SEIRModel: SEIR Model

In HHS/ASPR-flumodels: Deterministic compartmental models for influenza with mitigations.

SEIR Model

Description

A model for influenza that uses a SEIR framework with age structure

Usage

SEIRModel(population, populationFractions, contactMatrix, R0, latentPeriod,
  infectiousPeriod, seedInfections, priorImmunity, useCommunityMitigation,
  communityMitigationStartDay, communityMitigationDuration,
  communityMitigationMultiplier, simulationLength, seedStartDay, tolerance,
  method)

Arguments

population	Size of population; defaults to 1
populationFractions	Vector of population fractions (all non-negative, sum to 1); defaults to 1, representing a single population group
contactMatrix	A matrix whose (row i, column j) entry denotes the number of potentially infectious contacts a single individual from group j has with individuals from group i each day; defaults to proportional mixing
R0	Average number of secondary cases from a single infected individual in a completely susceptible population; must be specified
latentPeriod	Latent period in days; must be specified
infectiousPeriod	Infectious period in days; must be specified
seedInfections	Number of infections to seed; single number or vector of numbers by population group; defaults to 0
priorImmunity	Fraction of the population with prior immunity; single fraction, or vector of fractions by population group; defaults to 0
useCommunityMitigation	Whether or not to use community mitigation implemented by modulation of the contact matrix; defaults to FALSE
communityMitigationStartDay	If using community mitigation, day of the simulation on which to start mitigation; must be specified if applicable
communityMitigationDuration	If using community mitigation, duration of time during which mitigation is in effect; must be specified if applicable
communityMitigationMultiplier	If using community mitigation, the non-negative matrix of multipliers that will be used to modulate the contact matrix by elementwise multiplication; must be specified if applicable
simulationLength	Number of days to simulate after seeding infections; defaults to 240
seedStartDay	Day on which to seed initial infections; defaults to 0
tolerance	Absolute tolerance for numerical integration; defaults to 1e-8
method	Which integration method to use. Defaults to lsoda

Value

a SEIRModel object

HHS/ASPR-flumodels documentation built on Dec. 6, 2022, 12:20 p.m.