sim_contacts | R Documentation |
Simulate contacts for an infectious disease outbreak
sim_contacts(
contact_distribution = function(x) stats::dpois(x = x, lambda = 2),
infectious_period = function(x) stats::rlnorm(n = x, meanlog = 2, sdlog = 0.5),
prob_infection = 0.5,
outbreak_start_date = as.Date("2023-01-01"),
anonymise = FALSE,
outbreak_size = c(10, 10000),
population_age = c(1, 90),
contact_tracing_status_probs = c(under_followup = 0.7, lost_to_followup = 0.2, unknown
= 0.1),
config = create_config()
)
contact_distribution |
A The function can be defined or anonymous. The function must have a single
argument in the form of an An The default is an anonymous function with a Poisson probability mass function
( |
infectious_period |
A The function can be defined or anonymous. The function must return a vector of randomly generated real numbers representing sampled infectious periods. The function must have a single argument, the number of random infectious periods to generate. An The default is an anonymous function with a lognormal distribution random
number generator ( |
prob_infection |
A single |
outbreak_start_date |
A |
anonymise |
A |
outbreak_size |
A |
population_age |
Either a |
contact_tracing_status_probs |
A named |
config |
A list of settings to adjust the randomly sampled delays and
Ct values. See |
A contacts <data.frame>
Joshua W. Lambert, Carmen Tamayo
# quickly simulate contact tracing data using the function defaults
contacts <- sim_contacts()
head(contacts)
# to simulate more realistic contact tracing data load epiparameters from
# {epiparameter}
library(epiparameter)
contact_distribution <- epiparameter(
disease = "COVID-19",
epi_name = "contact distribution",
prob_distribution = create_prob_distribution(
prob_distribution = "pois",
prob_distribution_params = c(mean = 2)
)
)
infectious_period <- epiparameter(
disease = "COVID-19",
epi_name = "infectious period",
prob_distribution = create_prob_distribution(
prob_distribution = "gamma",
prob_distribution_params = c(shape = 1, scale = 1)
)
)
contacts <- sim_contacts(
contact_distribution = contact_distribution,
infectious_period = infectious_period,
prob_infection = 0.5
)
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