A Data-Driven Comparison of Linear Mixed Model and Mixed Effects Regression Tree Approaches for Dairy Productivity Analysis

Dairy productivity studies often involve hierarchical and longitudinal data structures that violate the assumptions of linear regression. This study compares two modeling approaches, Linear Mixed Model (LMM) and Mixed Effects Regression Tree (MERT), in predicting dairy productivity based on the 2024 National Dairy Productivity Survey data. Predictive performance was evaluated using MSEP, RMSEP, MAD, and MAPE, with MERT consistently outperforming LMM in accuracy and robustness. Permutational Multivariate Analysis of Variance (PERMANOVA) test results reinforced this finding, yielding a pseudo-F value of 224.7 and a p-value of 0.001, indicating statistically significant differences in model performance. Key predictors of MERT model included farm altitude, the previous week’s milk production, and the amounts of concentrate feed given, which are part of significant predictor variables in LMM. This finding underscores MERT’s superiority in modeling complex agricultural datasets while providing interpretable insights through data-driven segmentation. The study advocates policy focus in sustainable milk production as well as the availability of high quality of feed and altitude-based dairy farms location to improve milk productivity. Should these focuses implemented by the industry, combined with the MBG Program, Indonesia would be progressing better towards achievement of SDGs Goal 2 and 3.