Last updated: 2026-09-01
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Knit directory: covid_script/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 1c7efea | Ziang Zhang | 2026-09-01 | Refine supplementary table explorer views |
| html | ead8b95 | Ziang Zhang | 2026-09-01 | build: publish supplementary table explorer |
| Rmd | 3f3cefd | Ziang Zhang | 2026-09-01 | feat: add interactive supplementary table explorer |
| Rmd | c55510f | Ziang Zhang | 2026-09-01 | feat: add coverage-aware supplementary grouping |
| html | c55510f | Ziang Zhang | 2026-09-01 | feat: add coverage-aware supplementary grouping |
| Rmd | 755ef0a | Ziang Zhang | 2026-08-31 | feat: expand supplementary interactive explorers |
| html | 755ef0a | Ziang Zhang | 2026-08-31 | feat: expand supplementary interactive explorers |
| Rmd | 588e463 | Ziang Zhang | 2026-08-31 | feat: publish interactive supplementary analyses |
| html | 588e463 | Ziang Zhang | 2026-08-31 | feat: publish interactive supplementary analyses |
| html | 3e71c91 | Ziang Zhang | 2026-08-31 | build: publish Zenodo reproduction guidance |
| html | b47130b | Ziang Zhang | 2026-08-31 | build: refresh published site provenance |
| html | e5925a4 | Ziang Zhang | 2026-08-31 | build: publish workflowr analysis site |
| Rmd | b7bbc08 | Ziang Zhang | 2026-08-31 | fix: activate pinned environment for reproduction |
| Rmd | e87ff80 | Ziang Zhang | 2026-08-31 | feat: add publication workflowr website |
The frozen supplementary bundle presents every cohort in the current analysis contract without loading fitted models in the browser. It contains 1,119 registered geography-by-age-by-sex analyses: 1,118 successful compact posterior-predictive results and one explicitly retained historical model failure.
| Explorer | Available selections | Output |
|---|---|---|
| Time series and pointwise P-scores | Analysis family, geography, age group, sex, and display metric | Observed mortality, expected mortality with a 95% posterior predictive interval, or the pointwise P-score curve |
| Wave-specific maps | Region, age group, sex, Initial/Alpha/Delta/Omicron wave, and posterior summary | Interactive geographic P-score or excess-death maps with exact values in an accessible table |
| Vaccination-group trajectories | P-score or female-minus-male P-score difference, Europe or United States, original age group, two vaccination thresholds, and manual location membership | Recomputed low- and high-vaccination trajectories with panel-specific coverage screening, manuscript presets, uncertainty intervals, and downloadable current membership |
| Wave-specific P-score table | Switchable sex-stratified and total-population tables, global search, every-column filters, sorting, page size, and pagination | Wave-specific P-score summaries for all registered geographies and original age groups, with vaccination metadata where comparable |
The chart pages load only the shard required by the current selection, and the table page loads a compact sub-megabyte summary index. They therefore remain static GitHub Pages files rather than a server process, while still exposing the full registered stratification set. The vaccination explorer adds approximately 25 MB of summary-only browser assets; fitted objects remain local.
| Analysis family | Registered cohorts | Time scale |
|---|---|---|
| Eurostat Europe | 388 | Weekly |
| United States, non-sex-stratified | 204 | Monthly |
| United States, sex-stratified | 408 | Monthly |
| Canada, non-sex-stratified | 40 | Weekly |
| Canada, sex-stratified | 72 | Weekly |
| England and Wales | 3 | Weekly |
| Republic of Ireland | 4 | Quarterly |
The United States branch Vermont / 0-44 / female is
retained in the registry with status model_failed; no value
is imputed. Superseded Europe, England-and-Wales, and Ireland model
batches, and unregistered United States age_all files, are
not mixed into this frozen analysis contract.
For each successful cohort, the bundle records observed deaths, the expected posterior mean and median, the central 95% posterior predictive interval, and the pointwise P-score distribution. Interactive mortality charts use the posterior median as their center line. This matters for a small number of sparse cohorts where extreme posterior draws can pull the mean outside the central interval; the downloadable table retains both summaries without truncation.
Wave summaries use the four half-open intervals fixed in
config/analysis.yml:
For a wave with observed periods, the wave P-score is computed draw by draw as
\[ P = \frac{\sum_t Y_t - \sum_t E_t}{\sum_t E_t}, \]
before posterior quantiles are taken. It is not an average of pointwise P-scores.
The public files contain summary statistics only. Posterior draw matrices and fitted model objects are not included.
The bundle is derived from the registered observed-data snapshots and existing compact posterior-predictive objects. It does not refit a model.
system2(
"Rscript",
"scripts/supplementary/build_bundle.R"
)
system2(
"Rscript",
"scripts/supplementary/build_vaccination_groups.R"
)
system2(
"Rscript",
"scripts/supplementary/build_table_explorer.R"
)
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