Code repository for scripts and model output associated with sensitivity analysis of the VarroaPop honeybee hive simulation model. This dataset is associated with the following publication: Kuan, C., G. DeGrandi-Hoffman, R. Curry, K. Garber, A. Kanarek, M. Snyder, K. Wolfe, and T. Purucker. Sensitivity analyses for simulating pesticide impacts on honey bee colonies. ENVIRONMENTAL MODELLING AND SOFTWARE. Elsevier Science Ltd, New York, NY, USA, 376: 15-27, (2018).

The U.S. Environmental Protection Agency (USEPA) and U.S. Department of Agriculture (USDA) are developing the VarroaPop+Pesticide model which simulates the dynamics of honey bee colonies and how they respond to multiple stressors, including weather, Varroa mites and pesticides. To evaluate this model, we used Approximate Bayesian Computation to fit field data from an empirical study where honey bee colonies were fed the insecticide clothianidin. Model input data (Minucci 2021a) are available on Figshare: https://doi.org/10.6084/m9.figshare.c.5402901.v1. Scripts (Minucci 2021b) to run this analysis are available on Zenodo: https://doi.org/10.5281/zenodo.4721797. This dataset is associated with the following publication: Minucci, J., R.J. Curry, G. DeGrandi-Hoffman, C. Douglass, K. Garber, and S. Purucker. Inferring pesticide toxicity to honey bees from a field-based feeding study using a colony model and Bayesian inference. ECOLOGICAL APPLICATIONS. Ecological Society of America, Ithaca, NY, USA, 31(8): e02442, (2021).

The U.S. Environmental Protection Agency (USEPA) and U.S. Department of Agriculture (USDA) are developing the VarroaPop+Pesticide model which simulates the dynamics of honey bee colonies and how they respond to multiple stressors, including weather, Varroa mites and pesticides. To evaluate this model, we used Approximate Bayesian Computation to fit field data from an empirical study where honey bee colonies were fed the insecticide clothianidin. Model input data (Minucci 2021a) are available on Figshare: https://doi.org/10.6084/m9.figshare.c.5402901.v1. Scripts (Minucci 2021b) to run this analysis are available on Zenodo: https://doi.org/10.5281/zenodo.4721797. This dataset is associated with the following publication: Minucci, J., R.J. Curry, G. DeGrandi-Hoffman, C. Douglass, K. Garber, and S. Purucker. Inferring pesticide toxicity to honey bees from a field-based feeding study using a colony model and Bayesian inference. ECOLOGICAL APPLICATIONS. Ecological Society of America, Ithaca, NY, USA, 31(8): e02442, (2021).

,Toxicological data generated for Apis mellifera honey bees and an ectoparasitic mite (Varroa destructor) in laboratory toxicity trials are presented. Data were generated over a four-year period by members of the Varroacide Research and Testing Team (VRTT) as part of a foundational grant from the Foundation for Food and Agricultural Research (FFAR). Data may be used to explore toxicological responses of honey bees and Varroa mites to a wide range of natural and synthetic chemical treatments against Varroa infestations in honey bee colonies. Data may be collected and analyzed together with other data sets not generated by VRTT.,,

,These data represent V. destructor genomic annotations to be used for evolutionary comparison with other arthropods.,The ectoparasitic mite Varroa destructor has emerged as the primary pest of domestic honey bees (Apis mellifera). Here we present an initial survey of the V. destructor genome carried out to advance our understanding of Varroa biology and to identify new avenues for mite control. This sequence survey provides immediate resources for molecular and population-genetic analyses of Varroa-Apis interactions and defines the challenges ahead for a comprehensive Varroa genome project.,

,Varroa destructor are harmful ectoparasitic mites of Apis mellifera honey bees. Deformed wing-like viruses (DWV-A and B (VDV1)) are ubiquitous honey bee viruses that are vectored by Varroa; mite vectoring can cause an increase in virus infectivity and diversity of genetic variants. Beekeepers use both chemical (e.g., amitraz) and non-chemical (e.g., ‘brood break’) means to control mite populations in honey bee colonies, and these methods may be combined into an integrated pest management strategy. Here we explore how these control methods affected the DWV/VDV1 population in honey bee colonies, the diversity of viral genetic variants, and the competence of Varroa to transmit overt DWV infections. We found that ‘brood break’ treatment significantly elevated Varroa populations in colonies with a concomitant increase in DWV-A and VDV1 levels, but not when combined with amitraz application. Our results demonstrate negative implications to honey bee colony health from chemical treatment failures on the levels of DWV-like viruses in adult bees and mites, and the ability of mites to transmit overt infections.,

