infection_age_process: Infection process for age-structured models

In mrc-ide/individual: Framework for Specifying and Simulating Individual Based Models

Infection process for age-structured models

Description

Simulates infection for age-structured models, where individuals contact each other at a rate given by some mixing (contact) matrix. The force of infection on susceptibles in a given age class is computed as:

\lambda_{i} = p \sum\limits_{j} C_{i,j} \left( \frac{I_{j}}{N_{j}} \right)

Where C is the matrix of contact rates, p is the probability of infection per contact. The per-capita probability of infection for susceptible individuals is then:

1 - e^{-\lambda_{i} \Delta t}

.

Usage

infection_age_process(
  state,
  susceptible,
  exposed,
  infectious,
  age,
  age_bins,
  p,
  dt,
  mixing
)

Arguments

state	a CategoricalVariable object.
susceptible	a string representing the susceptible state (usually "S").
exposed	a string representing the state new infections go to (usually "E" or "I").
infectious	a string representing the infected and infectious state (usually "I").
age	a IntegerVariable giving the age of each individual.
age_bins	the total number of age bins (groups).
p	the probability of infection given a contact.
dt	the size of the time step (in units relative to the contact rates in mixing).
mixing	a mixing (contact) matrix between age groups.

Value

a function which can be passed as a process to simulation_loop.

mrc-ide/individual documentation built on Aug. 17, 2024, 2:10 p.m.