SI1) from MAGIC, Pond Permanence (SI3) from a Sentinel 2 time series, and Waterfowl Presence (SI7) from NBN Atlas in Remote Assessment.
Automatically calculated from your input layers: Pond Area (SI2), Terrestrial Habitat (SI4), Pond Count (SI5).
Entered manually: Shoreline Shade (SI6) and the Full Assessment site-visit inputs (Fish, Water Quality, Macrophyte). Waterfowl can also be entered manually in Full Assessment.

Any value you enter manually always overrides the automated value.

Required (both tools)

Parameter	Description
Candidate Pond(s)	Polygon layer — 1 to 10 ponds per run
Existing Ponds	All ponds within 1km of the candidate pond(s)
Terrestrial Habitats	UK Habitat polygons within 250m of the candidate pond(s)
Habitat Type Field	Field containing UKHab habitat classification strings

Optional — global defaults

Parameter	Description
GCN Risk Zone	Leave on `(auto-detect)` to determine automatically, or select Green / Amber / Red manually
Pond Permanence	Leave on `(auto-detect)` to determine automatically (see conditions below), or select a class manually
Shoreline Shade %	Percentage of shoreline shaded. Entered manually. Used for SI6 scoring

Optional — per-pond overrides

The Per-Pond Values table allows individual overrides per pond using its OID. Columns: Pond OID | Shade (%) | Permanence Override | Risk Zone Override. Leave any cell blank to use the global default or automated value.

GCN HSI (Full Assessment) tool only

These 4 site-visit inputs are shown only in the Full Assessment tool.

Parameter	Options
Waterfowl Presence	Absent / Minor / Major
Fish Presence	Absent / Possible / Minor / Major
Water Quality	Good / Moderate / Poor / Bad
Macrophyte Cover %	Percentage cover of aquatic macrophytes

Why these matter most: Waterfowl Presence (SI7) and Fish Presence (SI8) are the strongest predictors of GCN presence/absence — a Major impact from either can result in GCN absence even in an otherwise high-scoring pond. In Remote Assessment, Waterfowl is estimated from NBN Atlas occurrence records around the pond, but this is a coarse proxy and a site visit is still far more reliable. Fish cannot be determined remotely at all, so it is only available in Full Assessment. Running the Full Assessment with site-visit data produces a substantially more accurate and reliable HSI score than a Remote Assessment alone.

Pond Permanence automation conditions

Pond Permanence is estimated from a short Sentinel 2 NDWI time series (last ~18 months, 10 m resolution). The tool queries low cloud Sentinel 2 L2A scenes, samples the green and NIR bands at each pond and classifies the pond as Never Dries, Rarely Dries, Sometimes Dries or Dries Annually based on how many months had water. If there are not enough clear observations, the value is left unassessed and the log explains why. A manual selection always takes precedence over the automated value. Smaller ponds are still attempted, but very small or heavily shadowed ponds may not give a reliable result.

Outputs

A polygon layer copied from the candidate pond input, with these fields added:

Field	Description
ORIG_OID	Original feature OID from the input layer
HSI_SCORE	Overall HSI score (0.0 – 1.0). Always calculated from the full 10 variable weighting, with any missing variables filled by a neutral 0.5, so Remote and Full scores are directly comparable.
VARS_USED	Number of variables that had actual data for this pond. Missing variables are shown as Not assessed in the individual SI fields.
HSI_CLASS	High / Moderate / Low
ASSESS_MD	Assessment mode used
SI1_GEOG … SI6_SHADE	Individual suitability index scores (both tools)
SI7_WFOWL	Waterfowl suitability index (both tools; Remote uses NBN Atlas auto-detect, Full uses manual entry)
SI7_WFOWL_SRC	Source of the waterfowl value, e.g. NBN: Major, Manual: Minor, Not assessed
SI8_FISH … SI10_MACP	Site-visit scores (Full Assessment only; not assessed in Remote)

The output is symbolised with traffic-light colours:

High HSI ≥ 0.68 Moderate HSI 0.34–0.67 Low HSI < 0.34

Comparing Remote and Full scores: The HSI is always computed using the same 10 variable weighting. If a variable is not available, it is filled with a neutral 0.5 before the score is calculated. This means a Remote Assessment score (7 observed variables) and a Full Assessment score (up to 10 observed variables) use the same scale and are directly comparable. Individual suitability index fields still show Not assessed for any variable with no data.

Road barrier detection

The tool automatically detects linear road features within the 250m terrestrial habitat buffer. Habitat polygons or existing ponds located on the far side of a detected road from the candidate pond are excluded from SI4 and SI5 scoring respectively. Detections and exclusions are reported in the Processing Log.

Professional use and development sites

A Full HSI Assessment requires a physical site visit and should be carried out by a suitably licensed and experienced ecologist.
Where a pond scores Moderate or High, further survey work (e.g. eDNA or presence/absence surveys) will typically be required.
A low HSI score does not preclude GCN presence; survey work should not be ruled out on a low score alone.
This tool applies increased weighting to SI7 (Waterfowl) and SI8 (Fish) relative to the original Oldham et al. (2000) scoring.
Assessments for planning must comply with national and local policy and follow CIEEM guidelines. In England, consider Natural England's District Level Licensing where applicable.

References

Oldham, R.S., Keeble, J., Roberts, M.J. & Latham, D. (2000). Evaluating the suitability of habitat for the great crested newt (Triturus cristatus). Herpetological Journal, 10: 143–155.

ARG UK (2010). Advice Note 5: Great Crested Newt Habitat Suitability Index. Amphibian and Reptile Groups of the United Kingdom.

Buxton, A.S., Tracey, H. & Downs, N.C. (2021). How reliable is the habitat suitability index as a predictor of great crested newt presence or absence? The Herpetological Journal, 31(2): 111–117.