├── .Rbuildignore ├── .github ├── dependabot.yml └── workflows │ ├── R-CMD-check.yaml │ ├── pkgdown.yaml │ ├── render_readme.yml │ ├── test-coverage.yaml │ └── upload-coverage.yaml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── aux_functions.R ├── checking.R ├── globals.R ├── opts.R ├── outbreak_model.R ├── outbreak_setup.R ├── outbreak_step.R ├── ringbp-package.R ├── sample_offspring.R └── scenario_sim.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── codecov.yml ├── man ├── check_dist_func.Rd ├── delay_opts.Rd ├── event_prob_opts.Rd ├── extinction.Rd ├── figures │ └── README-plot-1.png ├── incubation_to_generation_time.Rd ├── intervention_opts.Rd ├── offspring_opts.Rd ├── outbreak_continue.Rd ├── outbreak_model.Rd ├── outbreak_setup.Rd ├── outbreak_step.Rd ├── presymptomatic_transmission_to_alpha.Rd ├── ringbp-package.Rd ├── sample_offspring.Rd ├── scenario_sim.Rd └── sim_opts.Rd ├── tests ├── testthat.R └── testthat │ ├── _snaps │ ├── 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