Last updated: 2026-09-01
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Knit directory: covid_script/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | c55510f | Ziang Zhang | 2026-09-01 | feat: add coverage-aware supplementary grouping |
| 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 | e87ff80 | Ziang Zhang | 2026-08-31 | feat: add publication workflowr website |
This website documents the data, statistical analyses, and publication outputs for a multi-country study of excess mortality during the COVID-19 pandemic. The repository contains the exact source snapshots used for the analysis and separates computationally intensive model fitting from lightweight reporting.
Each page provides the manuscript caption, the code used to construct the publication artifact from precomputed analysis results, and downloadable output.
| Publication item | Description |
|---|---|
| Figure 1 | Seasonally Adaptive Mortality Model illustration |
| Figure 2 | Initial- and Delta-wave P-scores in Europe |
| Figure 3 | Initial- and Delta-wave P-scores in North America |
| Figure 4 | P-scores by vaccination group over time |
| Figure 5 | Female-minus-male P-score differences over time |
| Table 1 | Wave-specific P-scores for selected regions |
The regional analyses page maps the common estimands to the source-specific pipelines for Europe, England and Wales, Ireland, Canada, and the United States. The statistical methods page records the shared model and summary definitions.
The supplementary overview provides a frozen inventory, summary definitions, and complete downloads. Interactive pages expose geography-specific mortality and P-score time series and all four wave-specific map summaries without loading posterior draws or fitted model objects in the browser.
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data/raw/. Provider-hosted data may subsequently be
revised; the optional access scripts retrieve current versions without
replacing the repository snapshots. See data
sources and reproduction
instructions for details.
Model fits and posterior draws are intentionally excluded from Git because they are large and computationally expensive to recreate. Website generation reads the tracked publication figures and table and does not refit any model.
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