Last updated: 2026-09-01
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Knit directory: covid_script/
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| html | ead8b95 | Ziang Zhang | 2026-09-01 | build: publish supplementary table explorer |
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Observed deaths are modelled using a log-Poisson model with a second-order integrated Wiener process for the long-term trend, an aggregated seasonal Gaussian process, and an independent observation-level component. Each jurisdiction-age-sex series is fitted independently; the primary analysis does not pool jurisdictions and does not include a population offset. The United States monthly model includes a calendar-days offset.
The baseline training period contains observations strictly before 1 January 2020. Frequency-specific seasonal construction is retained for weekly, monthly, and quarterly sources. Posterior predictive draws preserve uncertainty in the counterfactual baseline and observation process.
For time point (t), the P-score for posterior baseline draw (b) is
\[ P_t^{(b)} = \frac{Y_t - \widetilde{Y}_t^{(b)}} {\widetilde{Y}_t^{(b)}}, \]
where (Y_t) is the observed death count and \(\widetilde{Y}_t^{(b)}\) is a posterior-predicted baseline count. Posterior medians and 95% credible intervals are obtained from the draw-wise summaries.
Wave-level P-scores use the ratio of summed counts,
\[ P_W^{(b)} = \frac{\sum_{t \in W} Y_t} {\sum_{t \in W} \widetilde{Y}_t^{(b)}} - 1, \]
and are not averages of pointwise P-scores. Wave boundaries are
start-inclusive and end-exclusive. Their exact dates are defined in
config/analysis.yml.
Sex differences are computed as the female P-score minus the male P-score for the corresponding geography, age group, and time point.
Vaccination coverage is defined as people receiving at least one dose per 100 people, evaluated at 1 July 2021. European values use the latest observation on or before that date. The thresholds and region membership used by the publication outputs are stored in the tracked analysis configuration rather than inferred during plotting.
Model seeds are derived deterministically from the configured base
seed and analysis identifiers. Publication artifacts are linked to input
hashes, source code, and package versions. The complete model contract
is available in documentation/model-specification.md.
sessionInfo()R version 4.5.1 (2025-06-13)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.6.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1
locale:
[1] C.UTF-8/C.UTF-8/C.UTF-8/C/C.UTF-8/C.UTF-8
time zone: America/Chicago
tzcode source: internal
attached base packages:
[1] stats graphics grDevices datasets utils methods base
loaded via a namespace (and not attached):
[1] vctrs_0.7.3 cli_3.6.6 knitr_1.50 rlang_1.2.0
[5] xfun_0.55 stringi_1.8.9 otel_0.2.0 renv_1.1.5
[9] promises_1.5.0 jsonlite_2.0.0 workflowr_1.7.2 glue_1.8.1
[13] rprojroot_2.1.1 git2r_0.36.2 htmltools_0.5.9 httpuv_1.6.16
[17] sass_0.4.10 rmarkdown_2.30 evaluate_1.0.5 jquerylib_0.1.4
[21] tibble_3.3.0 fastmap_1.2.0 yaml_2.3.12 lifecycle_1.0.5
[25] whisker_0.4.1 stringr_1.6.0 compiler_4.5.1 fs_1.6.6
[29] Rcpp_1.1.1-1.1 pkgconfig_2.0.3 later_1.4.4 digest_0.6.39
[33] R6_2.6.1 pillar_1.11.1 magrittr_2.0.5 bslib_0.9.0
[37] tools_4.5.1 cachem_1.1.0