R/parameters.R

In mrc-ide/esft: WHO ESFT Calculations

#' @title Get baseline model parameters
#' @description
#' Gives baseline parameters from the inputs and user dashboard tab
#' in the WHO ESFT.
#'
#' @param overrides a named list of parameter values to use instead of defaults.
#' The parameters are defined below, and are taken from the default settings in
#' the ESFT.
#'
#' @details
#'
#' Case Severity Distributions:
#' \itemize{
#'  \item{mild_i_proportion}{ - proportion of cases that are mild, considered to
#'  be isolating to reduce onward transmission; default = 0.4}
#'  \item{mod_i_proportion}{ - proportion of cases that are moderate, considered
#'  to be isolating to minimize onward transmission; default = 0.4}
#'  \item{sev_i_proportion}{ - proportion of cases that are severe, depending on
#'  severe bed availability, are admitted to hospital and require oxygen;
#'  default = 0.15}
#'  \item{crit_i_proportion}{ - proportion of cases that are critical, depending
#'  on critical bed availability, admitted to hospital and require ventilation;
#'  default = 0.05}
#' }
#'
#' Weeks of Stay in Isolation (WHO recommendation based on incubation period of
#' COVID-19 and case management guidelines):
#' \itemize{
#'  \item{stay_mild}{ - average length of stay (in weeks) of mild cases in
#'  isolation; default = 2}
#'  \item{stay_mod}{ - average length of stay (in weeks) of moderate cases in
#'  isolation; default = 2}
#' }
#'
#' Weeks of Stay in Hospital (based on studies of case severity):
#' \itemize{
#'  \item{stay_sev}{ - average length of stay (in weeks) of severe cases in
#'  hospital; default = 1}
#'  \item{stay_crit}{ - average length of stay (in weeks) of critical cases in
#'  hospital; default = 2}
#' }
#'
#' Infection Fatality Rates (note: could be updated based on newer research):
#' \itemize{
#'  \item{ifr_sev}{ - infection fatality rate of severe cases, based on WHO
#'  China Joint Mission Report; default = 0.134}
#'  \item{ifr_crit}{ - infection fatality rate of critical cases, based on
#'  Imperial College Report nr. 9; default = 0.5}
#' }
#'
#' Miscellaneous Parameters:
#' \itemize{
#'  \item{perc_hcws_not_covid}{ - assumption of percentage of HCWs not working
#'  on COVID; default = 0.4}
#'  \item{n_hosp_beds_per_care_unit}{ - assumption, used to estimate triple
#'  packaging boxes (might not be necessary); default = 40}
#' }
#'
#' Healthcare Workers per Bed or Patient:
#' \itemize{
#' \item{ambulancews_per_bed}{ - ambulance personnel ratio assumes 1 ambulance
#' per 100 bed hospital with 2 operators (paramedic + driver) at all times
#' (3x8 hour shifts) so 6/100 beds; default = 0.06}
#' \item{bioengs_per_bed}{ - biomedical engineer ratio assumes 2 biomedical
#' engineers (on 8-hour shifts) per 100 bed hospital; default = 0.02}
#' \item{n_inf_caregivers_hosp}{ - reference assumption of zero is based on
#' current guidance that no family members or other caretakers should be in
#' hospitals; default = 0}
#' \item{n_inf_caregivers_isol}{ - reference is based on management of home
#' care guidance, with estimates of 1 caregiver per patient for the duration of
#' the roughly 2-week isolation - his calculation estimates the quantity of PPE
#' required (e.g., masks and gloves) for the patient and caregiver; default = 1}
#' }
#'
#' Percent of Critical Patients that are Mechanically Ventilated:
#' \itemize{
#' \item{perc_crit_inv_mv}{ - WHO recommendation; default = 0.667}
#' \item{perc_crit_noninv_mv}{ - WHO recommendation; default = 0.333}
#' }
#'
#' Oxygen Flow by Case Severity, in LPM:
#' \itemize{
#' \item{o2_flow_sev}{ - severe patients require 5-15 LPM, so median taken;
#' default = 10}
#' \item{o2_flow_crit_inv_mv}{ - critical patients with invasive mechanical
#' ventilation; default = 30}
#' \item{o2_flow_crit_noninv_mv}{ - critical patients with non-invasive
#' mechanical ventilation; default = 30}
#' }
#'
#' @export
get_parameters <- function(overrides = list()) {
  parameters <- list(
    # case severity distribution
    mild_i_proportion = 0.4,
    mod_i_proportion = 0.4,
    sev_i_proportion = 0.15,
    crit_i_proportion = 0.05,
    # days of stay in isolation
    stay_mild = 2,
    stay_mod = 2,
    # days of stay in hospital
    stay_sev = 1,
    stay_crit = 2,
    # IFRs
    ifr_sev = 0.134,
    ifr_crit = 0.5,
    # percentage allocation of HCWs
    perc_hcws_not_covid = 0.4,
    n_hosp_beds_per_care_unit = 40,
    # HCWs per bed or patient
    ambulancews_per_bed = 0.06,
    bioengs_per_bed = 0.02,
    n_inf_caregivers_hosp = 0,
    n_inf_caregivers_isol = 1,
    # cases_screened_per_hcw_per_day = ((8 * 60) / 48),
    # cleaners_per_bed = 0.6,
    # percent of critical patients mechanically ventilated
    perc_crit_inv_mv = 2 / 3,
    perc_crit_noninv_mv = 1 / 3,
    # o2 flow for severity
    o2_flow_sev = 10,
    o2_flow_crit_inv_mv = 30,
    o2_flow_crit_noninv_mv = 30
  )

  # Override parameters with any client specified ones
  if (!is.list(overrides)) {
    stop("overrides must be a list")
  }

  for (name in names(overrides)) {
    if (!(name %in% names(parameters))) {
      stop(paste("unknown parameter", name, sep = " "))
    }
    parameters[[name]] <- overrides[[name]]
  }

  props_infection <- c(
    parameters$mild_i_proportion,
    parameters$mod_i_proportion,
    parameters$sev_i_proportion,
    parameters$crit_i_proportion
  )

  if (!approx_sum(props_infection, 1)) {
    stop("Proportions of infection severity level do not sum to 1")
  }

  perc_mv <- c(
    parameters$perc_crit_inv_mv,
    parameters$perc_crit_noninv_mv
  )

  if (!approx_sum(perc_mv, 1)) {
    stop("Mechanical ventilation proportions do not sum to 1")
  }

  return(parameters)
}