Data and code for: Hidden Markov model identifies four phytoplankton regimes associated with seasonal forcing and monsoon disturbance in Jinhae Bay, Korea

Complete data and code supporting the manuscript submitted to Limnology and Oceanography (LO-26-0267). Contents: raw and processed daily HPLC pigment and environmental data; the frozen-state R pipeline (multi-start Gaussian HMM; biomass emission variable = log10[TChl-a + fucoxanthin + peridinin]; CZM zero replacement via zCompositions; CLR-PCA); fitted model objects; the decoded regime sequence and posterior probabilities; state-number selection (AIC/BIC/ICL, k=1-6) with k=4 vs k=5 cross-tabulation and fifth-state profile; CLR transformation-sensitivity; parametric bootstrap (summary and replicate-level); below-detection (censored) and conditional-independence sensitivity analyses; figure code; Supplementary Tables S1-S8; and an environment lockfile (R 4.5.2, package versions, random seeds). A clean environment can regenerate all principal figures, tables, and numerical results from README.md. Funding: NRF grants RS-2026-25468730 and RS-2026-25550603.