update_params_mistry: Update Mistry-based parameters

In bbolker/McMasterPandemic: Pandemic Model

Update Mistry-based parameters

Description

Recalculate beta0 and/or pmat if setting-specific contact rates and/or overall transmissiblity are changed

Usage

update_params_mistry(
  params,
  contact_rate_setting = NULL,
  transmissibility = NULL
)

Arguments

params	parameter list initialized using 'expand_params_mistry()'
contact_rate_setting	named list containing setting-specific contact rates (in units of average contacts in the given setting per individual of age i with individuals of age j per day)
transmissibility	probability of transmission upon contact with an infected (beta0 = transmissibility * contact_rate)

Details

For 'contact_rate_setting', a full list (initialized with 'mk_contact_rate_setting()') or a partial list (e.g. 'list(community = 0)') can be provided. If a partial list is provided, default values from Mistry et al. 2021 are assumed for the contact rates that have not been specified (see 'mk_contact_rate_setting()' for values).

Value

an object of class 'params_pansim'

See Also

Other classic_macpan: add_d_log(), add_updated_vaxrate(), aggregate_agecats(), calibrate_comb(), calibrate(), check_age_cat_compatibility(), check_contact_rate_setting(), col_multiply(), condense_age(), condense_params_vax(), condense_state(), condense_vax(), dev_is_tikz(), do_step(), expand_params_age(), expand_params_desc_age(), expand_params_desc_variant(), expand_params_desc_vax(), expand_params_mistry(), expand_params_variant(), expand_params_vax(), expand_state_age(), expand_state_vax(), expand_stateval_testing(), fix_pars(), fix_stored(), forecast_ensemble(), forecast_sim(), getData(), get_GI_moments(), get_Gbar(), get_R0(), get_doses_per_day(), get_evec(), get_kernel_moments(), get_opt_pars(), get_r(), invlink_trans(), make_betavec(), make_beta(), make_jac(), make_ratemat(), make_state(), make_test_wtsvec(), make_vaxrate(), mk_Nvec(), mk_agecats(), mk_contact_rate_setting(), mk_mistry_Nvec(), mk_pmat(), mk_vaxcats(), mle_fun(), non_expanded_states, rExp(), read_params(), repair_names_age(), restore(), run_sim_ageify(), run_sim_break(), run_sim_loglin(), run_sim_mobility(), run_sim_range(), run_sim(), show_ratemat(), testify(), texify(), trans_state_vars(), update_contact_rate_setting(), update_foi(), vis_model(), write_params()

Examples

params <- read_params("PHAC_testify.csv")
age_cat <- mk_agecats(min = 0, max = 80, da = 10)
params_mistry <- expand_params_mistry(params = params, province = "ON", age_cat = age_cat)
params_mistry <- update_params_mistry(params_mistry,
 contact_rate_setting = list(school = 0))

bbolker/McMasterPandemic documentation built on Aug. 25, 2024, 6:35 p.m.