run_sim: Run pandemic simulation

In bbolker/McMasterPandemic: Pandemic Model

Run pandemic simulation

Description

Run pandemic simulation

Usage

run_sim(
  params,
  state = NULL,
  start_date = "2020-03-20",
  end_date = "2020-05-1",
  params_timevar = NULL,
  dt = 1,
  ndt = 1,
  stoch = c(obs = FALSE, proc = FALSE),
  stoch_start = NULL,
  ratemat_args = NULL,
  step_args = list(),
  ode_args = list(),
  use_ode = FALSE,
  condense = TRUE,
  condense_args = NULL,
  verbose = FALSE,
  use_flex = FALSE,
  flexmodel = NULL,
  obj_fun = NULL
)

Arguments

params	named vector of parameters
state	named vector of states
start_date	starting date (Date or character, any sensible D-M-Y format)
end_date	ending date (ditto)
params_timevar	four-column data frame containing columns 'Date'; 'Symbol' (parameter name/symbol); 'Value'; and 'Type' (rel_orig (relative to value at time zero); rel_prev (relative to previous value); or abs (absolute value at specified time). If a 'Relative_value' column is present, it is renamed to 'Value' and 'Type' is set to rel_orig for back-compatibility.
dt	time step for do_step
ndt	number of internal time steps per time step
stoch	a logical vector with elements "obs" (add obs error?) and "proc" (add process noise?)
stoch_start	dates on which to enable stochasticity (vector of dates with names 'proc' and 'obs')
ratemat_args	additional arguments to pass to make_ratemat
step_args	additional arguments to pass to do_step
ode_args	additional arguments to ode
use_ode	integrate via ODE rather than discrete step?
condense	if TRUE, use condense.pansim to reduce the number of variables in the output (in particular, collapse subclasses and return only one I, H, and ICU variable)
condense_args	arguments to pass to condense (before adding observation error)
verbose	print messages (e.g. about time-varying parameters)?
use_flex	use flexmodel approach
flexmodel	optional flexmodel object
obj_fun	optional TMB objective function computed with tmb_fun

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_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(), 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")
paramsS <- update(params,c(proc_disp=0.1,obs_disp=100))
paramsSz <- update(paramsS, zeta=5)
state <- make_state(params=params)
time_pars <- data.frame(Date=c("2020-03-20","2020-03-25"),
                       Symbol=c("beta0","beta0"),
                       Relative_value=c(0.7,0.1),
                       stringsAsFactors=FALSE)
res1 <- run_sim(params,state,start_date="2020-02-01",end_date="2020-06-01")
res1X <- run_sim(params,state,start_date="2020-02-01",end_date="2020-06-01",
                 condense_args=list(keep_all=TRUE))
res1_S <- update(res1, params=paramsS, stoch=c(obs=TRUE, proc=TRUE))
res1_t <- update(res1, params_timevar=time_pars)
res1_S_t <- update(res1_S, params_timevar=time_pars)
res2_S_t <- update(res1_S_t,params=update(paramsS, proc_disp=0.5))
res3_S_t <- update(res2_S_t,stoch_start="2020-04-01")
res3_Sz <- update(res1_S, params=paramsSz)
plot(res3_Sz,log=TRUE,log_lwr=1e-4)

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