expand_params_vax: Expand parameter list to include vaccination

In bbolker/McMasterPandemic: Pandemic Model

Expand parameter list to include vaccination

Description

Expand parameter list to include vaccination

Usage

expand_params_vax(
  params,
  model_type = c("onedose", "twodose"),
  vax_doses_per_day = 1e+05,
  vax_prop_first_dose = 1,
  vax_efficacy_dose1 = 0.6,
  vax_efficacy_dose2 = 0.9,
  vax_avg_response_time = 14,
  vax_avg_response_time_R = 7,
  vax_alpha_dose1 = 0.5,
  vax_alpha_dose2 = 0.5,
  vax_mu_dose1 = 1,
  vax_mu_dose2 = 1
)

Arguments

params	parameter list (e.g. read in with 'read_params()')
model_type	choose either the one-dose or the two-dose model
vax_doses_per_day	total number of vaccine doses administered per day
vax_prop_first_dose	the proportion of vaccine doses administered per day that are first doses
vax_efficacy_dose1	infection-blocking vaccine efficacy for dose 1
vax_efficacy_dose2	infection-blocking vaccine efficacy for dose 2
vax_avg_response_time	average number of days it takes for a vaccine dose to confer protection for an individual that has never been infected
vax_avg_response_time_R	average number of days it takes for a vaccine dose to confer protection for an individual that has previously been infected (e.g. between being dosed and eliciting the protective immune response)
vax_alpha_dose1	proportion of infections that are asymptomatic in individuals that have received one dose of the vaccine
vax_alpha_dose2	proportion of infections that are asymptomatic in individuals that have received two doses of the vaccine
vax_mu_dose1	proportion of infections that are mild (vs. severe) in individuals that have received one dose of the vaccine
vax_mu_dose2	proportion of infections that are mild (vs. severe) in individuals that have received two doses of the vaccine

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_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(), update_params_mistry(), vis_model(), write_params()

Examples

params <- read_params("PHAC.csv")
params_vax <- expand_params_vax(params)

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