SEIR.penalty.function: Penalty function for SEIR-type models

In HHS/ASPR-flumodelsutil: Flumodels helper utilities

Description

Computes the penalty compared to preexisting incidence.

Usage

SEIR.penalty.function(
  model,
  incidence,
  attackRatesToMatch,
  populationFractions,
  population = 1,
  symptomaticIncidence = FALSE,
  fractionSymptomatic = 0.5,
  seedWeeksBeforeIncidence = 0,
  weightIncidenceTimeseries = 1,
  weightAttackRates = 1,
  weightOverallAttackRate = 30
)

Arguments

model	SEIR-type model
incidence	Array of weekly incidence
attackRatesToMatch	Attack rates for population groups
populationFractions	Population fractions
population	Total population, Default: 1
symptomaticIncidence	Is the incidence serological or symptomatic. Defaults to false (serological).
fractionSymptomatic	The fraction of cases that are symptomatic. Not a parameter to fit. Only used if symptomaticIncidence is set to true. Defaults to 0.5.
seedWeeksBeforeIncidence	Days before the start of the supplied incidence curve to seed initial infections.
weightIncidenceTimeseries	What relative weight to the penalty function should the incidence timeseries receive? Defaults to 1.
weightAttackRates	What relative weight to the penalty function should the age-specific attack rates receive? Defaults to 1.
weightOverallAttackRate	What relative weight to the penalty function should the overall attack rate receive? Defaults to 10.

Value

Total penalty

HHS/ASPR-flumodelsutil documentation built on Dec. 31, 2020, 12:58 p.m.