Run ODE Solver for SIRS model

Run ODE Solver for SIRS model

Usage

run(
  iter = NULL,
  initial_compartments = NULL,
  initial_compartments_steady = NULL,
  params = NULL,
  times = NULL,
  name = NULL
)

Arguments

iter

Number of iterations, often referred to as 'nsamples' in package examples

initial_compartments

Initial compartment sizes, including (proportions, stored as list)

initial_compartments_steady

Initial compartment sizes for steady state calculation (proportions, stored as list)

params

SIRS parameters, stored as a list

times

Length of projection (days)

name

Name of context being simulated

Value

List containing iteration details, including initial compartment sizes for ODE solver and steady state calculation, parameters, context name, and daily, proportional sizes of each SIRS compartment and cumulative infections during the 120 day projection, and whether the SARS-CoV-2 persists at equilibrium.

Examples

if (FALSE) {
nsamples = 10

example_inits <- c(S_wild = 1, I_wild = 0,
                   R_wild = 0, I_wild_cumulative = 0,
                   S_captive = 1, I_captive = 0,
                   R_captive = 0, I_captive_cumulative = 0)

example_inits_steady <- c(S_wild = 1, I_wild = 0,
                   R_wild = 0, S_captive = 1,
                   I_captive = 0, R_captive = 0)

# set the time to run
example_times <-  seq(0, 365, by = 1)
# Set parameters of transmission, immunity, recovery

example_params <- c(alpha_immunity = 0.03,
                    beta_aero_ww = 0.01,
                    beta_aero_cw = 0.01,
                    beta_aero_cc = 0.02,
                    beta_aero_hw = 0.01,
                    beta_aero_hc = 0.2,
                    beta_dc_ww = 0.01,
                    beta_dc_cw = 0.01,
                    beta_dc_cc = 0.01,
                    gamma_recov = 0.01,
                    I_human = 0.05,
                    boost = 0)

run(iter = nsamples,
initial_compartments = example_inits,
initial_compartments_steady = example_inits_steady,
params = example_params,
times = example_times,
name = Test)}