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Nimue format that returns just compartments/summaries requested

nimue_format.Rd

If a squire object is provided out it should be feed through to squire::format_output. However, please note that not all variables can be selected for squire.

Usage

nimue_format(
  out,
  var_select = NULL,
  reduce_age = TRUE,
  combine_compartments = TRUE,
  date_0 = NULL,
  mean_over_80_age = 82.5,
  case_to_infection_ratio = 0.195
)

Arguments

out

nimue_simulation or squire_simulation object

var_select

Vector of compartment names, e.g. c("S", "R"). In addition a number of summary compartment can be requested. These include:

  • "deaths" Daily Deaths

  • "infections" Daily Infections

  • "hospital_occupancy" See description

  • "ICU_occupancy" See description

  • "hospital_demand" See description

  • "ICU_demand" See description

  • "hospital_incidence" See description

  • "ICU_incidence" See description

  • "hospitalisations" See description

  • "vaccines", "unvaccinated", "vaccinated", "priorvaccinated" Vaccine outputs

  • "long_covid" Long COVID estimates

reduce_age

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

combine_compartments

Collapse compartments of same type together (e.g. E1 and E2 -> E)

date_0

Date of time 0, if specified a date column will be added

mean_over_80_age

Mean age of over 80 population for calculating long covid incidence. Default = 82.5

case_to_infection_ratio

Ratio of infections to cases for long covid calculation. Default = 0.195 from UK ONS analyses

Value

Formatted long data.frame

Details

To better define the summaries related to the healthcare pathway:

demand

The total number of requiring hospitalisation and ICU care at the given time, regardless of if they've received it

occupancy

The total number of those who received ICU or hospital care at the given time

incidence

The total number of new people who require hospital or ICU care

hospitalisations

Sum of new people recieving hospital or ICU care

Note: this is confusing and seemingly inconsistent i.e. hospital_incidence does not capture those recovering from ICU and hospitalisations is stated to equal the sum of the incidences elsewhere.

Examples

#generate some outputs for the afghanistan fit and pass through to format
#getting deaths and long covid estimates
if (FALSE) {
generate_draws(afg_fit) %>%
  nimue_format(var_select = c("deaths", "long_covid"))
}