Expand parameter list to include variant strain
expand_params_variant(
params,
variant_prop = 0.01,
variant_advantage = 1.5,
variant_vax_efficacy_dose1 = 0.3,
variant_vax_efficacy_dose2 = 0.8,
variant_vax_mu_dose1 = NULL,
variant_vax_mu_dose2 = NULL
)parameter list (e.g. read in with read_params())
current proportion of infections caused by the variant
transmissibility advantage of variant compared to current dominant strain (as a multiplicative factor), e.g., a 50% more transmissible variant would have variant_advantage = 1.5.
one-dose vaccine efficacy against variant (only used in vaxified model)
two-dose vaccine efficacy against variant (only used in vaxified model)
probability that an individual protected by one vaccine dose has a mild variant infection (if NULL, assume the same probability as for the resident strain)
probability that an individual protected by two vaccine doses has a mild variant infection (if NULL, assume the same probability as for the resident strain)
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_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(),
update_params_mistry(),
vis_model(),
write_params()
params <- read_params("PHAC.csv")
params_variant <- expand_params_variant(params)