make_state | R Documentation |
retrieve parameters from a CSV file
make_state(
N = params[["N"]],
E0 = params[["E0"]],
type = "ICU1h",
state_names = NULL,
use_eigvec = NULL,
params = NULL,
x = NULL,
normalize = FALSE,
ageify = NULL,
vaxify = NULL,
testify = NULL
)
N |
population size |
E0 |
initial number exposed |
type |
(character) specify what model type this is intended
for (e.g., |
state_names |
vector of state names, must include S and E |
use_eigvec |
use dominant eigenvector to distribute non-Susc values
to zero: default is to set this to |
params |
parameter vector (looked in for N and E0) |
x |
proposed (named) state vector; missing values will be set |
normalize |
(logical) should the state vector be normalized to sum to 1? |
ageify |
expand state vector to include different age groups (??) |
vaxify |
expand state vector to include groups that have 1-2 vaccine doses (??) |
testify |
expand state vector to include testing compartments (untested, neg waiting, pos waiting, pos received) ? |
The parameters that must be set are:
N:
population size
\beta_0:
transmission rate
1/\sigma:
mean latent period
1/\gamma_a:
mean infectious period for asymptomatic individuals
...
generate initial state vector
"CI"
refers to the Stanford group's
"covid intervention" model.
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_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()
p <- read_params("ICU1.csv")
make_state(N=1e6,E0=1)
make_state(params=p)
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