Expression List

Create a list of expressions for defining a compartmental model in TMB.

Usage

ExprList(
  before = list(),
  during = list(),
  after = list(),
  .simulate_exprs = character(0L)
)

Arguments

before

List of formulas to be evaluated in the order provided before the simulation loop begins. Each formula must have a left hand side that gives the name of the matrix being updated, and a right hand side giving an expression containing only the names of matrices in the model, functions defined in macpan2.cpp, and numerical literals (e.g. 3.14). The available functions are described in engine_functions. Names can be provided for the components of before, and these names do not have to be unique. These names are used by the .simulate_exprs argument.

during

List of formulas to be evaluated at every iteration of the simulation loop, with the same rules as before.

after

List of formulas to be evaluated after the simulation loop, with the same rules as before.

.simulate_exprs

Character vector of names of expressions to be evaluated within TMB simulate blocks. This is useful when an expression cannot be evaluated during the computation of the objective function and its gradients (e.g. if the expression contains randomness or other discontinuities that will break the automatic differentiation machinery of TMB).

Value

Object of class ExprList with the following methods.

Methods

• $data_arg(...): Return the following components of the data structure to pass to C++.

  • expr_output_id -- Indices into the list of matrices identifying the matrix being produced.

  • expr_sim_block -- Identified whether or not the expression should be evaluated inside a simulate macro within TMB.

  • expr_num_p_table_rows -- Number of rows associated with each expression in the parse table (p_table_*)

  • eval_schedule -- Vector giving the number of expressions to evaluate in each phase (before, during, or after) of the simulation.

  • p_table_x -- Parse table column giving an index for looking up either function, matrix, or literal.

  • p_table_n -- Parse table column giving the number of arguments in functions.

  • p_table_i -- Parse table column giving indices for looking up the rows in the parse table corresponding with the first argument of the function.

Method Arguments

• ...: Character vector containing the names of the matrices in the model.