Setup birds with SIRS infection model — setup_birds

This model interfaces with bloodmeals via the vector model$bird$h, giving the per-capita force of infection for birds in each patch.

Usage

setup_birds_SIRS(
  model,
  stochastic,
  fledge_disperse,
  theta,
  SIR,
  mu,
  wf = NULL,
  b = 0.55,
  c = 0.15,
  gamma = 1/5,
  r = 1/120,
  beta = 0.5
)

Arguments

model: an object from MicroMoB::make_MicroMoB
stochastic: should the model update deterministically or stochastically?
fledge_disperse: a dispersal matrix for fledglings; this parameter is part of the adult model rather than fledgling model because the handoff of responsibility between the two occurs at the moment a fledgling leaves its nest, which is exactly the point at which they decide where to disperse as a new adult.
theta: a matrix giving time spent in each bird's home range
SIR: matrix of initial states for each patch
mu: either a scalar, a vector of length tmax, or a vector of length 365 giving daily mortality rates
wf: biting weights, should be a vector of length p or NULL to use 1 for all places/patches.
b: transmission efficiency (mosquitoes to birds)
c: transmission efficiency (birds to mosquitoes)
gamma: inverse of infectious duration (recovery rate)
r: inverse of immune duration (rate of loss of immunity)
beta: number of eggs produced, per adult, per day