Pre-specification protocol for a three-tier hantavirus cardiopulmonary syndrome early warning system in Ñuble, Chile (S49, v1.0 + Addendum v1.1 + Addendum v1.2)

This archive contains the locked pre-specification protocol for the ecological analysis of a three-tier early warning system for Hantavirus Cardiopulmonary Syndrome (SCPH, Andes virus) in the Ñuble region of south-central Chile, covering the period 2002-2024. The bundle includes (1) the primary pre-specification v1.0 defining the GLMM nbinom2 model specification (S29-K), walk-forward validation protocol (14 folds, 2011-2024), anti-leakage standardization, baseline forecasts, and scoring metrics; (2) Addendum v1.1 formalizing a burn-in period (2011-2014) justified by the Poisson-limit behavior of nbinom2 in low-event regimes; (3) Addendum v1.2 establishing the logarithmic score and ranked probability score as primary metrics following scoring rule theory (Gneiting-Raftery 2007, Wilks 2011) and precedent in Emerging Infectious Diseases (Fox et al. 2024). All analytical decisions were locked on 2026-04-04 BEFORE any out-of-sample metric was computed. Filesystem timestamp ledger in Section 8 of Addendum v1.2 provides additional sequence evidence. This archive provides externally verifiable timestamp proof to neutralize post-hoc selection concerns (anti-HARKing, Nosek et al. 2018; Munafò et al. 2017). The full manuscript is in preparation for submission to Emerging Infectious Diseases (CDC, 2026).