Add Getting Started vignette

[joshwlambert]

This PR addresses #139 by adding a Getting started vignette (ringbp.Rmd) to the package.

The vignette gives an overview of the {ringbp} model and how to parameterise it, with an explanation of the model parameters. It runs a simple scenario_sim() example and shows how to plot the outbreak (both for weekly and cumulative cases), and summarise the results using extinct_prob().

As suggested in #139 it contains a simplified version of the analysis in Hellewell et al.

The plotting in ringbp.Rmd uses {tinyplot} which does not include any non-base R dependencies so it is a nice lightweight dependency and makes it easy to plot the outbreak data. {tinyplot} is added to Suggests in the DESCRIPTION file.

A references.bib file is added to vignettes/, this includes the Hellewell et al. citation which is cited in ringbp.Rmd.

Summary by CodeRabbit

• Documentation

  • Added a comprehensive "Getting started" vignette covering package workflows, model configuration, running simulations, visualising results, and calculating extinction probabilities.
  • Added bibliography reference.

• Chores

  • Updated package dependencies to include tinyplot.

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Walkthrough

The pull request adds tinyplot as a suggested package dependency, introduces a new bibliography reference entry, and includes a comprehensive "Getting started" vignette demonstrating ringbp package workflows encompassing model configuration, simulations, visualisations, and extinction probability analysis.

Changes

Cohort / File(s)	Change Summary
Package Dependencies DESCRIPTION	Added tinyplot to Suggests field alongside existing testthat (>= 3.0.0) with formatting adjustments
Vignette Resources vignettes/references.bib, vignettes/ringbp.Rmd	Added Hellewell2020 bibliography entry and new "Getting started with ringbp" vignette demonstrating package workflows including model configuration, scenario simulations, result visualisations using tinyplot, and extinction probability calculations

🚥 Pre-merge checks | ✅ 3

✅ 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 Getting Started vignette' directly and clearly describes the primary change in the pull request: adding a new Getting Started vignette file (vignettes/ringbp.Rmd) to the ringbp package.
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: 5

🤖 Fix all issues with AI agents

In `@vignettes/ringbp.Rmd`:
- Line 91: The sentence defining isolation is missing the word "of"; update the
line that starts with "Isolation is the separation infectious individuals from
others, with the aim to prevent further transmission." to read "Isolation is the
separation of infectious individuals from others, with the aim to prevent
further transmission." so the term "Isolation" definition is grammatical and
clear.
- Around line 60-62: Remove the duplicate word "the" in the sentence defining
the offspring distribution by editing the phrase "The mean of the the offspring
distribution is the basic reproduction number (R_0)" to "The mean of the
offspring distribution is the basic reproduction number (R_0)". Update this
occurrence in the vignette text around the sentence that begins "The mean of the
the offspring distribution..." in vignettes/ringbp.Rmd so the wording is correct
and runs as a single "the".
- Line 52: Fix the duplicated word "and and" in the sentence that links to the
[`ringbp-model.Rmd` vignette]; update the sentence text to read "...model and
non-pharmaceutical interventions influence disease transmission..." (or
optionally "...model and the influence of non-pharmaceutical interventions on
disease transmission...") so the duplicate "and" is removed.
- Line 99: In the vignette text referencing event_prob_opts(), correct the
misspelled parameter name "presymtomatic_transmission" to
"presymptomatic_transmission" so the documentation matches the actual parameter;
update the sentence mentioning `asymptomatic`, `presymptomatic_transmission`,
and `symptomatic_ascertained` accordingly.
- Around line 119-129: Fix wording and a misspelling in the quarantine
explanatory paragraph: rephrase to something like "Quarantine in the {ringbp}
model is isolation of individuals regardless of infection status: contacts are
quarantined as soon as the infector is confirmed and isolated, which can occur
before contacts become symptomatic. This differs from isolation, which requires
the infectee to be symptomatic." Correct the misspelling "qurantine" to
"quarantine", ensure the code example using intervention_opts(quarantine =
FALSE) and the sentence "By default, isolation of symptomatic cases is active
and quarantine is not active." remain clear and grammatically correct; update
the paragraph surrounding the variable interventions and function
intervention_opts() accordingly.

[sbfnk]

lgtm

[pearsonca]

Some minor notes; looks good overall