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Setup humans with MOI (multiplicity of infection) pathogen model

Source: R/humans_MOI.R
setup_humans_MOI.Rd

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.