flexmodel: Initialize Flexible Compartmental Model

In bbolker/McMasterPandemic: Pandemic Model

Initialize Flexible Compartmental Model

Description

https://canmod.net/misc/flex_specs

Usage

flexmodel(
  params,
  state = NULL,
  start_date = NULL,
  end_date = NULL,
  params_timevar = NULL,
  do_hazard = getOption("MP_default_do_hazard"),
  do_make_state = getOption("MP_default_do_make_state"),
  do_hazard_lin = getOption("MP_default_do_hazard_lin"),
  do_approx_hazard = getOption("MP_default_do_approx_hazard"),
  do_approx_hazard_lin = getOption("MP_default_do_approx_hazard_lin"),
  do_sim_constraint = getOption("MP_default_do_sim_constraint"),
  sim_lower_bound = getOption("MP_default_sim_lower_bound"),
  max_iters_eig_pow_meth = 8000,
  tol_eig_pow_meth = 1e-06,
  data = NULL,
  ...
)

init_model(...)

Arguments

params	a param_pansim object
state	a state_pansim object
start_date	simulation start date
end_date	simulation end date
params_timevar	data frame with scheduling for piece-wise constant parameter variation (TODO: direct to other help pages)
do_hazard	should hazard simulation steps be used? (https://canmod.net/misc/flex_specs#v0.0.5) – only used if spec_ver_gt('0.0.4')
do_make_state	should state be remade on the c++ size? (https://canmod.net/misc/flex_specs#v0.1.1) – only used if spec_ver_gt('0.1.0')
do_hazard_lin	like do_hazard but for the linearized model that is used to construct the initial state variable – only used when do_make_state == TRUE
do_approx_hazard	approximate the hazard transformation by a smooth function (experimental)
do_approx_hazard_lin	like do_approx_hazard but for the linearized model that is used to construct the initial state (experimental)
do_sim_constraint	should simulated values be smoothly constrained to be above sim_lower_bound when computing negative binomial (maybe others in the future?) loss functions? the smooth constraint function is y = x + \epsilon * \exp(-x / \epsilon), where \epsilon is sim_lower_bound and x is the simulated value.
sim_lower_bound	optional lower bound on the simulated values when computing negative binomial loss functions (only applicable when do_sim_constraint is TRUE.
max_iters_eig_pow_meth	maximum number of iterations to use in computing the eigenvector for initial state construction
tol_eig_pow_meth	tolerance for determining convergence of the power method used in initial state construction
data	optional observed data frame in long format to compare with simulated trajectories. must have the following columns: date, var, value. (currently this is not working)

Value

flexmodel object representing a compartmental model

See Also

Other flexmodels: make_ageified_model(), make_base_model(), make_hello_world_model(), make_omicron_model(), make_sir_model(), make_vaccination_model()

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