Published January 21, 2026 | Version v1.0
Software Open

Pesticide contamination in honey from organically managed colonies in the continental U.S. is comparable to certified organic imports

Authors/Creators

  • 1. ROR icon Cornell University
  • 2. ROR icon Pennsylvania State University

Description

Data and code relating to the manuscript "Pesticide contamination in honey from organically managed colonies in the continental U.S. is comparable to certified organic imports"

Background: Beekeepers in the continental United States do not have the option of USDA organic certification due to unfeasible apiculture standards. Interim recommendations require more organic-certified land for foraging than is available surrounding most apiaries. To test whether typical organic farms in New York and Pennsylvania (USA) provide sufficient forage for organic honey production, we established 72 colonies using organic management practices on six organic farms in 2023. In 2024, we screened the resulting honey for 96 pesticide residues and tested whether landscape features were associated with pesticide contamination. Additionally, we compared the levels of pesticide contamination to 20 brands of store-bought organic and conventional honey.

R Analysis

  1. We used R version 4.4.3.
  2. All data inputs required to run the analysis are located within the data directory.
  3. The R Markdown script, Analysis.Rmd generates all tables, figures, and statistics referenced in the manuscript. Results from this script can be viewed in either Analysis.html or Analysis.md.
  4. The functions directory contains some R scripts referenced by Analysis.Rmd. This is to keep code inside Analysis.Rmd concise.
  5. Running Analysis.Rmd creates a separate cache directory to store results of resource-intensive operations and save them for later use.
  6. The analysis script outputs figure images to the figures directory.

Packages

Package Version Purpose
tidyverse 2.0.0 Easier data manipulation and visualization
readxl 1.4.5 Import Excel files directly into R
sf 1.0-19 Handle spatial data
crawlUtils 0.1.62 Provides function to expand st_bbox limits
basemaps 0.0.8 Downloads base map imagery for ggplot map
ggspatial 1.1.9 Provides legend scale and north arrow for map
ggrepel 0.9.6 Provides geom_text_repel function
khroma 1.16.0 Colors for heatmap
patchwork 1.3.0 Arrange plots in grids
ggedit 0.4.2 Remove a geom from a ggplot for visual abstract
gt 1.0.0 Formatted tables
glmmTMB 1.1.10 Generalized linear mixed effects models
performance 1.13.0 Provides check_overdispersion function
emmeans 1.10.7 Pairwise tests
indicspecies 1.8.0 Indicator Species Analysis
vegan 2.6-10 For ordinations
ggordiplots 0.4.4 Generates hulls for ordination plots
colorspace 2.1-1 Provides darken color function
pairwiseAdonis 0.4.1 Pairwise PERMANOVA
units 0.8-6 Support units in R vectors, for set_units()
CropScapeR 1.1.5 Download landscape data from the USDA Cropland Data Layer
MuMIn 1.48.11 AICC comparison for landscape models
ggeffects 2.2.1 GLMM predictions

Files

ben393/orei-organic-honey-v1.0.zip

Files (5.1 MB)

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Additional details

Related works

Is supplement to
Software: https://github.com/ben393/orei-organic-honey/tree/v1.0 (URL)

Funding

United States Department of Agriculture
Organic Agriculture Research and Extension Initiative 51300-26814

Software

Repository URL
https://github.com/ben393/orei-organic-honey
Programming language
R