pybeepop+: A Python Interface for the BeePop+ Honey Bee Colony Model

Jeffrey Minucci

doi:10.5334/jors.550

Abstract

The BeePop+ honey bee colony model, developed by the U.S. Environmental Protection Agency (US EPA) and U.S. Department of Agriculture (USDA), simulates how pesticides, pathogens, and other stressors impact colony dynamics. The pybeepop+ package provides a Python interface to BeePop+ through a ctypes-based wrapper that communicates with the compiled C++ library. It exposes BeePop+’s functionality through an intuitive API for setting parameters, loading weather and pesticide data, running simulations, and retrieving results as pandas DataFrames. The package includes pre-compiled binaries for Windows/Linux, automated testing, and comprehensive documentation. By enabling programmatic access to BeePop+, pybeepop+ facilitates high-throughput analyses, sensitivity testing, and integration with Python scientific computing workflows previously unavailable with the standalone model.

References

Reilly JR, Artz DR, Biddinger D, Bobiwash K, Boyle NK, Brittain C, Brokaw J, Campbell JW, Daniels J, Elle E, Ellis JD, Fleischer SJ, Gibbs J, Gillespie RL, Gundersen KB, Gut L, Hoffman G, Joshi N, Lundin O, … Winfree R. Crop production in the USA is frequently limited by a lack of pollinators. Proceedings of the Royal Society B: Biological Sciences. 2020;287(1931):20200922. DOI: 10.1098/rspb.2020.0922
Open DOI Search in Google Scholar Back to article
Zapata-Hernández G, Gajardo-Rojas M, Calderón-Seguel M, Muñoz AA, Yáñez KP, Requier F, Fontúrbel FE, Ormeño-Arriagada PI, Arrieta H. Advances and knowledge gaps on climate change impacts on honey bees and beekeeping: A systematic review. Global Change Biology. 2024;30(3):e17219. DOI: 10.1111/gcb.17219
Open DOI Search in Google Scholar Back to article
Evans JD, Schwarz RS. Bees brought to their knees: microbes affecting honey bee health. Trends in Microbiology. 2011;19(12):614–620. DOI: 10.1016/j.tim.2011.09.003
Open DOI Search in Google Scholar Back to article
Donkersley P, Rhodes G, Pickup RW, Jones KC, Wilson K. Honeybee nutrition is linked to landscape composition. Ecology and Evolution. 2014;4(21):4195–4206. DOI: 10.1002/ece3.1293
Open DOI Search in Google Scholar Back to article
Goulson D, Nicholls E, Botı́as C, Rotheray EL. Bee declines driven by combined stress from parasites, pesticides, and lack of flowers. Science. 2015;347(6229):1255957. DOI: 10.1126/science.1255957
Open DOI Search in Google Scholar Back to article
Woodcock BA, Bullock JM, Shore RF, Heard MS, Pereira MG, Redhead J, Ridding L, Dean H, Sleep D, Henrys P, Peyton J, Hulmes S, Hulmes L, Sárospataki M, Saure C, Edwards M, Genersch E, Knäbe S, Pywell RF. Country-specific effects of neonicotinoid pesticides on honey bees and wild bees. Science. 2017;356(6345):1393–1395. DOI: 10.1126/science.aaa1190
Open DOI Search in Google Scholar Back to article
Garber K, DeGrandi-Hoffman G, Curry R, Minucci JM, Dawson DE, Douglass C, Milone JP, Purucker ST. Simulating the effects of pesticides on honey bee (Apis mellifera L.) colonies with BeePop+. Ecologies. 2022;3(3):275–291. DOI: 10.3390/ecologies3030022
Open DOI Search in Google Scholar Back to article
DeGrandi-Hoffman G, Curry R. The population dynamics of varroa mites in honey bee colonies: Part I-The VARROAPOP program. American Bee Journal. 2005;145(7):592–595.
Search in Google Scholar Back to article
Kuan AC, DeGrandi-Hoffman G, Curry RJ, Garber KV, Kanarek AR, Snyder MN, Wolfe KL, Purucker ST. Sensitivity analyses for simulating pesticide impacts on honey bee colonies. Ecological Modelling. 2018;376:15–27. DOI: 10.1016/j.ecolmodel.2018.02.010
Open DOI Search in Google Scholar Back to article
Curry B. quanted/VPopLib: Code to support Garber et al 2022 (v0.1.0-beta) [Computer software]. Zenodo; 2022. DOI: 10.5281/zenodo.6856426
Open DOI Search in Google Scholar Back to article
United States Department of Agriculture, ARS. BEEPOP+. 2023. https://www.ars.usda.gov/pacific-west-area/tucson-az/carl-hayden-bee-research-center/research/beepopplus/beepopplus/
Search in Google Scholar Back to article
The pandas development team. pandas-dev/pandas: Pandas (latest) [Computer software]. Zenodo; 2020. DOI: 10.5281/zenodo.3509134
Open DOI Search in Google Scholar Back to article
Minucci JM, Curry R, DeGrandi-Hoffman G, Douglass C, Garber K, Purucker ST. Inferring pesticide toxicity to honey bees from a field-based feeding study using a colony model and Bayesian inference. Ecological Applications. 2021;31(8):e02442. DOI: 10.1002/eap.2442
Open DOI Search in Google Scholar Back to article
Klinger E, Rickert D, Hasenauer J. pyABC: distributed, likelihood-free inference. Bioinformatics. 2018; 34(20):3591–3593. DOI: 10.1093/bioinformatics/bty361
Open DOI Search in Google Scholar Back to article
Dask Development Team. Dask: Library for dynamic task scheduling; 2016. http://dask.pydata.org
Search in Google Scholar Back to article

pybeepop+: A Python Interface for the BeePop+ Honey Bee Colony Model

Abstract

Paradigm

My account