simulate_si: Simulate serial interval
In mrc-ide/hermione: Robust estimation of COVID-19 Serial Interval

Description Usage Arguments Details Value Author(s)

Simulate serial interval

simulate_si(
  mean_ip,
  sd_ip,
  mean_inf,
  sd_inf,
  mean_iso = NULL,
  sd_iso = NULL,
  offset = 0,
  nsim = 50
)

`mean_ip`	Mean Incubation Period
`sd_ip`	Standard deviation of the incubation period
`mean_inf`	Infectious Period
`sd_inf`	Standard deviation of the infectious period
`mean_iso`	Mean delay from symptom onset to case isolation. If this is null, then isolation is not simulated.
`sd_iso`	Standard deviation of the delay from symptom onset to case isolation
`offset`	Numeric - days before symptom onset that infectiousness is assumed to begin. If `offset` is NULL, then asymptomatic infectiousness is assumed to be absent.
`nsim`	Number of transmission pairs to simulate

This function simulates serial interval with or without case isolation, and with or without pre-symptomatic infectiousness. At the moment, infectious period, incubation period and onset to isolation distributions are assumed to be gamma distributed.

a data frame with columns t_1, t_2, si t_1 corresponds to draws from the infectious period, t_2 corresponds to draws from the incubation period, and si is the serial interval (t_1 + t_2). If mean_iso and sd_iso are not NULL, then the output also contains a column nu corresponding to draws from the distribution of onset to isolation.

Sangeeta Bhatia

mrc-ide/hermione documentation built on Aug. 15, 2020, 9:16 a.m.