Reproducibility package: Typhoid fever in the Republic of Korea, 2001–2024 — long-term decline, residual annual periodicity, and southeastern coastal spatial clustering

This Zenodo deposit is the reproducibility package accompanying the manuscript: Lee G and Kim S. Typhoid fever in the Republic of Korea, 2001–2024: long-term decline, residual annual periodicity and southeastern coastal spatial clustering in 24 years of nationwide surveillance. Submitted to Foodborne Pathogens and Disease (Sage Journals, R2 revision). Contents:- /tables/ — 14 source CSV files underlying main and supplementary tables (annual rates, age-specific Mann–Kendall, Sen slope confidence intervals, wavelet stability, breakpoint bootstrap, LISA FDR, Empirical Bayes sigungu shrinkage, 12-weighting Moran's I sensitivity, n=1,000 power simulations).- /figures/ — 2 main composite figures (Figure 1: 6 panels; Figure 2: 5 panels) and 4 supplementary figures (S1 STL decomposition, S2 elderly share, S3 NB GLM fit overlay, S4 sigungu animated MP4 + interactive HTML).- /scripts/ — 11 Python and JavaScript analysis and figure-rendering scripts (typhoid_r2_analyses.py, recompute_weights.py, rerun_power_n1000.py, rebuild_combined_figs.py, build_sigungu_mp4.py, etc.).- /docs/ — manuscript, supplementary material, cover letter (final R2 versions). Data sources:- Korea Disease Control and Prevention Agency (KDCA) Infectious Disease Portal (https://dportal.kdca.go.kr/) — typhoid notifications, weekly × sigungu, 2001–2024.- Korean Statistical Information Service (KOSIS) — annual mid-year resident registration population by sigungu, 2001–2024. Methods (summary):Hamed–Rao modified Mann–Kendall test with rank-based Sen slope 95% CIs; negative-binomial GLM (NB2, dispersion α = 0.154); Morlet continuous wavelet transform with 1,000-simulation AR(1) red-noise null; exhaustive BIC breakpoint search with 200-replicate parametric bootstrap; direct age-standardisation to the 2005 Korean Standard Population; global Moran's I (9,999 permutations) under Queen + KNN-2 baseline plus 11 alternative weighting schemes; LISA with Benjamini–Hochberg FDR; Empirical Bayes (Marshall 1991) sigungu shrinkage; period-stratified analysis (2001–2012 vs 2013–2024). Reproducibility:All Monte-Carlo procedures use seed = 42. Python 3.12 with pandas, numpy, statsmodels, scipy, geopandas, plotly, matplotlib, PyMannKendall. License: Creative Commons Attribution 4.0 International (CC-BY-4.0)