Recalculate beta0 and/or pmat if setting-specific contact rates and/or overall transmissiblity are changed
update_params_mistry(
params,
contact_rate_setting = NULL,
transmissibility = NULL
)
parameter list initialized using `expand_params_mistry()`
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)
probability of transmission upon contact with an infected (beta0 = transmissibility * contact_rate)
an object of class `params_pansim`
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).
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()
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))