Add testing to the outbreak model with test sensitivity

[joshwlambert]

This PR addresses #176 by adding testing to the epidemic model. The testing is assumed to be conducted for all symptomatic individuals in the model and the test_sensitivity argument added to intervention_opts() controls which proportion of individuals get a false negative test result using binomial sampling.

Symptomatic individuals in the model that are tested and get a false negative are not isolated throughout their infectious period (the same as asymptomatic individuals).

The variable missed is renamed to traced and the boolean inverted. The argument symptomatic_ascertained is renamed to symptomatic_traced. These two changes harmonise the variable naming in the simulation code, addressing #208.

Summary by CodeRabbit

Release Notes

• New Features

  • Added test sensitivity parameter to intervention options (0–1 range) for diagnostic test accuracy configuration; false negative results now prevent case isolation and contact tracing.

• Documentation

  • Updated intervention options documentation to describe the new test sensitivity parameter and its impact on isolation behaviour.

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[coderabbitai]

Walkthrough

The changes introduce test sensitivity as a new intervention option. A test_sensitivity parameter (default 1) is added to intervention_opts and documented. The outbreak simulation logic now models test outcomes using rbinom sampling, applying false negative rates to adjust isolation behaviour for symptomatic cases, alongside related dependency imports and global variable declarations.

Changes

Cohort / File(s)	Summary
Core Options Infrastructure R/opts.R, man/intervention_opts.Rd	Added test_sensitivity parameter (numeric, 0-1, default 1) to intervention_opts function. Updated function signature and documentation to describe parameter behaviour regarding false negatives in testing.
Simulation Logic R/outbreak_step.R	Added rbinom import. Introduced test_positive temporary column in new_cases sampling pipeline. For symptomatic non-missed cases, generates test results using rbinom with interventions\$test_sensitivity probability. Sets isolation time to Inf on false negatives to model missed isolation. Removes test_positive column from final output.
Package Configuration NAMESPACE	Added importFrom directive for rbinom from stats package.
Global Declarations R/globals.R	Added test_positive to globalVariables declaration under outbreak_step category.
Test Updates tests/testthat/test-opts.R	Updated test expectations to validate new test_sensitivity field in ringbp_intervention_opts structure returned by intervention_opts.

Possibly related PRs

• Improve package test suite #160: Adds tests for intervention_opts function, directly corresponding to the new test_sensitivity parameter additions.
• Add latent_period to control minimum generation time #142: Modifies the same outbreak_step.R and opts.R implementation paths affected by these changes.

Suggested labels

testing

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title accurately summarizes the main change: adding test sensitivity functionality to the outbreak model for testing symptomatic individuals.
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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[coderabbitai]

Actionable comments posted: 0

Caution

Some comments are outside the diff and can’t be posted inline due to platform limitations.

⚠️ Outside diff range comments (1)

R/outbreak_step.R (1)

17-22: Update the interventions parameter doc to include test_sensitivity.
The description still says it contains only quarantine, which is now outdated.

✏️ Proposed doc tweak

-#'   [intervention_opts()]. Contains one element: `quarantine`
+#'   [intervention_opts()]. Contains two elements: `quarantine` and
+#'   `test_sensitivity`

[sbfnk]

looks good to me except minor doc comments - for future issue testing of contacts (irrespective of symptoms) would be a good addition.

[pearsonca]

Minor items to consider

[pearsonca]

extracted one remaining concern i had as new issue; otherwise LGTM