Last updated: 2026-08-31
Checks: 7 0
Knit directory: covid_script/
This reproducible R Markdown analysis was created with workflowr (version 1.7.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
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The results in this page were generated with repository version e5925a4. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for
the analysis have been committed to Git prior to generating the results
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file, but you know if there are other scripts or data files that it
depends on. Below is the status of the Git repository when the results
were generated:
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These are the previous versions of the repository in which changes were
made to the R Markdown (analysis/data_sources.Rmd) and HTML
(docs/data_sources.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 |
|---|---|---|---|---|
| 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