Probabilistic Co-Occurrence Tool (APCOAT)

Version 3.0.0

APCOAT (Automated Probabilistic Co-Occurrence Assessment Tool) produces probabilistic pesticide-use footprints, runs species distribution models (SDM) with MaxEnt, and generates probabilistic co-occurrence reports for terrestrial and aquatic species in the contiguous United States.

APCOAT was developed by Stone Environmental in collaboration with Syngenta Crop Protection, LLC.

https://www.stone-env.com/apcoat/

---

Repository contents

Path	Description
src/	Python source code
ui/	Qt Designer UI files
build/	Build and distribution scripts
UserDataTemplates/	Input data templates (CSV)
testdata/	Minimal test dataset
distribution_files.json	Manifest of all files required for a full distribution
CHANGELOG.txt	Version history
LICENSE.txt	License

---

What is NOT included

The following dependencies are required to run APCOAT but are not distributed through this repository. They are bundled in the official installer.

Runtime dependencies

Dependency	Description	How to obtain
jre/	Java Runtime Environment	Adoptium — JRE 11 or later, Windows x64
maxent/maxent.jar	MaxEnt species distribution modeling software	MaxEnt homepage

Data dependencies

These large geospatial and database files are required at runtime. They are distributed separately via the APCOAT installer and are not tracked in this repository.

Path	Description
db/	SQLite databases and supporting rasters
cdl/	USDA Cropland Data Layer rasters (2019–2024, 30 m)
cooccZones/	Co-occurrence zone rasters and shapefiles (HUC8/12, states, counties, CRDs)
maxentPredictors/terrestrial/	Bioclimatic and environmental predictor rasters (WorldClim/CHELSA/NLCD)
maxentPredictors/aquaticflowing/	NHD flowline geodatabase (APCOAT_flowline.gdb)
maxentPredictors/aquaticstatic/	NHD waterbody geodatabase (APCOAT_waterbody.gdb)

A full listing of required files is in distribution_files.json.

---

Installation (recommended)

Download and run the official installer (ProbCoOccTool_Setup_<version>.exe) from https://www.stone-env.com/apcoat/. The installer bundles Python, all data dependencies, JRE, and MaxEnt into a self-contained application — no separate installation of Python or data files is required.

---

Running from source

1. Install Python 3.11+ (64-bit).

2. Install dependencies:

   pip install PyQt5>=5.15 shapely>=2.0 geopandas>=0.14 numpy>=1.26 pandas>=2.1 scipy>=1.11 matplotlib>=3.8 seaborn>=0.13 pyodbc>=5.0
   

   GDAL is also required. On Windows, install via a pre-built wheel (e.g., from Christoph Gohlke's collection).

3. Supply data dependencies listed above in the project root directory.

4. Supply jre/ and maxent/maxent.jar in the project root.

5. Launch:

   python src/main.py
   

---

Building the installer

See build/ for scripts. Prerequisites: Python 3.11+, Inno Setup 6, and either MSVC or MSYS2 MinGW for the C++ launcher.

build\build_distribution.bat   # assemble distribution files
build\build.bat                 # compile installer with Inno Setup

Output directories (ProbabilisticCoOccurrenceToolDist/, ProbabilisticCoOccurrenceToolInstaller/) are created as siblings of this repository root.

---

License

MIT License — Copyright (c) 2022-2026 Stone Environmental and Syngenta Crop Protection, LLC