Update vignette to reference epidist and primarycensored packages

[jamesmbaazam]

NOTE: To be merged after #1140

Summary

• Updated the workflow vignette to point to the current {epidist} and {primarycensored} packages instead of the outdated {dynamicaltruncation} reference
• Clarified that estimate_delays() is a wrapper around {primarycensored}
• Added both package names to the WORDLIST for spell-checking

Fixes #1173

Test plan

• Built the vignette using knitr to ensure it renders correctly
• Pre-commit hooks passed (spell-check, style, etc.)

🤖 Generated with Claude Code

Summary by CodeRabbit

• Documentation
  • Enhanced vignette documentation with updated information on delay estimation methodologies and expanded recommendations for supplementary tools and approaches.

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Walkthrough

The pull request expands the WORDLIST with new entries and reorganises existing items, whilst updating vignette documentation to reference the primarycensored and epidist R packages instead of dynamicaltruncation.

Changes

Cohort / File(s)	Summary
WORDLIST expansion inst/WORDLIST	Added numerous new entries including user/project names, terms, and variants (e.g., Dirichlet, Dockerfile, ECDC, EpiEstim, EpiNow, GauriSaran, Nowcasts, Poisson, Wellcome); reorganised and replaced previous entries to broaden lexical coverage.
Vignette documentation updates vignettes/estimate_infections_workflow.Rmd, vignettes/estimate_infections_workflow.Rmd.orig	Updated descriptions of delay estimation to describe estimate_delays() as a wrapper around primarycensored package; replaced citations of dynamicaltruncation with references to epidist R package.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

• WORDLIST additions are repetitive and cosmetic in nature
• Vignette updates are straightforward documentation rewording with no functional logic changes

Suggested reviewers

• seabbs

Pre-merge checks and finishing touches

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	The PR title accurately summarizes the main change: updating vignette references to epidist and primarycensored packages instead of outdated alternatives.
Linked Issues check	✅ Passed	The PR successfully addresses issue #1173 by updating vignette content to reference primarycensored and epidist instead of dynamicaltruncation, and adding both packages to WORDLIST.
Out of Scope Changes check	✅ Passed	All changes are directly scoped to the stated objective: vignette content updates and WORDLIST additions for spell-checking, with no extraneous modifications.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.

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Actionable comments posted: 1

📜 Review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between b6f7a10 and 34e7e37.

📒 Files selected for processing (3)

• inst/WORDLIST (3 hunks)
• vignettes/estimate_infections_workflow.Rmd (1 hunks)
• vignettes/estimate_infections_workflow.Rmd.orig (1 hunks)

🧰 Additional context used

🧠 Learnings (1)

📚 Learning: 2025-07-23T20:57:00.615Z

Learnt from: jamesmbaazam
Repo: epiforecasts/EpiNow2 PR: 695
File: vignettes/benchmarks.Rmd:45-45
Timestamp: 2025-07-23T20:57:00.615Z
Learning: In the EpiNow2 project, vignettes/benchmarks.Rmd is a rendered output file generated from vignettes/benchmarks.Rmd.orig. The source .Rmd.orig file uses proper dynamic core detection with inline R expressions, and the rendered .Rmd shows the evaluated results from when it was knitted.

Applied to files:

• vignettes/estimate_infections_workflow.Rmd.orig

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🔇 Additional comments (3)

vignettes/estimate_infections_workflow.Rmd.orig (1)

109-110: Source file updated correctly.

The documentation changes in the source file match those in the rendered output. The references to primarycensored and epidist are correctly updated.

Note: Verification of URLs and the wrapper claim was requested in the review of the rendered file (vignettes/estimate_infections_workflow.Rmd).

inst/WORDLIST (2)

52-52: Good addition for spell-checking.

The epidist package name is correctly added to the wordlist, supporting the vignette documentation updates.

---

162-162: Good addition for spell-checking.

The primarycensored package name is correctly added to the wordlist, supporting the vignette documentation updates.

Note: The wordlist also includes many other additions throughout the file, which appear to be general maintenance to expand lexical coverage for the package's terminology. These are appropriate housekeeping changes.