,In 2014–2022, USDA-ARS Tucson, AZ, by itself and in collaboration with other precision apiculture (PA) research programs, including the PA program at Utah State University, and several commercial operations, acquired a large reservoir of multi-sensor data, including thousands of frame photographs and sensor measurements, from field experiments with managed honey bee colonies. This reservoir is a loose collection of hive frame photos, CSV files, spreadsheets, and hive inspection text logs. Our project explores and exploits this reservoir and makes public its curated subsets. This dataset is the first such subset we curated in 2024-25 under USDA-NIFA Award 205732 "DSFAS - Exploration and Exploitation of the 2014-2022 USDA-ARS Tucson, AZ Digital Data Reservoir of Field Experiments with Managed Honey Bee Colonies.",The zipped directory ANNOTATED_HIVE_FRAMES includes 13 image subdirectories with annotated images.,1) 2013_07_28_CHBRC -- 57 Files,2) 2014_07_30_12_CHBRC -- 111 Files,3) 2015_02_11_MAC_RR -- 660 Files,4) 2016_03_30_HOOPS -- 153 Files,5) 2017_02_01_SRER_BEAR_CAGE -- 87 Files,6) 2018_02_13_SRER_SC_complete_3_9_25 -- 195 Files,7) 2018_04_18_SRER_SC_Methoxy -- 366 Files,8) 2019_07_11_SRER_BC_Neonic -- 60 Files,9) 2020_02_27_RR_Hive_Directions -- 36 Files,10) 2021_06_08_CHBRC_VLAD -- 282 Files,11) 2021_09_27_RR_ColdStor -- 855 Files,12) 2021_02_11_CT_ColdStor -- 111 Files,13) 2014_12_15_50_CHBRC --- 30 files,The name of each subfolder includes a year, a month, and a date on which the frame photos were taken, followed by the location of the apiary where the photos were taken. The de-abbreviations are as follows:,CHBRC -- Carl Hayden Bee Research Center,MAC -- Maricopa Agriculture Center,RR -- Red Rock Agriculture Center,HOOPS -- one of the apiaries at CHBRC,SRER -- Santa Rita Experimental Range,SRER -- Shipping Corrals,CT -- Cow Town,Each of the 13 subdirectories has three subsubdirectories: PNG/, XML/, TXT/.,PNG/ -- hive frame photos in PNG format;,XML/ -- XML annotations of images in PNG/ with LabelImg,TXT/ -- TXT annotations of images in PNG/ for YOLO training,Thus, in each of the 13 folders, each PNG image has two annotation files. E.g.,,2020_02_27_RR_Hive_Directions_IMG_2540_VK.PNG,2020_02_27_RR_Hive_Directions_IMG_2540_VK.xml,2020_02_27_RR_Hive_Directions_IMG_2540_VK.txt,Each PNG is annotated for the following categories:,(1) CappedHoneyCell,(2) CappedWorkerBroodCell,(3) EmptyCombCell,(4) PollenCell,(5) UncappedNectarCell,(6) UncappedWorkerLarvaCell,(7) BeeHiveFrame,The counts on the number of annotated region of interest (ROI) images are as follows:,CappedHoneyCell: 19,723,CappedWorkerBroodCell: 21,456,EmptyCombCell: 20,655,PollenCell: 13,406,UncappedNectarCell: 11,009,UncappedWorkerLarvaCell: 18,283,BeeHiveFrame: 1001,Each such ROI can be extracted into a separate image and used in training machine learning algorithms.,The subdirectory SRC/ contains two Python scripts that can convert XML to TXT and TXT to XML: xml_to_txt_converter.py and txt_to_xml_converter.py.,USDA_ARZ_DATA_YOLO_19june2025.zip is a 3GB zip version of these images prepared for YOLO training. It is available at https://usu.box.com/s/dh75xkinwfyl3sqgb9vugy1ahf6z9mrh.,SRC/ also contains the following Python scripts that we used for training YOLO networks:,(a) train_valid_split.py -- splits all alldata.txt in USDA_ARZ_DATA_YOLO_19june2025.zip into train.txt and valid.txt for YOLO training.,(b) tune_y8n.py --- tunes YOLOv8-nano,(c) tune_y8s.py --- tunes YOLOv8-small,(d) tune_y11n.py -- tunes YOLOv11-nano,(e) tune_y11s.py -- tunes YOLOv11-small,The folder METADATA/ contains two files: METADATA.txt and PapersDataSets_DrMeikle.xlsx. These files provide the metadata on the the USDA-ARS Tucson, AZ reservoir.,

Pesticide concentrations determined in honey bee hive matrices from GC/qToF-MS analysis. Including neonicotinoid concentrations determined by LC-MS/MS as published in Lin et al., 2021. This dataset is associated with the following publication: Glinski, D., S. Purucker, J. Minucci, R. Richardson, C. Lin, R. Johnson, and W. Henderson. Analysis of contaminant residues in honey bee hive matrices. SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM, NETHERLANDS, 954: 176329, (2024).