parse_country_severity: Parse country severity parameters

In mrc-ide/squire: SEIR transmission model of COVID-19

Parse country severity parameters

Description

Parse country severity parameters

Usage

parse_country_severity(
  country = NULL,
  prob_hosp = NULL,
  prob_severe = NULL,
  prob_non_severe_death_treatment = NULL,
  prob_severe_death_treatment = NULL,
  prob_non_severe_death_no_treatment = NULL,
  prob_severe_death_no_treatment = NULL,
  walker_params = FALSE
)

Arguments

country	Character for country beign simulated. WIll be used to generate population and contact_matrix_set if unprovided. Either country or population and contact_matrix_set must be provided.
prob_hosp	Probability of hospitalisation by age. Default, NULL, will use c(0.000840764, 0.001182411, 0.001662887, 0.002338607, 0.003288907, 0.004625365, 0.006504897, 0.009148183, 0.012865577, 0.018093546, 0.025445917, 0.035785947, 0.050327683, 0.0707785, 0.099539573, 0.1399878, 0.233470395)
prob_severe	Probability of developing severe symptoms by age. Default, NULL, will use c(0.000840764, 0.001182411, 0.001662887, 0.002338607, 0.003288907, 0.004625365, 0.006504897, 0.009148183, 0.012865577, 0.018093546, 0.025445917, 0.035785947, 0.050327683, 0.0707785, 0.099539573, 0.1399878, 0.233470395)
prob_non_severe_death_treatment	Probability of death from non severe treated infection. Default, NULL, will use c(0.181354223, 0.181354223, 0.181354223, 0.137454906, 0.121938236, 0.122775613, 0.136057441, 0.160922182, 0.196987378, 0.242011054, 0.289368845, 0.326537862, 0.337229819, 0.309082553, 0.243794865, 0.160480254, 0.057084366)
prob_severe_death_treatment	Probability of death from severe infection that is treated. Default, NULL, will use c(0.226668959, 0.252420241, 0.281097009, 0.413005389, 0.518451493, 0.573413613, 0.576222065, 0.54253573, 0.493557696, 0.447376527, 0.416666608, 0.411186639, 0.443382594, 0.538718871, 0.570434076, 0.643352843, 0.992620047)
prob_non_severe_death_no_treatment	Probability of death in non severe hospital inections that aren't treated. Default, NULL, will use rep(0.5, 17)
prob_severe_death_no_treatment	Probability of death from severe infection that is not treated. Default, NULL, will use rep(0.95, 17)
walker_params	Boolean for using parameters in Walker et al. Default = FALSE, which uses parameter update as of November 2020. For full information see parameters vignette

mrc-ide/squire documentation built on Sept. 10, 2022, 1:11 a.m.