Agroecological Zoning of Bangkalan Regency Using K-Means and HDBSCAN Based on Integrated Soil Fertility and Climate Features
https://doi.org/10.26594/register.v12i1.5969
Keywords:
Agroecological Zoning, Soil Fertility, Climate Variability, K-Means Clustering, Process InnovationAbstract
Agroecological heterogeneity poses challenges for agricultural planning in Bangkalan Regency, Indonesia. This study aimed to delineate agroecological zones by integrating soil fertility, climate, and topographic variables using K-Means clustering and Hierarchical Density-Based Spatial Clustering of Applications with Noise (HDBSCAN). A total of 11,000 geospatial observations obtained from Google Earth Engine were aggregated into 277 village-level units. The dataset included soil nutrients (nitrogen, phosphorus, and potassium), the Soil Quality Index, temperature, rainfall, humidity, elevation, and slope. Data preparation, modeling, and evaluation were performed as the primary methodological steps. Min-Max Scaling was applied to normalize the data. The optimal K-Means configuration (K = 3) achieved a Silhouette Score of 0.2668, an Inertia value of 294.5529, and a Calinski-Harabasz Index (CHI) of 75.8821. The resulting clusters were classified as High-Potential (52 villages), Moderate-Potential (142 villages), and Environmental-Constraint (83 villages) zones. HDBSCAN was used to validate clustering patterns and detect environmental anomalies. The optimal HDBSCAN configuration identified two density-based clusters and five noise villages. These villages showed exceptionally high nitrogen, phosphorus, and Soil Quality Index values, indicating localized agroecological hotspots. The integration of K-Means and HDBSCAN offers a comprehensive framework for agricultural planning, resource allocation, and sustainable land management.
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[1] R. Virtriana et al., “Effects of extreme climate on agriculture in paddy field area in West Java Province (Indonesia) using multitemporal scenarios, GIS, and remote sensing,” Geomatics, Natural Hazards and Risk, vol. 16, no. 1, p. 2455487, Dec. 2025, doi: 10.1080/19475705.2025.2455487.
[2] M. S. Farooq et al., “Partial replacement of inorganic fertilizer with organic inputs for enhanced nitrogen use efficiency, grain yield, and decreased nitrogen losses under rice-based systems of mid-latitudes,” BMC Plant Biol., vol. 24, no. 1, p. 919, 2024, doi: 10.1186/s12870-024-05629-w.
[3] W. J. Brownlie, P. Alexander, M. Maslin, M. Cañedo-Argüelles, M. A. Sutton, and B. M. Spears, “Global food security threatened by potassium neglect,” Nat. Food, vol. 5, no. 2, pp. 111–115, 2024, doi: 10.1038/s43016-024-00929-8.
[4] X. Fan et al., “Impacts of Extreme Temperature and Precipitation on Crops during the Growing Season in South Asia,” Remote Sens. (Basel)., vol. 14, no. 23, Dec. 2022, doi: 10.3390/rs14236093.
[5] W. Utama et al., “Application of Flow Coefficients to Support High Economical Plant Cultivation (Case Study: Kwanyar Bangkalan, Indonesia),” Jurnal Penelitian Pendidikan IPA, vol. 9, no. 9, pp. 6828–6833, Sep. 2023, doi: 10.29303/jppipa.v9i9.3307.
[6] E. Fauziyah, I. Maflahah, and D. R. Hidayati, “Policy Impacts on Farm Efficiency: Fertilizer Subsidies in Corn Production in Madura Island, Indonesia,” Research on World Agricultural Economy, Sep. 2025, doi: 10.36956/rwae.v6i4.2264.
[7] W. I. Susanti, S. N. Cholidah, and F. Agus, “Agroecological Nutrient Management Strategy for Attaining Sustainable Rice Self-Sufficiency in Indonesia,” Jan. 01, 2024, Multidisciplinary Digital Publishing Institute (MDPI). doi: 10.3390/su16020845.
[8] J. Chavez, V. Nijman, D. K. T. Sukmadewi, M. D. Sadnyana, S. Manson, and M. Campera, “Impact of Farm Management on Soil Fertility in Agroforestry Systems in Bali, Indonesia,” Sustainability (Switzerland), vol. 16, no. 18, Sep. 2024, doi: 10.3390/su16187874.
[9] D. Selvida, A. F. Pulungan, and A. S. Huzaifah, “Optimization Of Garlic Cultivation Land Selection Using Pca And K-Means Approach In Spatial Intelligent System,” Eastern-European Journal of Enterprise Technologies, vol. 3, no. 2, pp. 54–64, 2025, doi: 10.15587/1729-4061.2025.325340.
