SEIRTModel: SEIR+T Model

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

SEIR+T Model

Description

A model for influenza that uses a SEIR framework with age structure and that allows for antiviral treatment

Usage

SEIRTModel(population, populationFractions, contactMatrix, R0, latentPeriod,
  infectiousPeriod, seedInfections, priorImmunity, useCommunityMitigation,
  communityMitigationStartDay, communityMitigationDuration,
  communityMitigationMultiplier, fractionSymptomatic, fractionSeekCare,
  fractionDiagnosedAndPrescribedOutpatient, fractionAdhere, fractionAdmitted,
  fractionDiagnosedAndPrescribedInpatient, AVEi, AVEp, 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	Fraction of the population to seed with infections; single fraction or vector of fractions 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
fractionSymptomatic	Fraction of the infections that are symptomatic cases; single fraction or vector of fractions by population group; defaults to 0.5
fractionSeekCare	Fraction of the symptomatic cases that seek medical care; single fraction or vector of fractions by population group; defaults to 0.6
fractionDiagnosedAndPrescribedOutpatient	Fraction of the outpatient medical care seeking cases that are diagnosed and prescribed antiviral drugs; single fraction or vector of fractions by population group; defaults to 0.7
fractionAdhere	Fraction of the cases that are prescribed antiviral drugs that adhere to the regimen; single fraction or vector of fractions by population group; defaults to 0.8
fractionAdmitted	Fraction of the cases that require hospitalization that are admitted; single fraction or vector of fractions by population group; defaults to 1
fractionDiagnosedAndPrescribedInpatient	Fraction of the hospitalized cases that are diagnosed and prescribed antiviral drugs; single fraction or vector of fractions by population group; defaults to 1
AVEi	Antiviral efficacy: prevention of transmission from infected individuals taking antiviral drugs; single fraction or vector of fractions by population group; defaults to 0
AVEp	Antiviral efficacy: probability that antiviral treatment averts hospitalization and/or death; single fraction or vector of fractions by population group; defaults to 0
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 SEIRTModel object

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