R/ageify.R
expand_params_desc_age.RdEdit parameter description attribute to include age-specific definitions (helper function for `expand_params_age()`)
expand_params_desc_age(params_desc)parameter descriptions, as initialized in `read_params()`
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_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(),
update_params_mistry(),
vis_model(),
write_params()
params <- read_params("PHAC_testify.csv")
params_desc <- attr(params, "description")
expand_params_desc_age(params_desc)
#> beta0
#> "Baseline (non-intervention) transmission across categories per age category (if single value, this same value is taken for all age groups)"
#> Ca
#> "relative asymptomatic transmission (or contact)"
#> Cp
#> "relative presymptomatic transmission (or contact)"
#> Cm
#> "relative mildly symptomatic transmission (or contact)"
#> Cs
#> "relative severely symptomatic transmission (or contact)"
#> alpha
#> "Fraction of cases asymptomatic"
#> sigma
#> "1/time in exposed class"
#> gamma_a
#> "1/time for asymptomatic recovery"
#> gamma_m
#> "1/time for mildly symptomatic recovery"
#> gamma_s
#> "1/time for severely symptomatic transition to hospital/death"
#> gamma_p
#> "1/time in pre-symptomatic class"
#> rho
#> "1/time in hospital (acute care)"
#> delta
#> "Fraction of acute-care cases that are fatal"
#> mu
#> "Fraction of symptomatic cases that are mild"
#> N
#> "Population size per age category"
#> E0
#> "Initial number exposed"
#> nonhosp_mort
#> "probability of mortality without hospitalization"
#> iso_m
#> "Relative self-isolation/distancing of mild cases"
#> iso_s
#> "Relative self-isolation/distancing of severe cases"
#> phi1
#> "Fraction of hospital cases to ICU"
#> phi2
#> "Fraction of ICU cases dying"
#> psi1
#> "Rate of ICU back to acute care"
#> psi2
#> "Rate of ICU to death"
#> psi3
#> "Rate of post-ICU to discharge"
#> c_prop
#> "fraction of incidence reported as positive tests"
#> c_delay_mean
#> "average delay between incidence and test report"
#> c_delay_cv
#> "coefficient of variation of testing delay"
#> proc_disp
#> "dispersion parameter for process error (0=demog stoch only)"
#> zeta
#> "phenomenological heterogeneity parameter"
#> W_asymp
#> " asymptomatic weights"
#> P_S
#> " probability of positive in S"
#> P_E
#> " probability of positive in E"
#> P_Ia
#> "probability of positive in Ia"
#> P_Ip
#> "probability of positive in Ip"
#> P_Im
#> "probability of positive in Im"
#> P_Is
#> "probability of positive in Is"
#> P_H
#> " probability of positive in H"
#> P_H2
#> " probability of positive in H2"
#> P_ICUs
#> " probability of positive in ICUs"
#> P_ICUd
#> "probability of positive in ICUd"
#> P_R
#> "probability of positive in R"
#> omega
#> "1/waiting time for tests to be returned"
#> testing_intensity
#> "tests per capita per day"
#> iso_t
#> "Relative self-isolation/distancing of tested-positives"
#> testing_tau
#> "tests per capita per infected person per day"
#> pmat
#> "Contact probability matrix: the entry in row i and column j represents the probability that an individual of age i contacts an individual of age j (but not necessarily the other way around---only matrix rows must sum to 1)"