Pesticide Mixture Toxic Pressure as a Driver of Soil Biodiversity Loss Across European Agroecosystems

Overview This repository contains the R scripts and data used to analyze the relationship between pesticide mixture toxic pressure and soil biodiversity patterns across Europe. The analyses integrate chemical exposure estimates, species occurrence records, and spatially explicit environmental data to evaluate ecological impacts at the landscape scale. The repository includes scripts to: Process and harmonize biodiversity datasets. Calculate and analyze mixture toxic pressure metrics, including multi-substance Potentially Affected Fraction (msPAF) and summed Hazard Units (∑HU). Investigate relationships between chemical mixture pressure and species richness using Generalized Additive Models (GAMs). Estimate Potentially Disappeared Fraction (PDF) of species relative to baseline conditions. Quantify dominant chemical drivers contributing to mixture toxic pressure across agricultural landscapes. Generate publication-ready figures, maps, and summary statistics for Europe and individual countries (i.e., the Netherlands). Software Requirements Analyses were carried out in R (version 4.3.2). All scripts automatically check for and install missing package dependencies before execution. Data Description The scripts require input datasets containing: "10x10grids.gpkg"- created 10 × 10 km grid-cell resolution across Europe "Biota_Toxicpressure_df_EU.rds" -Species occurrence records aggregated at 10 × 10 km grid-cell resolution. "ChemicalSpecific_PAFs.rds"Chemical-specific per-site calculated Potentially Affected Fraction of Species (PAFs). "Europe.shp"European country boundary data for map visualization. "list_of_invasive_alien_species_of_union_concern.tsv" -Lists of invasive alien species used for biodiversity filtering. "sum_HU_msPAF_site_output.rds" -Spatially explicit mixture toxic pressure estimates. The following datasets are not currently shared because they are associated with manuscripts under review or in preparation. However, placeholder file paths are retained in the scripts to ensure reproducibility once the datasets become publicly available: a. Europe_Catchment_Intersect_16_12_2026.gpkg and Pesticidesconc_with_xy.rds (to be released upon publication of Zhang et al.) b. matched_data_SSD.rds- (to be released upon publication of Tripathi et al.) Reproducibility All file paths are relative to the repository root to facilitate reproducibility across operating systems. Users can reproduce the analyses by downloading the repository, placing the required datasets within the Data/ directory, and executing the scripts in the order described in the manuscript and accompanying documentation. Associated Publication This repository accompanies the manuscript: Oginah et al. Pesticide Mixture Toxic Pressure as a Driver of Soil Biodiversity Loss Across European Agroecosystems.