ringbp: Simulate infectious disease transmission with contact tracing

ringbp is an R package that provides methods to simulate infectious disease transmission in the presence of contact tracing. It was initially developed to support a paper written in early 2020 to assess the feasibility of controlling COVID-19. For more details on the methods implemented here, see the associated paper.

Installation

The current development version of ringbp can be installed from GitHub using the pak package.

if(!require("pak")) install.packages("pak")
pak::pak("epiforecasts/ringbp")

Quick start

The main functionality of the package is in the scenario_sim() function. Here is an example for running 10 simulations of a given scenario:

library("ringbp")
library("ggplot2")

res <- scenario_sim(
  n = 10, ## 10 simulations
  initial_cases = 1, ## one initial case in each of the simulations
  prop_asymptomatic = 0, ## no asymptomatic infections
  prop_ascertain = 0.2, ## 20% probability of ascertainment by contact tracing
  cap_cases = 4500, ## don't simulate beyond 4500 infections
  cap_max_days = 350, ## don't simulate beyond 350 days
  r0_isolated = 0.5, ## isolated individuals have R0 of 0.5
  r0_community = 2.5, ## non-isolated individuals have R0 of 2.5
  disp_community = 0.16, ## dispersion parameter in the community
  disp_isolated = 1, ## dispersion  parameter of those isolated
  onset_to_isolation = \(x) stats::rweibull(n = x, shape = 1.651524, scale = 4.287786), ## time from onset to isolation
  incubation_period = \(x) stats::rweibull(n = x, shape = 2.322737, scale = 6.492272), ## incubation period
  prop_presymptomatic = 0.5, ## probability of onward infection time being before symptom onset
  quarantine = FALSE ## whether quarantine is in effect
)

Plot of weekly cases

ggplot(
  data = res, aes(x = week, y = cumulative, col = as.factor(sim))
) +
  geom_line(show.legend = FALSE, alpha = 0.3) +
  scale_y_continuous(name = "Cumulative number of cases") +
  theme_bw()

Estimate extinction probability

extinct_prob(res, cap_cases = 4500)
#> [1] 0.8

Contributors

All contributions to this project are gratefully acknowledged using the allcontributors package following the all-contributors specification. Contributions of any kind are welcome!

Code

seabbs, sbfnk, jhellewell14, timcdlucas, amygimma, joshwlambert, Bisaloo, actions-user

Issue Authors

pearsonca, sophiemeakin

Issue Contributors

thimotei, adamkucharski, dcadam, jamesmbaazam