Last updated: 2026-08-31
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Knit directory: covid_script/
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Modified: analysis/supplementary.Rmd
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Modified: analysis/supplementary_app.js
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| 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 | e87ff80 | Ziang Zhang | 2026-08-31 | feat: add publication workflowr website |
The regional pipelines retain source-specific time scales and age definitions while applying the common training-period, model, and P-score contracts.
The European analysis uses weekly Eurostat deaths by geography, age,
and sex. The canonical snapshot covers 2000-W01 through 2024-W19.
Source-specific model code is in code/regions/europe,
and the production entry point is scripts/model_fitting/europe/refit_eurostat.R.
The England-and-Wales analysis combines daily deaths by occurrence
through 2020 with weekly registered deaths for 2021–2023. These two
source definitions are recorded explicitly in the data contract. The
fitted analysis uses weekly age groups UNDER65,
65-84, and GE85.
The production entry point is scripts/model_fitting/england_wales/refit.R.
The Ireland analysis uses quarterly registered deaths from CSO PxStat
table VSQ20, with age groups 25-44,
45-64, 65-84, and GE85. The
production entry point is scripts/model_fitting/ireland/refit.R.
The Canadian analysis uses weekly provisional deaths from Statistics
Canada Table 13-10-0768-01, stratified by province or
territory, age, and sex. The production entry point is scripts/model_fitting/canada/refit.R.
The United States analysis uses monthly CDC WONDER exports grouped by
residence state and age, with a separate sex-stratified export. Calendar
days per month enter the fitted model as an offset. The target graph is
defined in _targets.R,
and the production runner is scripts/pipeline/run_pipeline.R.
Each pipeline writes standardized summaries below the ignored
output/ directory. The reporting scripts then construct the
manuscript figures and tables from those summaries. No regional model is
fitted when this website is built.
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