setup_humans_MOI: Setup humans with MOI (multiplicity of infection) pathogen...

In MicroMoB: Discrete Time Simulation of Mosquito-Borne Pathogen Transmission

Setup humans with MOI (multiplicity of infection) pathogen model

Description

This is a queueing model (M/M/inf) of superinfection in humans.

Usage

setup_humans_MOI(
  model,
  stochastic,
  theta,
  wf = NULL,
  H,
  MOI,
  b = 0.55,
  c = 0.15,
  r = 1/200,
  sigma = 1
)

Arguments

model	an object from make_MicroMoB
stochastic	should the model update deterministically or stochastically?
theta	a time spent matrix
wf	biting weights
H	vector of strata population sizes
MOI	a matrix giving the distribution of persons across strata (columns) and multiplicity of infection (rows).
b	transmission efficiency (mosquito to human)
c	transmission efficiency (human to mosquito)
r	recovery rate (inverse of infectious duration)
sigma	control non-independence of pathogen clearance; sigma > 1 indicates competition (clearance is faster than independent) and sigma < 1 indicates facilitation (clearance is slower than independent).

Value

no return value

Note

The step_humans method for the MOI model will grow the MOI matrix (add rows) if an individual's MOI exceeds the size of the matrix; therefore it's a good idea to pad the input matrix with extra empty rows to avoid reallocating memory during the simulation as much as possible.

MicroMoB documentation built on Jan. 17, 2023, 9:06 a.m.