simulate_infections {EpiNow2} | R Documentation |
Simulate infections using the renewal equation
Description
Simulations are done from given initial infections and, potentially
time-varying, reproduction numbers. Delays and parameters of the observation
model can be specified using the same options as in estimate_infections()
.
Usage
simulate_infections(
R,
initial_infections,
day_of_week_effect = NULL,
generation_time = generation_time_opts(),
delays = delay_opts(),
truncation = trunc_opts(),
obs = obs_opts(),
CrIs = c(0.2, 0.5, 0.9),
backend = "rstan",
seeding_time = NULL,
pop = 0
)
Arguments
R |
a data frame of reproduction numbers (column |
initial_infections |
numeric; the initial number of infections (i.e.
before |
day_of_week_effect |
either |
generation_time |
A call to |
delays |
A call to |
truncation |
A call to |
obs |
A list of options as generated by |
CrIs |
Numeric vector of credible intervals to calculate. |
backend |
Character string indicating the backend to use for fitting stan models. Supported arguments are "rstan" (default) or "cmdstanr". |
seeding_time |
Integer; the number of days before the first time point
of |
pop |
Integer, defaults to 0. Susceptible population initially present. Used to adjust Rt estimates when otherwise fixed based on the proportion of the population that is susceptible. When set to 0 no population adjustment is done. |
Details
In order to simulate, all parameters that are specified such as the mean and standard deviation of delays or observation scaling, must be fixed. Uncertain parameters are not allowed.
Value
A data.table of simulated infections (variable infections
) and
reported cases (variable reported_cases
) by date.
Examples
R <- data.frame(
date = seq.Date(as.Date("2023-01-01"), length.out = 14, by = "day"),
R = c(rep(1.2, 7), rep(0.8, 7))
)
sim <- simulate_infections(
R = R,
initial_infections = 100,
generation_time = generation_time_opts(
fix_parameters(example_generation_time)
),
delays = delay_opts(fix_parameters(example_reporting_delay)),
obs = obs_opts(family = "poisson")
)