simeq: Mutliple age and titer class final size equation system

In jameshay218/episize: Epidemic Final Size Calculator

Description

Given an attack rate matrix, R0, contact matrix, population proportions and immunity, gives the difference of the final size equation(see Kucharski PLoS Pathogens 2014; Andreasen 2011 and Wallinga 2006). This should return zero if the attack rate matrix is correct.

Usage

simeq(A, R0, G, P, Z)

Arguments

A	an NxM matrix of attack rates, where N is the number of age classes and M the number of immunity classes
R0	the disease specific R0 ie. beta/gamma. Note that another parameter will mediate the contact rate
G	the normalised contact rate matrix scaled by population sizes. See setup_C
P	NxM matrix of population proportions; number of each age and titre class as proportion of entire population
Z	NxM matrix of immunity. ie. each element is the proportion of infection prevented due to immunity for that age/titre class

Value

difference between the LHS and RHS of the final size equation

jameshay218/episize documentation built on May 18, 2019, 11:20 a.m.