load_params_init: Base-case initial parameter set

In SC-COSMO/sccosmomcma: Stanford-CIDE COronavirus Simulation MOdel (SC-COSMO) for Mexico City Metropolitan Area Analysis

Description

load_params_init generates the initial values of the SC-COSMO parameters.

Usage

load_params_init(
  n_t = 30,
  time_step = 1,
  comp = TRUE,
  v_init_age_grps = c(0, 5, 15, 25, 45, 55, 65, 70),
  v_inf_init_ages = NULL,
  ctry = "Mexico",
  ste = "Mexico City",
  cty = "Mexico City",
  l_contact_info = l_contact_matrices,
  r_birth = 0,
  r_beta = 0.0536,
  v_sigma = rep(1/3, length(v_init_age_grps)),
  v_gamma = rep(1/3.1, length(v_init_age_grps)),
  v_omega = rep(0, length(v_init_age_grps)),
  l_nu_exp1_dx = add_period(l_period_def = NULL, l_period_add =
    make_period(functional_form = "constant", time_start = 0, time_stop = n_t, val_start
    = 0, val_end = 0)),
  l_nu_exp2_dx = add_period(l_period_def = NULL, l_period_add =
    make_period(functional_form = "constant", time_start = 0, time_stop = n_t, val_start
    = 1/12, val_end = 1/12)),
  l_nu_inf1_dx = add_period(l_period_def = NULL, l_period_add =
    make_period(functional_form = "constant", time_start = 0, time_stop = n_t, val_start
    = 0, val_end = 0)),
  l_nu_inf2_dx = add_period(l_period_def = NULL, l_period_add =
    make_period(functional_form = "constant", time_start = 0, time_stop = n_t, val_start
    = 1/12, val_end = 1/12)),
  l_phi_exp1_dx = add_period(l_period_def = NULL, l_period_add =
    make_period(functional_form = "constant", time_start = 0, time_stop = n_t, val_start
    = 0, val_end = 0)),
  l_phi_exp2_dx = add_period(l_period_def = NULL, l_period_add =
    make_period(functional_form = "constant", time_start = 0, time_stop = n_t, val_start
    = 0, val_end = 0)),
  l_phi_inf1_dx = add_period(l_period_def = NULL, l_period_add =
    make_period(functional_form = "constant", time_start = 0, time_stop = n_t, val_start
    = 0, val_end = 0)),
  l_phi_inf2_dx = add_period(l_period_def = NULL, l_period_add =
    make_period(functional_form = "constant", time_start = 0, time_stop = n_t, val_start
    = 0, val_end = 0)),
  l_cfr = get_const_multiage_list(n_t, c(1.3e-05, 8.7e-05, 0.000374, 0.00146, 0.007725,
    0.0262, 0.05145, 0.134)),
  l_ifr = get_const_multiage_list(n_t, c(8.05e-06, 4.28e-05, 0.00018925, 0.000844,
    0.00378, 0.012625, 0.025175, 0.078)),
  l_interventions = add_intervention(interventions = NULL, intervention =
    make_intervention(intervention_type = "StatusQuo", time_start = 0, time_stop = n_t)),
  l_idx_scale_factor = get_const_multiage_list(n_t, rep(0.2, 8)),
  v_reduced_sus = rep(1, 8),
  v_alpha_dx = NULL,
  l_p_hosp = get_const_multiage_list(n_t, c(1e-05, 2e-04, 0.005, 0.035, 0.06, 0.095,
    0.13, 0.17)),
  v_p_s_hosp = c(0.1111, 0.1111, 0.1202, 0.1202, (0.1202 + 0.1746)/2, (0.1746 +
    0.2875)/2, 0.2875, 0.2875),
  v_p_icu_s_hosp = c(0.191, 0.191, 0.191, 0.191, 0.191, 0.191, 0.191, 0.191),
  v_p_icu_ns_hosp = c(0.024, 0.024, 0.024, 0.024, 0.024, 0.024, 0.024, 0.024),
  m_r_exit_tot = c(1/3.1, 1/3.1, 1/((3.1 + 4.2)/2), 1/4.2, 1/4.3, 1/4.3, 1/4.6, 1/4.6),
  m_r_exit_icu = c(1/7.7, 1/7.7, 1/((7.7 + 7.2)/2), 1/7.2, 1/7.3, 1/7.3, 1/7.1, 1/7.1),
  m_r_exit_nonicu = 0.5 * m_r_exit_tot + 0.5 * m_r_exit_icu,
  m_sigma_tot = c(2, 2, 2, 2, 2, 2, 2, 2),
  m_sigma_nonicu = c(2, 2, 2, 2, 2, 2, 2, 2),
  m_sigma_icu = c(1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.5),
  n_hhsize = 3,
  r_tau = 0,
  r_sigma = v_sigma[1],
  r_gamma = v_gamma[1],
  r_omega = v_omega[1]
)