[10] C. Zhu et al., “Digital Mapping of Soil Organic Carbon Based on Machine Learning and Regression Kriging,” Sensors, vol. 22, no. 22, Nov. 2022, doi: 10.3390/s22228997.
[11] X. Li et al., “A zoning-based machine learning framework for accurate soil organic matter prediction across Mollisol and non-Mollisol regions,” J. Integr. Agric., 2026, doi: https://doi.org/10.1016/j.jia.2026.01.016.
[12] R. A. Purnamasari, “Land suitability evaluation for sugarcane cultivation based on agroecological zoning system in East Java Indonesia,” Buitenzorg: Journal of Tropical Science, vol. 1, no. 2, pp. 42–50, Dec. 2024, doi: 10.70158/buitenzorg.v1i2.12.
[13] A. Filintas, N. Gougoulias, N. Kourgialas, and E. Hatzichristou, “Management Soil Zones, Irrigation, and Fertigation Effects on Yield and Oil Content of Coriandrum sativum L. Using Precision Agriculture with Fuzzy k-Means Clustering,” Sustainability (Switzerland), vol. 15, no. 18, Sep. 2023, doi: 10.3390/su151813524.
[14] L. Poggio et al., “SoilGrids 2.0: Producing soil information for the globe with quantified spatial uncertainty,” SOIL, vol. 7, no. 1, pp. 217–240, Jun. 2021, doi: 10.5194/soil-7-217-2021.
[15] J. Muñoz-Sabater et al., “ERA5-Land: a state-of-the-art global reanalysis dataset for land applications,” Earth Syst. Sci. Data, vol. 13, no. 9, pp. 4349–4383, 2021, doi: 10.5194/essd-13-4349-2021.
[16] C. Funk et al., “The Climate Hazards Center Infrared Precipitation with Stations, Version 3,” Sci. Data, vol. 13, no. 1, Dec. 2026, doi: 10.1038/s41597-026-07096-4.
[17] M. Simard, M. Denbina, C. Marshak, and M. Neumann, “A Global Evaluation of Radar-Derived Digital Elevation Models: SRTM, NASADEM, and GLO-30,” J. Geophys. Res. Biogeosci., vol. 129, no. 11, Nov. 2024, doi: 10.1029/2023JG007672.
[18] P. Rautenstrauch and U. Ohler, “Shortcomings of silhouette in single-cell integration benchmarking,” Nat. Biotechnol., 2025, doi: 10.1038/s41587-025-02743-4.
[19] F. Ros, R. Riad, and S. Guillaume, “PDBI: A partitioning Davies-Bouldin index for clustering evaluation,” Neurocomputing, vol. 528, pp. 178–199, 2023, doi: https://doi.org/10.1016/j.neucom.2023.01.043.
[20] A. Rykov, R. C. De Amorim, V. Makarenkov, and B. Mirkin, “Inertia-Based Indices to Determine the Number of Clusters in K-Means: An Experimental Evaluation,” IEEE Access, vol. 12, pp. 11761–11773, 2024, doi: 10.1109/ACCESS.2024.3350791.
[21] L. E. Ekemeyong Awong and T. Zielinska, “Comparative Analysis of the Clustering Quality in Self-Organizing Maps for Human Posture Classification,” Sensors, vol. 23, no. 18, Sep. 2023, doi: 10.3390/s23187925.
[22] I. Djalovic et al., “Maize and heat stress: Physiological, genetic, and molecular insights,” Mar. 01, 2024, John Wiley and Sons Inc. doi: 10.1002/tpg2.20378.
[23] W. Zhu, E. E. Rezaei, Z. Sun, J. Wang, and S. Siebert, “Soil-climate interactions enhance understanding of long-term crop yield stability,” European Journal of Agronomy, vol. 161, p. 127386, 2024, doi: https://doi.org/10.1016/j.eja.2024.127386.
[24] X. He et al., “Global patterns and drivers of phosphorus fractions in natural soils,” Biogeosciences, vol. 20, no. 19, pp. 4147–4163, Oct. 2023, doi: 10.5194/bg-20-4147-2023.
[25] J. Delfim, A. Moreira, L. A. C. Moraes, J. F. Silva, P. A. M. Moreira, and O. F. Lima Filho, “Soil Phosphorus Availability Impacts Chickpea Production and Nutritional Status in Tropical Soils,” J. Soil Sci. Plant Nutr., vol. 24, no. 2, pp. 3115–3130, 2024, doi: 10.1007/s42729-024-01738-5.
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