simulate_infection_histories: Simulate infection histories

In seroanalytics/serosolver: Inference Framework for Serological Data

Simulate infection histories

Description

Given a vector of infection probabilities and potential infection times, simulates infections for each element of ages (ie. each element is an individual age. Only adds infections for alive individuals)

Usage

simulate_infection_histories(
  p_inf,
  strain_isolation_times,
  sampling_times,
  DOBs
)

Arguments

p_inf	a vector of attack rates (infection probabilities) for each year
strain_isolation_times	the vector of possible infection times
sampling_times	vector of potential sampling times
DOBs	a vector of ages for each individual

Value

a list with a matrix of infection histories for each individual in ages and the true attack rate for each epoch

See Also

Other simulation_functions: simulate_attack_rates(), simulate_data(), simulate_group(), simulate_individual_faster(), simulate_individual()

Examples

p_inf <- runif(40,0.1,0.4)
strain_isolation_times <- seq_len(40) + 1967
n_indivs <- 100
sampling_times <- rep(max(strain_isolation_times), n_indivs)
DOBs <- rep(min(strain_isolation_times), n_indivs)
inf_hist <- simulate_infection_histories(p_inf, strain_isolation_times, sampling_times, DOBs)

seroanalytics/serosolver documentation built on April 24, 2023, 9:52 a.m.