ode_model: Create an ODE model

In jtimonen/odemodeling: Building, fitting, and validating Bayesian ODE models in 'Stan'

Create an ODE model

Description

Generate model given the declarations of variables, parameters, functions etc. The arguments odefun_vars, loglik_vars and other_vars must be lists whose elements must have one of the following three types:

• StanDeclaration - can be created using stan_var(), stan_vector(), stan_array() etc.

• StanParameter - can be created using stan_param()

• StanTransformation - can be created using stan_transform()

These will go to different blocks of the 'Stan' model code so that

• StanDeclarations go to data

• StanParameters go to parameters

• StanTransformations with origin "data" go to ⁠transformed data⁠

• StanTransformations with origin "parameters" go to ⁠transformed parameters⁠

• StanTransformations with origin "model" go to ⁠generated quantities⁠

Usage

ode_model(
  N,
  odefun_vars = list(),
  odefun_body = "",
  odefun_init = NULL,
  loglik_vars = list(),
  loglik_body = "",
  other_vars = list(),
  verbose = FALSE,
  compile = TRUE,
  sig_figs = 18
)

Arguments

N	A StanDimension variable describing the number of time points.
odefun_vars	Data and parameters needed by the ODE function. Must be a list of StanDeclaration, StanParameter, or StanTransformation objects. These will be defined in Stan model code blocks
odefun_body	ODE function body (Stan code string).
odefun_init	Initial value for ODE system at t0. Has to be a StanVector, or alternatively a StanParameter or a StanTransformation with StanVector base declaration.
loglik_vars	Data and parameters needed by the log likelihood function.
loglik_body	Log likelihood function body (Stan code string).
other_vars	Other variables.
verbose	Should this print more information?
compile	Should the model be compiled?
sig_figs	Number of significant figures to use in all 'CmdStan' calls.

Value

An object of class OdeModel.

See Also

Other model constructor functions: example_ode_model()

jtimonen/odemodeling documentation built on Sept. 15, 2024, 4:29 a.m.