simulate_contacts: Simulate contacts of cases

In reconhub/simulacr: Outbreak simulation using branching processes

Description

Under development. Do not use. This simulator adds contacts to the cases of an outbreak object, using user-defined distributions for numbers and duration of contacts. It returns an outbreaks object with cases and contacts, identifying entries in the linelist as cases or contacts, and links as exposures or transmissions.

Usage

simulate_contacts(x, n_contacts, dist_time_to_contact, dist_duration)

Arguments

x	an outbreak object as returned by simulate_outbreak
n_contacts	a vector of values to be used as average number of contacts; values will be drawn at random from this vector to determine the expected number of contacts for each new case
dist_time_to_contact	the distribution of the delay to new exposures, in days after the onset of symptoms
dist_duration	the distribution of duration of the exposure period after the first day, i.e. the time interval between the start and the end of the exposure window

Author(s)

Thibaut Jombart [e-mail]

See Also

simulate_outbreak

Examples

## first simulate an outbreak
## (see example in ?simulate_outbreak)
incubation <- c(0, 1, 1, 1, 1) # numbers = unscaled PMF
infectious_period <- make_disc_gamma(10, 7) # distcrete object
reporting <- function(x) dpois(x, 5) # PMF function
set.seed(1)
x <- simulate_outbreak(R = runif(100, 1, 3), # random values on [1;3]
                       dist_incubation= incubation,
                       dist_infectious_period = infectious_period,
                       dist_reporting = reporting)

## simulate contacts: inputs

## exposure starts 0-2 days post onset
time_to_contact = c(1, 1, 1)

## geom dist for duration of exposure
duration <- function(x) dgeom(x, prob = .9)

x_with_contacts <- simulate_contacts(
    x[1:10, ],
    n_contacts = 1:10, # 1 to 10 contacts
    dist_time_to_contact = time_to_contact,
    dist_duration = duration)

## check output
class(x_with_contacts)
dim(x_with_contacts)
head(x_with_contacts)

plot(x_with_contacts)

reconhub/simulacr documentation built on Dec. 9, 2020, 7:57 p.m.