Machine learning (ML) has become more prevalent as a tool used for biogeochemical analysis in agricultural management. However, a common drawback of ML models is the lack of interpretability, as they are black boxes that provide little insight into agricultural management. To overcome this limitation, we compared three tree-based models (decision tree, random forest, and gradient boosting) to explain soil organic matter content through Shapley additive explanations (SHAP). Here, we used nationwide data on field crops, soil, terrain, and climate across South Korea (n = 9584). Using the SHAP method, we identified common primary controls of the models, for example, regions with precipitation levels above 1400 mm and exchangeable potassium levels exceeding 1 cmol⁺ kg⁻¹, which favor enhanced organic matter in the soil. Different models identified different impacts of macronutrients on the organic matter content in the soil. The SHAP method is practical for assessing whether different ML models yield consistent findings in addressing these inquiries. Increasing the explainability of these models means determining essential variables related to soil organic matter management and understanding their associations for specific instances.

Machine learning has become more prevalent as a tool used for biogeochemical analysis in agricultural management. However, a common drawback of machine learning models is the lack of interpretability, as they are black boxes that provide little insight into agricultural management. To overcome this limitation, we compared three tree-based models (decision tree, random forest, and gradient boosting) to explain soil organic matter content through Shapley additive explanations (SHAP). Here, we used nationwide data on field crops, soil, terrain, and climate across South Korea (n = 9,584). Using the SHAP method, we identified common primary controls of the models, for example, regions with precipitation levels above 1400 mm and exchangeable potassium levels exceeding 1 cmol+ kg-1, which favor enhanced organic matter in the soil. Different models identified different impacts of nutrients on the organic matter level in the soil. The SHAP method is practical for assessing whether different machine learning models yield consistent findings in addressing these inquiries. Increasing the explainability of these models means determining essential variables related to soil organic matter management and understanding their associations for specific instances.