Arguments

n_t	Time horizon in days.
time_step	Model evaluations per day.
comp	Flag (default TRUE) of whether the compiled version of SC-COSMO should be used.
v_init_age_grps	Vector with initial ages of age groups.
v_inf_init_ages	Vector with number of individuals in first infectious class for each age group. Default will assign 1 for each age group.
ctry	Country.
ste	State.
cty	County or municipality.
l_contact_info	A list with overall and setting specific contact matrices.
r_birth	Daily birth rate (crude).
r_beta	Transmission parameters.
v_sigma	Age-specific daily rate of progression of exposed individuals (Latent period).
v_gamma	Age-specific daily rate of recovery of infectious individuals (Infectiousness period).
v_omega	Age-specific daily rate of waning immunity of recovered individuals.
l_nu_exp1_dx	List specifying time-varying case detection when exposed l = 1.
l_nu_exp2_dx	List specifying time-varying case detection when exposed l = 2.
l_nu_inf1_dx	List specifying time-varying case detection when infectious l = 1.
l_nu_inf2_dx	List specifying time-varying case detection when infectious l = 2.
l_phi_exp1_dx	List specifying time-varying screen detection when exposed l = 1.
l_phi_exp2_dx	List specifying time-varying screen detection when exposed l = 2.
l_phi_inf1_dx	List specifying time-varying screen detection when infectious l = 1.
l_phi_inf2_dx	List specifying time-varying screen detection when infectious l = 2.
l_cfr	Age-specific case fatality rate.
l_ifr	Age-specific infection fatality rate.
l_interventions	List of intervention "objects" defining type, timing, and effects of interventions.
l_idx_scale_factor	Age-specific infectiousness reduction factor on detected cases.
v_reduced_sus	Age-specific reduction factor on susceptibility.
v_alpha_dx	Age-specific reduction in mortality on detected infectious vs undetected infectious.
l_p_hosp	Age-specific probability of hospitalization for detected (prevalent or incident) cases.
v_p_s_hosp	Age-specific proportion of hospitalizations that are severe based on NEJM definition.
v_p_icu_s_hosp	Age-specific probability of going to ICU given that you are severe hospitalization.
v_p_icu_ns_hosp	Age-specific probability of going to ICU given that you are non-severe hospitalization.
m_r_exit_tot	Age-specific rate of non-severe hospital exit
m_r_exit_icu	Age-specific rate of ICU hospital exit
m_r_exit_nonicu	Age-specific rate of severe hospital exit
m_sigma_tot	Age-specific sigma (gamma distribution) total hospitalization duration.
m_sigma_nonicu	Age-specific sigma (gamma distribution) non ICU hospitalizations duration.
m_sigma_icu	Age-specific sigma (gamma distribution) ICU hospitalization duration.
n_hhsize	Household size (integer).
r_tau	Transmission rate in the household model.
r_sigma	Daily rate of progression of exposed individuals (Latent period). Default to the first entry of the age-specific v_sigma.
r_gamma	Daily rate of recovery of infectious individuals (Infectiousness period). Default to the first entry of the age-specific v_gamma.
r_omega	Waning rate for the household model (default to the first entry of the age-specific v_omega). Default will assign a reduction factor of 1 (i.e., no social distancing).

Value

List of all parameters

SC-COSMO/sccosmomcma documentation built on Dec. 18, 2021, 11:56 a.m.