Format vaccine model output

Take raw odin vaccine model output and formats in long format with the option to select variables and summarise over age groups. Output variables are ordered as in argument ordering.

format(
  x,
  compartments = c("S", "E", "IMild", "ICase", "IICU", "IHospital", "IRec", "R", "D"),
  summaries = c("N", "hospitalisations", "hospital_demand", "hospital_occupancy",
    "ICU_demand", "ICU_occupancy", "vaccines", "unvaccinated", "vaccinated",
    "priorvaccinated", "infections", "deaths"),
  reduce_age = TRUE,
  date_0 = NULL,
  replicate = 1
)

Arguments

x

squire_simulation object
compartments

Vector of compartment names, e.g. c("S", "R"), or sub-compartment names, e.g. c("S", "E1", "E2")
summaries

Vector of summary names, which may be:

  • "deaths" Deaths per day

  • "infections" Infections per day. New infections (note this is currently a slightly different definitionto the main Squire mode)

  • "hospitilisations" Hospitalisations per day (Note this takes into account hospital capacity)

  • "hospital_occupancy" Occupied Hospital Beds

  • "ICU_occupancy" Occupied ICU Beds

  • "hospital_demand Required Hospital Beds

  • "ICU_demand Required ICU Beds

  • "vaccinated" Vaccines administered per day
reduce_age

Collapse age-dimension, calculating the total in the compartment.
date_0

Date of time 0 (e.g. "2020-03-01"), if specified a date column will be added
replicate

Which replicate is being formatted. Default = 1

Value

Formatted long data.frame