Expand case studies vignette with new examples and literature

[seabbs-bot]

Summary

Expands vignettes/case-studies.Rmd with new case studies, a public health surveillance entry, and ten additional peer-reviewed papers in the "By others" literature section.

New case study

• Charniga et al. (CDC) mpox nowcasting — github.com/kcharniga/mpox_nowcasting. Code and data for nowcasting/forecasting the 2022 U.S. mpox outbreak; results were shared in real time with the CDC Mpox Response.

New public health surveillance entry

• CDC CFA — Current Epidemic Trends (ongoing) — cdc.gov/cfa-modeling-and-forecasting/rt-estimates. The page explicitly names EpiNow2 as one of the tools used to estimate weekly Rt for COVID-19, influenza, and RSV across U.S. states from NSSP emergency department visit data.

New literature — By others

All papers were verified by fetching the source page (PubMed, PMC, or publisher) before inclusion. Evidence of EpiNow2 use for each:

Paper	Journal	Evidence of EpiNow2 use
Binny et al. 2022	PeerJ	PMC9583856: "used the EpiNow2 package to estimate time-varying Rt during Aotearoa New Zealand's August 2021 Delta outbreak"
Parker et al. 2022	Nature Communications	PMC9376901: "We estimated the time-varying effective reproduction number with the Epinow2 package, fitting the time series of cases using MCMC sampling"
Ranoa et al. 2022	Nature Communications	PMC9184485: "The calculations were done using the package EpiNow2 which implements several open-source tools and current best practices"
Aravamuthan et al. 2023	BMC Public Health	PMC9937741: "used EpiNow2 to estimate the time-varying effective reproduction number Rt using a Bayesian latent variable model"
Kerr et al. 2023	GeoHealth	PMC10030230: "The time-varying reproductive number of COVID-19 (Rt) was generated with EpiNow2 for each Brazilian state"
Charniga et al. 2024	Epidemics	PubMed 38452454: "performed nowcasting and forecasting for the 2022 mpox outbreak in the United States using the R package EpiNow2"
Richard et al. 2024	MMWR	mm7346a3: "EpiNow2 (version 1.4.0) in R (version 4.3.1)" used to estimate Rt and Pr(Rt > 1) from nowcasted ED visit data
Costa et al. 2025	Ciência Rural	scielo.br: "a Bayesian latent variable approach using back-calculation to estimate the time-varying reproduction number via the EpiNow2 package" — applied to foot-and-mouth disease outbreaks
Pekar et al. 2025	Nature Medicine	PMC12092259: EpiNow2 used to infer Re and growth rate during NYC mpox outbreak, "assuming a gamma-distributed generation time with a mean of 12.6 days"

This was opened by a bot. Please ping @seabbs for any questions.

Summary by CodeRabbit

• Documentation
  • Expanded case studies vignette with additional literature references and public health surveillance examples
  • Added work-in-progress status notice to case studies documentation
  • Enhanced bibliography with recent publications, including mpox transmission studies, CDC forecasting resources, and EpiNow2 usage examples for infectious disease monitoring

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Walkthrough

This pull request expands the case studies vignette documentation across two files. The NEWS.md entry announces updates to the case studies vignette, whilst the vignette itself adds a work-in-progress notice, includes new case study examples (including mpox outbreak), expands the public health surveillance section with CDC and Rt-states references, and substantially extends the literature citations in both author and community-contributed sections.

Changes

Case Studies Vignette Documentation

Layer / File(s)	Summary
NEWS Entry Update NEWS.md	Development-version announcement expanded to reference additional literature and public health surveillance content in the case studies vignette.
Case Studies and Work-in-Progress Notice vignettes/case-studies.Rmd	Work-in-progress notice added after knitr setup; case studies section expanded with new bullet entries including an mpox outbreak example.
Public Health Surveillance Content vignettes/case-studies.Rmd	Public health surveillance subsection expanded with CDC technical report and Rt-states citations, and descriptive text on EpiNow2 application to time-varying reproduction number estimation across COVID-19, influenza, and RSV.
Literature References vignettes/case-studies.Rmd	Literature section substantially expanded under "By package authors" and "By others" subsections, with new citations through recent years and entries covering mpox transmission and contemporary epidemiological studies.

Possibly related PRs

• epiforecasts/EpiNow2#1304: Prior PR that also modifies the same vignette and NEWS files with documentation content updates.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The pull request title directly and accurately summarises the main change: expanding the case studies vignette with new examples and additional literature references.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch add-case-studies

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[seabbs]

@sbfnk I got a team of @seabbs-bot to look into this via searching github and cross checking. I haven't manually followed up yet. I think its useful. If I manually check the citation info for each one are we happy?

Note that the Charniga one enters twice but that seems reasonable?