get_parameters: Get baseline model parameters

In mrc-ide/esft: WHO ESFT Calculations

Get baseline model parameters

Description

Gives baseline parameters from the inputs and user dashboard tab in the WHO ESFT.

Usage

get_parameters(overrides = list())

Arguments

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:

• mild_i_proportion - proportion of cases that are mild, considered to be isolating to reduce onward transmission; default = 0.4

• mod_i_proportion - proportion of cases that are moderate, considered to be isolating to minimize onward transmission; default = 0.4

• sev_i_proportion - proportion of cases that are severe, depending on severe bed availability, are admitted to hospital and require oxygen; default = 0.15

• 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):

• stay_mild - average length of stay (in weeks) of mild cases in isolation; default = 2

• 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):

• stay_sev - average length of stay (in weeks) of severe cases in hospital; default = 1

• 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):

• ifr_sev - infection fatality rate of severe cases, based on WHO China Joint Mission Report; default = 0.134

• ifr_crit - infection fatality rate of critical cases, based on Imperial College Report nr. 9; default = 0.5

Miscellaneous Parameters:

• perc_hcws_not_covid - assumption of percentage of HCWs not working on COVID; default = 0.4

• 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:

• 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

• bioengs_per_bed - biomedical engineer ratio assumes 2 biomedical engineers (on 8-hour shifts) per 100 bed hospital; default = 0.02

• 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

• 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:

• perc_crit_inv_mv - WHO recommendation; default = 0.667

• perc_crit_noninv_mv - WHO recommendation; default = 0.333

Oxygen Flow by Case Severity, in LPM:

• o2_flow_sev - severe patients require 5-15 LPM, so median taken; default = 10

• o2_flow_crit_inv_mv - critical patients with invasive mechanical ventilation; default = 30

• o2_flow_crit_noninv_mv - critical patients with non-invasive mechanical ventilation; default = 30

mrc-ide/esft documentation built on July 31, 2023, 2:30 p.m.