align: Align deaths

In mrc-ide/squire: SEIR transmission model of COVID-19

Align deaths

Description

Quick method to align a set of simulations to a cumulative deaths total

Usage

align(
  deaths,
  reporting_fraction = 1,
  country = NULL,
  population = NULL,
  contact_matrix_set = NULL,
  seeding_age_groups = c("35-40", "40-45", "45-50", "50-55"),
  min_seeding_cases = 5,
  max_seeding_cases = 50,
  R0 = 3,
  R0_scan = NULL,
  replicates = 100,
  ...
)

Arguments

deaths	Number of observed deaths
reporting_fraction	Reporting fraction. Numeric for what proportion of the total deaths the reported deaths represent. E.g. 0.5 results in the model calibrating to twice the deaths provided by deaths
country	Character for country beign simulated. WIll be used to generate population and contact_matrix_set if unprovided. Either country or population and contact_matrix_set must be provided.
population	Population vector (for each age group). Default = NULL, which will cause population to be sourced from country
contact_matrix_set	Contact matrices used in simulation. Default = NULL, which will generate this based on the country.
seeding_age_groups	Age groups for seeding
min_seeding_cases	Minimum seeding cases
max_seeding_cases	Maximum seeding cases
R0	R0 to be passed to run_explicit_SEEIR_model. Default = 3
R0_scan	Vector or R0 values to sample from to introduce uncertainty in predictions. Default = NULL, which will not scan. If provided, the first value in R0 will be drawn from R0_scan
replicates	Replicates to be passed to run_explicit_SEEIR_model. Default = 100
...	Further aguments for run_explicit_SEEIR_model()

Value

List of time adjusted squire_simulations

mrc-ide/squire documentation built on Sept. 10, 2022, 1:11 a.m.