Simulate Aggregate Expected Deaths

Agesim_infxn_2_death(
  fatalitydata,
  infections,
  m_od = 14.26,
  s_od = 0.79,
  curr_day,
  spec,
  sens,
  demog,
  sero_delay_rate,
  simulate_seroreversion,
  sero_rev_shape = NULL,
  sero_rev_scale = NULL,
  smplfrac = 1,
  return_linelist = FALSE
)

Arguments

fatalitydata	dataframe; The strata-specific fatalities to simulate given a probability of infection and a noise effect. The column names: strata, ifr, rho, and Ne correspond to (patient) strata, infection-fatality ratio, the probability of infection (i.e. a probalistic attack rate), and a noise effect, respectively.
infections	integer vector; The infections for each day up to the current day.
m_od	double; The mean of the onset of infection to death (gamma distribution).
s_od	double; The coefficient of variation of the onset of infection to death (gamma distribution).
curr_day	numeric; Current day of epidemic (considered up to but not including this day).
spec	double; Specificity of the Seroprevalence Study
sens	double; Sensitivity of the Seroprevalence Study
demog	dataframe; Strata-specific population (demographic) counts. The columns names strata and popN correspond to (patient) strata and the number of individuals within that strata. The demography strata must match the fatalitydata strata. Only considered if `simulate_seroprevalence = TRUE`
sero_delay_rate	double; Rate of time from infection to seroconversion, assumed to be exponentially distributed
simulate_seroreversion	logical; Whether seroreversion (due to waning of antibodies) should be simulated or not
sero_rev_shape	double; The shape parameter of the Weibull seroreversion distribution
sero_rev_scale	double; The scale parameter of the Weibull seroreversion distribution
smplfrac	numeric; Sampling fraction for the observed seroprevalence study (assumed to be a simple random sample of all infected)
return_linelist	logical; Whether or not the linelist that was used to create the observed marginal data should be returned. N.B. the linelist can be quite large/burdensome for memory depending on population size and number of days considered.