Estimate Initial R Compartment for Single Location

Estimates the recovered population at time t0 for a single location based on historical infection data, accounting for waning immunity.

Usage

est_initial_R_location(
  cases,
  dates,
  population,
  t0,
  epsilon,
  sigma = 0.01,
  rho = 0.1,
  chi = 0.5,
  iota,
  gamma_1,
  gamma_2
)

Arguments

cases

Vector of reported suspected cholera cases

dates

Vector of dates corresponding to cases

population

Population size at t0

t0

Target date for estimation

epsilon

Waning immunity rate (per day)

sigma

Proportion of infections that are symptomatic

rho

Reporting rate of symptomatic cases

chi

Diagnostic positivity rate

iota

Incubation rate (per day)

gamma_1

Symptomatic recovery rate (per day)

gamma_2

Asymptomatic recovery rate (per day)

Value

Numeric value of R compartment size at t0