Hepatitis E in the Republic of Korea, 2020–2025: reproducibility package (data, scripts, intermediate outputs, tables, figures)

This Zenodo deposit accompanies the manuscript "Hepatitis E in the Republic of Korea, 2020–2025: rising incidence, modest annual seasonality, and sub-province spatial co-clustering with commercial pig populations in 5.25 years of mandatory notification" submitted to Memórias do Instituto Oswaldo Cruz. Contents:- scripts/ — Analysis pipeline (Python 3.10/3.12, custom NB IRLS routines)- intermediate/ — Cleaned KDCA weekly + annual cross-tab data, sigungu-pop merged data, and all session-generated analysis outputs (weekly NB GLM, sensitivity windows, Lomb-Scargle, weekly segmented NB, sigungu NB regression, bivariate Moran's I, 12-scheme Queen+KNN-2 Moran's I, LISA, EB shrinkage, Getis-Ord Gi*, Spatial Lag/Durbin NB, AR(1)-NB hybrid, VIF/correlation, alternative pig-exposure metrics)- tables/ — All 5 main-text + 17 supplementary CSV tables- figures/ — Figure 1 (6 panels) + Figure 2 (6 panels) at 300 dpi (PNG + TIF) + Supplementary Movie S1 (sigungu-level annual choropleth animation, 2020–2025)- README.md — File index, key results summary, and reproducibility notes Data sources:- Korea Disease Control and Prevention Agency (KDCA) Infectious Disease Statistics System — 3,122 weekly laboratory-confirmed domestic HEV cases, 2020 W27 – 2025 W38- Statistics Korea (KOSIS) resident-registration mid-year populations- KOSIS Livestock Trend Survey (가축동향조사, Statistic ID DT_1ED0001) — sigungu commercial pig populations, 2019–2023- KOSIS demographic, land-use, healthcare-use, fiscal-autonomy and groundwater-use sigungu-level series, 2020–2024 mean Reproducibility:- Random seed: np.random.default_rng(42)- 9,999 permutations for global Moran's I (12 schemes) and bivariate Moran's I- Queen contiguity computed via direct shapefile vertex-adjacency at 1-metre tolerance (identical 6-isolate set as the libpysal/esda implementation)- 5.25-year surveillance window (2020 W27 – 2025 W38; n = 273 weeks; 229 sigungu) Key results:- Weekly NB GLM annual IRR = 1.175 (95% CI 1.141–1.210), robust at 1.16–1.19 across four sensitivity windows- Sigungu Moran's I = 0.246 (Queen + KNN-2 baseline, p = 4 × 10⁻⁴), preserved across 11/12 weighting schemes- Bivariate Moran's I (HEV × log commercial pig population) = 0.179 (p < 10⁻⁴)- Spatial Lag NB pig coefficient IRR = 1.034 (p = 0.007); five alternative pig-exposure metrics all p < 10⁻⁴ License: CC-BY-4.0 Citation: Lee G, Kim S. Hepatitis E in the Republic of Korea, 2020–2025: reproducibility package. Zenodo; 2026. https://doi.org/10.5281/zenodo.20097377