Last updated: 2026-08-31

Checks: 7 0

Knit directory: covid_script/

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R Markdown file: up-to-date

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Environment: empty

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Seed: set.seed(20260831)

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Session information: recorded

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File paths: relative

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Repository version: 588e463

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The results in this page were generated with repository version 588e463. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

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Ignored files:
    Ignored:    .DS_Store
    Ignored:    analysis/assets/
    Ignored:    analysis/site_libs/
    Ignored:    code/regions 2/
    Ignored:    data/raw 2/
    Ignored:    documentation/validation 2/
    Ignored:    figures/manuscript 2/
    Ignored:    output/
    Ignored:    renv/library/
    Ignored:    renv/staging/
    Ignored:    scratch/
    Ignored:    scripts/data_access 2/
    Ignored:    scripts/model_fitting 2/
    Ignored:    scripts/publication 2/
    Ignored:    scripts/reporting 2/
    Ignored:    scripts/submission 2/
    Ignored:    scripts/supplementary 2/
    Ignored:    scripts/validation 2/
    Ignored:    tables/manuscript 2/
    Ignored:    tests/testthat 2/
    Ignored:    tests/testthat/_snaps/
    Ignored:    tmp/

Untracked files:
    Untracked:  R/supplementary_vaccination_groups.R
    Untracked:  analysis/supplementary_vaccination_app.css
    Untracked:  analysis/supplementary_vaccination_app.js
    Untracked:  analysis/supplementary_vaccination_groups.Rmd
    Untracked:  scripts/supplementary/build_vaccination_groups.R
    Untracked:  tests/testthat/test-supplementary-vaccination-groups.R

Unstaged changes:
    Modified:   R/vaccination.R
    Modified:   analysis/_site.yml
    Modified:   analysis/supplementary.Rmd
    Modified:   analysis/supplementary_app.css
    Modified:   analysis/supplementary_app.js
    Modified:   analysis/supplementary_timeseries.Rmd
    Modified:   scripts/publication/build_site.R
    Modified:   scripts/publication/validate_site_inputs.R
    Modified:   tests/testthat/test-supplementary-site.R

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (docs/index.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
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.

Manuscript figures and table

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

Regional analyses

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.

Supplementary analyses

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.

Reproducibility

Exact reproduction uses the versioned files under 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