Simulate a SIR Model with Vaccination and Variants

sirv() simulates a SIR model with vaccinations, a variant type with increased transmissibility, and a variant type with immunity resistance. For simplicity, vaccine- and naturally-acquired immunity are considered equivalent.

sirv(
  start = Sys.Date(),
  end = Sys.Date() + 60L,
  rt = 1,
  r0 = NULL,
  pop = 937166,
  active_cases = 500,
  total_cases = 91350,
  total_vac = 222550,
  vac_per_day = 3500,
  pct_vac_s = 0.8,
  vac_eff = 0.9,
  vac_eff_ek = 0.6,
  pct_var = 0.1/0.85,
  pct_var_uk = 0.85,
  pct_var_ek = 0,
  detect = 1/3
)

Arguments

start

Date or coercible to Date. The start date for simulation.

end

Date or coercible to Date. The end date for simulation.

rt

numeric. The observed reproduction number at the start of simulation; assumed constant other than population and variant effects.

r0

numeric. The baseline reproduction number of the non-variant strains. If this is supplied, rt is ignored.

pop

numeric. The size of the population being modeled.

active_cases

numeric. The observed number of active cases at the start of simulation.

total_cases

numeric. The observed number of total cases at the start of simulation.

total_vac

numeric. The number of vaccinated people at the start of simulation.

vac_per_day

numeric. The number of people vaccinated per day during simulation.

pct_vac_s

numeric between 0 and 1. The fraction of vaccinated people vaccinated who have never had COVID (i.e. are in the susceptible, or "S", compartment).

vac_eff

numeric between 0 and 1. Efficacy of vaccination and natural immunity for non-resistant variants.

vac_eff_ek

numeric between 0 and 1. Efficacy of vaccination and natural immunity for resistant variants (with the E484K mutation).

pct_var

numeric between 0 and 1. Percent of active cases that are variants of some form.

pct_var_uk

numeric between 0 and 1. Percent of variants that are B.1.1.7 (UK) variant or similarly highly transmissible. Assumed to not overlap with pct_var_ek.

pct_var_ek

numeric between 0 and 1. Percent of variants that possess the E484K mutation (vaccine resistance). Assumed to not overlap with pct_var_uk.

detect

numeric between 0 and 1. The percent of true cases detected; applies to both past and future cases.

Value

A tibble with columns time <date>, S <dbl>, I <dbl>, R <dbl>, pct_uk <dbl>, pct_ek <dbl>