make_ratemat: Create transition matrix

In bbolker/McMasterPandemic: Pandemic Model

Create transition matrix

Description

Defines rates (per day) of flow from compartment i (row) to compartment j (column).

Usage

make_ratemat(
  state,
  params,
  do_ICU = TRUE,
  sparse = FALSE,
  symbols = FALSE,
  indices = FALSE
)

Arguments

state	named vector of states
params	named vector of parameters
do_ICU	include additional health utilization compartments
sparse	return sparse matrix?
symbols	return character (symbol) form? (FIXME: call adjust_symbols here rather than in show_ratemat()?)
indices	return indices for lower-level stuff?

Details

The rates are as follows:

S to E: - (\beta_0 / N) S (C_a I_a + C_p I_p + (1-iso_m)C_m I_m + (1-iso_s)C_s I_s) E to I_a: E to I_p: ...

See read_params for parameter definitions.

Value

matrix of (daily) transition rates

Note

Base version matches structure of Stanford/Georgia models

• flow diagram: see http://covid-measures.stanford.edu/ 'model details' tab or ../pix/model_schematic.png

• parameter definitions: see params_CI_base.csv, params_ICU_diffs.csv

See Also

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_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()

Examples

params <- read_params("ICU1.csv")
state <- make_state(params[["N"]],E0=params[["E0"]], use_eigvec=FALSE)
M <- make_ratemat(state,params)
if (require(Matrix)) {
   image(Matrix(M))
}
make_ratemat(state,params,symbols=TRUE)

bbolker/McMasterPandemic documentation built on Aug. 25, 2024, 6:35 p.m.