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 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. 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. In a clean validation run, all six principal scripts completed. Twenty-two of 23 regenerated outputs were byte-identical to the live validated results; the remaining adjusted-regression table differed only by floating-point serialization, with a maximum absolute difference of 9.3e-12 and no change in signs or inferential decisions. MANIFEST.txt provides SHA-256 checksums and byte counts for every file. Version 2.0.0 This version supersedes v1.0.0 for the submitted manuscript. It excludes the incomplete final Jalisco week, aligns all three panels to 81 complete-week analytic cells through 2026-07-20, applies the documented 0 < Cq < 40 criterion, adds the final sensitivity analysis, and updates authorship metadata. 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.