Last updated: 2026-09-01
Checks: 7 0
Knit directory: covid_script/
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Ignored files:
Ignored: .DS_Store
Ignored: analysis/assets/
Ignored: code/regions 2/
Ignored: data/raw 2/
Ignored: documentation/validation 2/
Ignored: figures/manuscript 2/
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Ignored: renv/staging/
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Ignored: scripts/data_access 2/
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Ignored: scripts/reporting 2/
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made to the R Markdown (analysis/data_sources.Rmd) and HTML
(docs/data_sources.html) files. If you’ve configured a
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hyperlinks in the table below to view the files as they were in that
past version.
| 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 |
| 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 |
Exact reproduction uses the files committed under
data/raw/, verified against their SHA-256 manifest. Data
providers may revise provisional counts, historical records, schemas, or
download URLs after the repository snapshot date. The provider-access
scripts therefore download current versions to a separate, ignored
directory and never silently replace the canonical inputs.
| Provider | Region | Frequency | Geography | Provider identifier | Repository snapshot |
|---|---|---|---|---|---|
| Eurostat | europe | weekly | country | DEMO_R_MWK_20 | data/raw/eurostat/demo_r_mwk_20_linear.csv |
| CDC WONDER | united_states | monthly | state | Multiple Cause of Death 1999-2020 and provisional mortality | data/raw/cdc_wonder/sex_stratified |
| CDC WONDER | united_states | monthly | state | Multiple Cause of Death 1999-2020 and provisional mortality | data/raw/cdc_wonder/non_sex_stratified |
| Statistics Canada | canada | weekly | province_or_territory | 13-10-0768-01 | data/raw/statcan/13100768.csv |
| Office for National Statistics | england_wales | daily | England and Wales | ONS reference 14173 | data/raw/ons/daily_deaths_occurrences_1981_2020.xlsx |
| Office for National Statistics | england_wales | weekly | England and Wales | 2021 week 52 edition | data/raw/ons/weekly_deaths_2021_week52.xlsx |
| Office for National Statistics | england_wales | weekly | England and Wales | 2022 week 52 edition | data/raw/ons/weekly_deaths_2022_week52.xlsx |
| Office for National Statistics | england_wales | weekly | England and Wales | 2023 v37 week 35 edition | data/raw/ons/weekly_deaths_2023_week35.xlsx |
| Central Statistics Office Ireland | ireland | quarterly | Ireland | VSQ20 | data/raw/cso/ireland_quarterly_deaths.csv |
| Our World in Data | europe | daily | country | archived COVID-19 vaccination extract | data/raw/owid/europe_vaccination_snapshot.rda |
| Our World in Data | united_states | daily | state | us_state_vaccinations.csv | data/raw/owid/us_state_vaccination_snapshot.rda |
| United States Census Bureau | united_states | static | state | GENZ2018 cb_2018_us_state_500k | data/raw/us_census/cb_2018_us_state_500k.zip |
system2(
"Rscript",
"scripts/data_access/verify_snapshots.R"
)| Provider | Versioned files | Size (MB) |
|---|---|---|
| CDC WONDER | 14 | 58.1 |
| Central Statistics Office Ireland | 1 | 0.1 |
| Eurostat | 1 | 54.5 |
| Office for National Statistics | 4 | 8.2 |
| Our World in Data | 2 | 0.0 |
| Statistics Canada | 1 | 28.4 |
| United States Census Bureau | 1 | 3.2 |
The scripts in scripts/data_access
document how to retrieve current provider versions where automated
access is available. CDC WONDER exports require acceptance of the
provider’s data-use terms and are retained as saved query exports.
Source-specific details are recorded in documentation/data-sources.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 here_1.0.2 later_1.4.4
[33] digest_0.6.39 R6_2.6.1 pillar_1.11.1 magrittr_2.0.5
[37] bslib_0.9.0 tools_4.5.1 cachem_1.1.0