formula.hpp File Reference

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Functions
void	defm_motif_parser (std::string formula, std::vector< size_t > &locations, std::vector< bool > &signs, size_t m_order, size_t y_ncol, std::string &covar_name, std::string &vname)
	Parses a motif formula. More...

Function Documentation

defm_motif_parser()

void defm_motif_parser ( std::string  formula, std::vector< size_t > &  locations, std::vector< bool > &  signs, size_t  m_order, size_t  y_ncol, std::string &  covar_name, std::string &  vname  )

inline

Parses a motif formula.

This function will take the formula and generate the corresponding input for defm::counter_transition(). Formulas can be specified in the following ways:

• Intercept effect: {...} No transition, only including the current state.
• Transition effect: {...} > {...} Includes current and previous states.

The general notation is [0]y[column id]_[row id]. A preceeding zero means that the value of the cell is considered to be zero. The column id goes between 0 and the number of columns in the array - 1 (so it is indexed from 0,) and the row id goes from 0 to m_order.

Intercept effects

Intercept effects only involve a single set of curly brackets. Using the 'greater-than' symbol (i.e., '>') is only for transition effects. When specifying intercept effects, users can skip the row_id, e.g., y0_0 is equivalent to y0. If the passed row id is different from the Markov order, i.e., row_id != m_order, then the function returns with an error.

Examples:

• "{y0, 0y1}" is equivalent to set a motif with the first element equal to one and the second to zero.

Transition effects

Transition effects can be specified using two sets of curly brackets and an greater-than symbol, i.e., {...} > {...}. The first set of brackets, which we call LHS, can only hold row id that are less than m_order.

Parameters

formula
locations
signs
m_order
y_ncol

Definition at line 46 of file formula.hpp.