nimue_format: Nimue format that returns just compartments/summaries...

In mrc-ide/squire.page: Functions used in global-lmic-reports-orderly and other repos

Nimue format that returns just compartments/summaries requested

Description

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

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.

Value

Formatted long data.frame

Examples

#generate some outputs for the afghanistan fit and pass through to format
#getting deaths and long covid estimates
## Not run: 
generate_draws(afg_fit) %>%
  nimue_format(var_select = c("deaths", "long_covid"))

## End(Not run)

mrc-ide/squire.page documentation built on May 27, 2023, 11:20 a.m.