Data and code for "Soil context shapes biodiversity associations with global crop nutrient production

This repository contains the processed analytical dataset and custom code used to reproduce the analyses reported in the manuscript “Soil context shapes biodiversity associations with global crop nutrient production”. The code includes data processing, module construction, machine-learning model training, SHAP-based attribution, structural path analysis, generalized additive modelling, response-type clustering, counterfactual analyses and bootstrap uncertainty estimation. Analyses were conducted in R 4.4.2 and Python 3.12.4. Original source datasets are publicly available from the repositories and sources cited in the manuscript and Supplementary Table 1.