Analysis code and de-identified weekly aggregated data for: Population-level measles RT-PCR cycle threshold values and their relationships with disease severity, transmission, and incidence metrics (Mexico, 2025-2026)

Analysis code and de-identified weekly aggregated data supporting the accompanying article on population-level measles RT-PCR quantification cycle (Cq) values and outbreak metrics in Chihuahua and Jalisco, Mexico. This deposit contains no individual-level records. Data and canonical primary output Three panels aggregated by state and epidemiological week, each with 81 rows and spanning 2025-02-03 through 2026-07-20: weekly Cq, incidence and transmission measures; weekly hospitalization and recorded-pneumonia measures; and weekly specimen-composition measures. Six composition and completeness fields are suppressed in five state-weeks with fewer than five analyzable Cq determinations. All three panels contain the same 81 analytic state-week keys. The archive also includes the 144-row canonical M1-M4 primary-model output used by Supplementary Table S2, the primary/reference rows of Tables S9-S10, Figure 4 and the numerical results in the manuscript. Code and reproducibility The archive contains 33 R analysis scripts. Nineteen run on the deposited aggregate data alone, including the complete reported time-series chain: cross-correlation and lagged regression, adjusted models, supplementary tables, Toda-Yamamoto Granger/VAR analysis, out-of-sample predictive-gain assessment, and prewhitening, endpoint, composition, unsplit-Chihuahua and dmax=2 sensitivities. Fourteen scripts require the restricted individual-level extract and are included to document how the aggregate panels and individual-level analyses were produced. Script 18 generates the single canonical primary-model file. Scripts 21 and 24 read it directly, while script 40 imports it for rows labelled primary or reference instead of repeating the same bootstrap. In a clean archive-only validation run, regeneration reproduced the canonical file byte-for-byte and the complete consumer chain through Figure 4 and Tables S9-S12 completed successfully. MANIFEST.txt provides SHA-256 checksums and byte counts for every file. Version 2.1.0 This version supersedes v2.0.0 for the submitted manuscript. It preserves the complete-week panels and scientific estimates, adds the canonical primary-model output, and revises the analysis scripts so every reader-facing occurrence of a primary moving-block bootstrap interval comes from that single saved result rather than from independent resampling sequences. Licensing Aggregate data are released under CC BY 4.0; analysis code is released under the MIT License. See README.md, LICENSE and LICENSE-CODE.