Last updated: 2026-08-31
Checks: 6 1
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.
The R Markdown is untracked by Git. To know which version of the R
Markdown file created these results, you’ll want to first commit it to
the Git repo. If you’re still working on the analysis, you can ignore
this warning. When you’re finished, you can run
wflow_publish to commit the R Markdown file and build the
HTML.
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(20260831) was run prior to running
the code in the R Markdown file. Setting a seed ensures that any results
that rely on randomness, e.g. subsampling or permutations, are
reproducible.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
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.
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
(you can use wflow_publish or
wflow_git_commit). workflowr only checks the R Markdown
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:
Ignored files:
Ignored: .DS_Store
Ignored: analysis/assets/
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.
There are no past versions. Publish this analysis with
wflow_publish() to start tracking its development.
This explorer extends Figure 4 and Figure 5 to every original age stratum with an available fitted result. Choose separate low- and high-vaccination thresholds, then add, remove, or reassign individual countries or states. The default grouping uses vaccination coverage as of July 1, 2021 (or the latest available European record on or before that date); the manuscript preset is also available for direct comparison.
Selections update the chart immediately. Choose Excluded to remove a location, or Low/High to add it to either group.
| Country or state | Vaccinated (%) | Measurement date | Model status | Group |
|---|
Both groups are aggregated date by date with inverse-variance fixed-effect weights, using dates shared by every selected location. Figure 4 shows the normal-approximation interval as a ribbon. Figure 5 shows the female-minus-male P-score difference with dashed interval bounds; European Figure 5 trajectories use the same centered 14-day box smoother as the manuscript figure. Locations without the required paired sex-stratified result are shown explicitly and cannot be assigned for that panel.
All browser assets are summary-only. The frozen extension contains geography- level means and variances, not fitted models or posterior draw matrices.
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] stringr_1.6.0 compiler_4.5.1 fs_1.6.6 Rcpp_1.1.1-1.1
[29] pkgconfig_2.0.3 later_1.4.4 digest_0.6.39 R6_2.6.1
[33] pillar_1.11.1 magrittr_2.0.5 bslib_0.9.0 tools_4.5.1
[37] cachem_1.1.0