make weights vector for tests

make vector of test positivity

make_test_wtsvec(params, var_names = NULL)

make_test_posvec(params, var_names = NULL)

Arguments

params: parameter vector
var_names: variables names, in matching order to state vector/rate matrix

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_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

pp <- read_params("PHAC_testify.csv")
state1 <- state0 <- make_state(params=pp, testify=FALSE)   ## unexpanded

state1[] <- 1  ## occupy all states
state <- expand_stateval_testing(state0, params=pp)
#> Warning: CHECK: may not be working properly for testify?
vn <- setdiff(names(state0),non_expanded_states)
wtsvec <- make_test_wtsvec(pp, vn)
posvec <- make_test_posvec(pp, vn)
## need to make_ratemat() with *unexpanded* state, then expand it
ratemat <- testify(make_ratemat(state1,pp), pp)
betavec <- make_betavec(state,pp)
tt2 <- ratemat
tt2[tt2>0] <- 1 ## make all edges == 1
show_ratemat(tt2)

show_ratemat(ratemat,aspect="fill")

if (require(igraph)) {
   g <- igraph::graph_from_adjacency_matrix(tt2)
   plot(g, layout=igraph::layout_nicely)
}
#> Loading required package: igraph
#> 
#> Attaching package: ‘igraph’
#> The following objects are masked from ‘package:dplyr’:
#> 
#>     as_data_frame, groups, union
#> The following object is masked from ‘package:TMB’:
#> 
#>     normalize
#> The following objects are masked from ‘package:stats’:
#> 
#>     decompose, spectrum
#> The following object is masked from ‘package:base’:
#> 
#>     union

make weights vector for tests

Arguments

See also

Examples