parameters_explicit_SEEIR: Parmaters for explicit SEEIR model
In mrc-ide/squire: SEIR transmission model of COVID-19

parameters_explicit_SEEIR

R Documentation

Parmaters for explicit SEEIR model

Description

Parmaters for explicit SEEIR model

Usage

parameters_explicit_SEEIR(
  country = NULL,
  population = NULL,
  tt_contact_matrix = 0,
  contact_matrix_set = NULL,
  R0 = 3,
  tt_R0 = 0,
  beta_set = NULL,
  time_period = 365,
  dt = 0.1,
  init = NULL,
  seeding_cases = NULL,
  prob_hosp = NULL,
  prob_severe = NULL,
  prob_non_severe_death_treatment = NULL,
  prob_non_severe_death_no_treatment = NULL,
  prob_severe_death_treatment = NULL,
  prob_severe_death_no_treatment = NULL,
  p_dist = probs$p_dist,
  walker_params = FALSE,
  dur_E = NULL,
  dur_IMild = NULL,
  dur_ICase = NULL,
  dur_get_ox_survive = NULL,
  tt_dur_get_ox_survive = NULL,
  dur_get_ox_die = NULL,
  tt_dur_get_ox_die = NULL,
  dur_not_get_ox_survive = NULL,
  dur_not_get_ox_die = NULL,
  dur_get_mv_survive = NULL,
  tt_dur_get_mv_survive = NULL,
  dur_get_mv_die = NULL,
  tt_dur_get_mv_die = NULL,
  dur_not_get_mv_survive = NULL,
  dur_not_get_mv_die = NULL,
  dur_rec = NULL,
  dur_R = NULL,
  hosp_bed_capacity = NULL,
  ICU_bed_capacity = NULL,
  tt_hosp_beds = 0,
  tt_ICU_beds = 0
)

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.
`population`	Population vector (for each age group). Default = NULL, which will cause population to be sourced from `country`
`tt_contact_matrix`	Time change points for matrix change. Default = 0
`contact_matrix_set`	Contact matrices used in simulation. Default = NULL, which will generate this based on the `country`.
`R0`	Basic Reproduction Number. Default = 3
`tt_R0`	Change time points for R0. Default = 0
`beta_set`	Alternative parameterisation via beta rather than R0. Default = NULL, which causes beta to be estimated from R0
`time_period`	Length of simulation. Default = 365
`dt`	Time Step. Default = 0.1
`init`	Data.frame of initial conditions. Default = NULL
`seeding_cases`	Initial number of cases seeding the epidemic
`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_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_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_severe_death_no_treatment`	Probability of death from severe infection that is not treated. Default, NULL, will use `rep(0.95, 17)`
`p_dist`	Preferentiality of age group receiving treatment relative to other age groups when demand exceeds healthcare capacity.
`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
`dur_E`	Mean duration of incubation period (days). Default = 4.6
`dur_IMild`	Mean duration of mild infection (days). Default = 2.1
`dur_ICase`	Mean duration from symptom onset to hospitil admission (days). Default = 4.5
`dur_get_ox_survive`	Mean duration of oxygen given survive. Default = 9
`tt_dur_get_ox_survive`	Times at which dur_get_ox_survive changes (Default = 0 = doesn't change)
`dur_get_ox_die`	Mean duration of oxygen given death. Default = 9
`tt_dur_get_ox_die`	Times at which dur_get_ox_die changes (Default = 0 = doesn't change)
`dur_not_get_ox_survive`	Mean duration without oxygen given survive. Default = 4.5
`dur_not_get_ox_die`	Mean duration without oxygen given death. Default = 4.5
`dur_get_mv_survive`	Mean duration of ventilation given survive. Default = 14.8
`tt_dur_get_mv_survive`	Times at which dur_get_mv_survive changes (Default = 0 = doesn't change)
`dur_get_mv_die`	Mean duration of ventilation given death. Default = 11.1
`tt_dur_get_mv_die`	Times at which dur_get_mv_die changes (Default = 0 = doesn't change)
`dur_not_get_mv_survive`	Mean duration without ventilation given survive. Default = 7.4
`dur_not_get_mv_die`	Mean duration without ventilation given death. Default = 1
`dur_rec`	Duration of recovery after coming off ventilation. Default = 3
`dur_R`	Mean duration of immunity (days). Default = Inf
`hosp_bed_capacity`	General bed capacity. Can be single number or vector if capacity time-varies.
`ICU_bed_capacity`	ICU bed capacity. Can be single number or vector if capacity time-varies.
`tt_hosp_beds`	Times at which hospital bed capacity changes (Default = 0 = doesn't change)
`tt_ICU_beds`	Times at which ICU bed capacity changes (Default = 0 = doesn't change)

Details

All durations are in days.

Value

Paramater List

Parameter Updates

Parameters detailing the age-dependent probability of disease severity and durations of hospital durations have been updated in v0.5.0 of squire to reflect the changing understanding of COVID-19 transmission. Parameter arguments are by default equal to NULL, which causes the new updated parameters specified in default_probs and default_durations to be used. If any provided parameters are not NULL, these will be used. In order to ease previous fits and code, function argument walker_params will use the parameters described in Walker et al. Science. 2020 which can be viewed within the function parse_country_severity