How to test - SIR script example refactored

sir_script_refactored.R

# parameters --------------------------------------------------------------
N <- 1000      # network size
avk <- 7       # desired average degree
gamma <- 0.25  # recovery rate
tau <- 0.27    # per-edge infection rate
max_time <- 50 # maximum simulation length
i0 <- 10       # initial number of infected individuals


# -------------------------------------------------------------------------

# build erdos-renyi random-graph
network <- erdos_matrix(N, avk)

# initialise infected
initially_infected <- init_infected(N, i0)

# initialise status
status <- init_status(N, initially_infected)

# initialise_rates
rates <- init_rates(network, gamma, tau, status)

# initial conditions
times <- rep(NA_real_, 2 * N)   # preallocate for output (R thing)
INF <- rep(NA_integer_, 2 * N)
SUS <- rep(NA_integer_, 2 * N)

t <- 0   # time
i <- 1   # index
INF[i] <- i0
SUS[i] <- N - i0
times[i] <- 0

while((t < max_time) && (INF[i] > 0)) {

  # which node is the vent happening to
  event <- which_event(rate)

  # update values (note order as can effect function requirements)
  t <- t + step_update(rate)
  status[event] <- status_update(status(event))
  rate <- rate_update(event, rate, status, graph)

  # update times, INF and SUS
  if (status[event] == 1) {
    # S -> I
    INF[i + 1] <- INF[i] + 1
    SUS[i + 1] <- SUS[i] - 1
  } else {
    # I -> R
    INF[i + 1] <- INF[i] - 1
    SUS[i + 1] <- SUS[i]
  }
  times[i + 1] <- t

  # increment index
  i <- i + 1
}