Add epidemic model description vignette

[joshwlambert]

This PR addresses #140 by adding a new vignette to the package (ringbp-model.Rmd), and 5 images (.svg) with model schematics.

The vignette includes descriptions and illustrations of how disease transmission and interventions are structured in the {ringbp} model.

The vignette explains each of the three invention types in the model: isolation, contact tracing and quarantine.

There are two types of model schematic included, one is a multi-transmission scenario and the other is a simpler single-transmission scenario that examine specific transmission and interventions scenarios that can occur in the {ringbp} model.

At the end of the vignette there is a link between the epidemiological parameters that control the interventions, disease transmissibility and delay distributions with the R code for parameterising a {ringbp} simulation. Lastly, there is a link to outbreak_step() for readers that want to inspect the code implementing the scenarios outlined in the vignette.

Summary by CodeRabbit

• Documentation
  • Added comprehensive vignette documenting the ringbp epidemiological model. Covers isolation, contact tracing, and quarantine interventions, transmission scenarios with and without presymptomatic transmission, and detailed model parameters including incubation periods, onset-to-isolation delays, and asymptomatic proportions.

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Walkthrough

A new R Markdown vignette is added documenting the ringbp epidemiological model. The vignette describes isolation, contact tracing, and quarantine interventions; transmission scenarios with varying presymptomatic transmission; model parameters including incubation distributions and delays; and references the scenario_sim() function for simulations.

Changes

Cohort / File(s)	Change Summary
Ringbp model vignette vignettes/ringbp-model.Rmd	New vignette providing comprehensive documentation of the ringbp model, including overview of interventions, transmission scenarios, parameter configurations, and simulation workflow using scenario_sim() function

Suggested reviewers

• sbfnk

Pre-merge checks and finishing touches

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'Add epidemic model description vignette' directly and accurately summarizes the main change—addition of a new vignette documenting the ringbp epidemiological model.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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Actionable comments posted: 1

🧹 Nitpick comments (5)

vignettes/ringbp-model.Rmd (5)

21-21: Please verify that relative figure paths work for installed vignettes

You are referencing schematics via relative paths such as ../man/figures/model_schematic_iso_prevent.svg. These will work when knitting from the package source, but can break once the vignette is installed (HTML moved into doc/ while images stay elsewhere). Consider either:

• using knitr::include_graphics(system.file("figures", "model_schematic_iso_prevent.svg", package = "ringbp")) in a chunk, or
• placing figures under vignettes/ (or inst/) in a layout known to work for installed vignettes and pkgdown.

At minimum, please build and install the package locally and open the installed vignette to confirm all schematics render correctly.

---

34-35: Tidy wording in the contact tracing/quarantine description

Minor grammatical tweaks would improve readability here:

-In the scenarios that contacts are being traced in the model (i.e. the proportion of contacts ascertained > 0%), or quarantine is active, then the infectee is isolated at the earliest of the either the infectors isolation time or an onset-to-isolation delay after their symptom onset time.
+In scenarios where contacts are being traced in the model (i.e. the proportion of contacts ascertained > 0%), or quarantine is active, the infectee is isolated at the earliest of either the infector's isolation time or an onset-to-isolation delay after their symptom onset time.

This removes redundancy (“the earliest of the either”), fixes the possessive (“infector's”), and streamlines the sentence slightly.

---

44-45: Subject–verb agreement in description of scenarios (3a) and (3b)

Very small grammar nit:

-Scenarios (3a) and (3b) shows when a symptomatic infector transmits to a symptomatic infectee.
+Scenarios (3a) and (3b) show when a symptomatic infector transmits to a symptomatic infectee.

This keeps the text polished without changing meaning.

---

66-67: Fix article in description of scenario (5b)

Another small wording improvement:

-Scenario (5b) is equivalent to scenario (5), illustrating what happens if a infectee is not traced because contact tracing ascertainment is not 100%, but for (5b) the transmission is presymptomatic.
+Scenario (5b) is equivalent to scenario (5), illustrating what happens if an infectee is not traced because contact tracing ascertainment is not 100%, but for (5b) the transmission is presymptomatic.

---

80-81: Clarify timing phrasing in scenario (8)

Minor clarity/grammar suggestion:

-Scenario (8) shows the case where Person A infects Person B after Person A enters isolation, and Person B isolates a delay after becoming symptomatic.
+Scenario (8) shows the case where Person A infects Person B after Person A enters isolation, and Person B isolates after a delay following symptom onset.

This avoids the slightly awkward “isolates a delay after” phrasing.

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Reviewing files that changed from the base of the PR and between 85d794f and ae6e5df.

⛔ Files ignored due to path filters (5)

• man/figures/model_schematic_iso_infect.svg is excluded by !**/*.svg
• man/figures/model_schematic_iso_prevent.svg is excluded by !**/*.svg
• man/figures/model_schematic_scenario_postiso.svg is excluded by !**/*.svg
• man/figures/model_schematic_scenario_postsym.svg is excluded by !**/*.svg
• man/figures/model_schematic_scenario_presym.svg is excluded by !**/*.svg

📒 Files selected for processing (1)

• vignettes/ringbp-model.Rmd (1 hunks)

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[joshwlambert]

Tip: it might be easier to read and review the vignette by pulling theses changes locally and running pkgdown::build_site() to see the vignette in the preview of the package website.