custom_moves {o2geosocial}

Customise samplers for outbreaker

Description

This function is used to specify customised movement functions (a.k.a. samplers) for outbreaker. Custom functions are specified as a named list or series of comma-separated, named arguments, indicating which type of movement they implement. Values currently available are:

Usage

custom_moves(...)

Arguments

...

A list or a series of named, comma-separated functions implementing movements of parameters or augmented data.

Details

• pi: movement of the reporting probability; by default, the function cpp_move_pi is used.

• a: movement of the first spatial parameter; by default, the function cpp_move_a is used.

• b: movement of the second spatial parameter; by default, the function cpp_move_b is used.

• alpha: movement of the transmission tree, by randomly proposing infectors in the pool of cases infected before; by default, the function cpp_move_alpha is used.

• swap_cases: movement of the transmission tree, by swapping infectors and infected cases; by default, the function cpp_move_swap_cases is used.

• ancestors: movement of the transmission tree, by changing the ancestors of the different trees in a cluster; by default, the function cpp_move_ancestors is used.

• t_inf: movement of the date of infection; by default, the function cpp_move_t_inf is used.

• kappa: movement of the number generations between cases; by default, the function cpp_move_kappa is used.

Movement functions must have an argument param, which is a list of parameters and augmented data of the class create_param. Each movement function will be enclosed with its other arguments, so that the resulting function will have a single argument 'param'. For non-standard movements (i.e. none of the names specified above), the closure will contain:

• data: a list of named items containing input data as returned by outbreaker_data

• config: a list of named items containing input data as returned by create_config

• likelihoods: a list of named custom likelihood functions as returned by custom_likelihoods

• priors: a list of named custom prior functions as returned by custom_priors

Value

A named list of movement functions with a single argument 'param', with class outbreaker_moves.

Author(s)

Initial version by Thibaut Jombart, rewritten by Alexis Robert ([e-mail])