pybeepop+ 🐝

About

pybeepop+ provides the Python implementation of BeePop+, an agent-based model for simulating honey bee (Apis mellifera L.) colony dynamics. The model is designed for ecological risk assessment and research applications.

References:

Minucci, J. (2025). "pybeepop+: A Python Interface for the BeePop+ Honey Bee Colony Model." Journal of Open Research Software, 13(1). https://doi.org/10.5334/jors.550

Garber, K., et al. (2022). "Simulating the Effects of Pesticides on Honey Bee (Apis mellifera L.) Colonies with BeePop+." Ecologies, 3(3), 22. https://doi.org/10.3390/ecologies3030022

Package author: Jeffrey Minucci, U.S. Environmental Protection Agency

Table of Contents

• Requirements
• Quick Start Guide
• Minimal Working Example
• Example Notebook
• API Documentation
• Contributing to pybeepop+

Requirements

pybeepop+ is pure Python and runs on Windows, Linux, and macOS.

Note: The optional C++ engine was removed in version 0.3.0. If you previously passed engine='cpp' or lib_file=..., remove those arguments — the Python engine is now the only option. See the release notes for details.

Quick Start Guide

Installation

pip install pybeepop-plus

Basic Usage

from pybeepop import PyBeePop

# 1. Create a BeePop+ instance
beepop = PyBeePop()

# 2. Configure simulation parameters
params = {
    "ICWorkerAdults": 10000,
    "ICWorkerBrood": 8000,
    "SimStart": "04/13/2015",
    "SimEnd": "09/15/2015",
    "AIAdultLD50": 0.04
}
beepop.set_parameters(params)

# 3. Load weather data
beepop.load_weather('path/to/weather.txt')

# 4. (Optional) Load pesticide exposure data
beepop.load_residue_file('path/to/residues.txt')

# 5. Run simulation
results = beepop.run_model()
print(results)

Working with Results

# Get results as DataFrame
results_df = beepop.get_output()

# Get results as JSON
results_json = beepop.get_output(json_str=True)

# Visualize time series
beepop.plot_output()  # default columns
beepop.plot_output(["Colony Size", "Adult Workers"])  # custom columns

Updating Parameters Between Runs

# Update specific parameters (others remain unchanged)
beepop.set_parameters({"ICWorkerAdults": 22200, "InitColPollen": 4000})
results_updated = beepop.run_model()

Loading Parameters from File

# Parameters file format (key=value per line)
# Example: my_parameters.txt
#   RQEggLayDelay=10
#   RQReQueenDate=06/25/2015
#   RQEnableReQueen=False

beepop.load_parameter_file('my_parameters.txt')
params = beepop.get_parameters()

Additional Resources

• Parameter Reference: BeePop+ Parameters
• Weather File Format: docs/weather_readme.txt
• Residue File Format: docs/residue_file_readme.txt
• Example Files: example_data/

Note: Parameters not explicitly set will use BeePop+ default values. See the parameter list for details.

Note: Numeric parameters are validated when they are set. A value outside the range listed for it in the parameter reference, or a fractional value for an integer parameter, raises BeepopParameterError and leaves the previously set parameters unchanged.

Minimal Working Example

from pybeepop import PyBeePop
import tempfile
import os

# Create minimal synthetic weather data
weather_data = """04/01/2023, 20.0, 10.0, 15.0, 3.0, 0.0, 12.0
04/02/2023, 22.0, 12.0, 17.0, 2.5, 0.0, 12.1
04/03/2023, 21.0, 11.0, 16.0, 3.2, 2.0, 12.2
04/04/2023, 19.0, 9.0, 14.0, 2.8, 0.0, 12.3
04/05/2023, 23.0, 13.0, 18.0, 2.1, 0.0, 12.4"""

# Write to temporary file
with tempfile.NamedTemporaryFile(mode="w", suffix=".txt", delete=False) as f:
    f.write(weather_data)
    temp_weather_file = f.name

try:
    # Create BeePop+ instance and run simulation
    beepop = PyBeePop()
    beepop.set_parameters(
        {"ICWorkerAdults": 10000, "ICWorkerBrood": 5000, "SimStart": "04/01/2023", "SimEnd": "04/05/2023"}
    )
    beepop.load_weather(temp_weather_file)

    # Run model and display results
    results = beepop.run_model()
    print(results[["Date", "Colony Size", "Adult Workers"]].head())

finally:
    # Clean up temporary file
    os.unlink(temp_weather_file)

Example Notebook

A Jupyter notebook demonstrating pybeepop+ usage is available here:

→ pybeepop_example.ipynb

API Documentation

Complete API reference and usage guide:

→ https://usepa.github.io/pybeepop/

Contributing

We welcome community contributions. Here's how you can help:

Code Contributions

Fork the repository and submit pull requests. All submissions will be reviewed by maintainers.

Bug Reports

Found a bug? Please open an issue with:

• Description of the problem
• Steps to reproduce
• Expected vs. actual behavior
• System information (OS, Python version, etc.)

Support & Questions

Need help? Open an issue on GitHub.

Disclaimer

This software is provided "as is" without warranty of any kind. The views expressed in this package are those of the authors and do not necessarily represent the views or policies of the U.S. Environmental Protection Agency.