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.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
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 5370cb2. 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: output/
Ignored: renv/library/
Ignored: renv/staging/
Ignored: scratch/
Ignored: tests/testthat/_snaps/
Ignored: tmp/
Untracked files:
Untracked: R/supplementary_bundle.R
Untracked: analysis/supplementary_app.css
Untracked: analysis/supplementary_app.js
Untracked: analysis/supplementary_timeseries.Rmd
Untracked: analysis/supplementary_wave_maps.Rmd
Untracked: scripts/supplementary/
Untracked: tests/testthat/test-supplementary-bundle.R
Untracked: tests/testthat/test-supplementary-site.R
Unstaged changes:
Modified: analysis/_site.yml
Modified: analysis/index.Rmd
Modified: analysis/supplementary.Rmd
Modified: scripts/publication/build_site.R
Modified: scripts/publication/validate_site_inputs.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/reproduction.Rmd) and HTML
(docs/reproduction.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 | 3e71c91 | Ziang Zhang | 2026-08-31 | build: publish Zenodo reproduction guidance |
| Rmd | 9b2893c | Ziang Zhang | 2026-08-31 | feat: prepare Zenodo results deposit |
| 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 |
Run all commands from the repository root.
renv::restore()system2(
"Rscript",
"scripts/data_access/verify_snapshots.R"
)
system2("Rscript", "tests/testthat.R")The first command verifies file sizes and SHA-256 hashes for the exact source snapshots used by the analysis.
The following commands validate source-specific preprocessing and construct manifests without fitting models:
system2(
"Rscript",
c(
"scripts/model_fitting/europe/refit_eurostat.R",
"--manifest-only=true"
)
)
system2(
"Rscript",
c(
"scripts/model_fitting/england_wales/refit.R",
"--manifest-only=true"
)
)
system2(
"Rscript",
c(
"scripts/model_fitting/ireland/refit.R",
"--manifest-only=true"
)
)
system2(
"Rscript",
c(
"scripts/model_fitting/canada/refit.R",
"--manifest-only=true"
)
)Regional runners fit models when --manifest-only=true is
omitted. The United States target graph is started with:
system2(
"Rscript",
"scripts/pipeline/run_pipeline.R"
)These computations may require substantial memory and wall time. They
write fitted objects and posterior draws below the ignored
output/ directory and are not part of website
generation.
Canonical fitted objects are distributed separately from Git because model fitting is computationally intensive. A checksum-verified Zenodo package can be prepared from the completed local analysis without rerunning any model:
system2(
"Rscript",
"scripts/submission/prepare_zenodo_deposit.R"
)The package retains final production fits, compact diagnostics, reporting inputs, configuration, and provenance. Validation duplicates, compiler products, failed runs, stale freezes, and private manuscript files are excluded. The DOI is added after creator metadata, license, and the article relationship are confirmed.
After the required standardized summaries are present locally:
system2(
"Rscript",
c(
"scripts/reporting/run_all.R",
"--include_caption_review=true",
"--strict=true"
)
)Figures are written as editable PDF and 300-dpi PNG files. Table 1 is written as CSV and HTML. A completed, validated release freeze can then be synchronized to the tracked publication directories.
system2(
"Rscript",
"scripts/publication/build_site.R"
)This final command verifies the tracked artifact hashes and builds the website directly from those files. It does not read fitted model objects or posterior draws.
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