custom_moves: Customise samplers for outbreaker
In o2geosocial: Reconstruction of Transmission Chains from Surveillance Data

Description Usage Arguments Details Value Author(s)

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:

1	custom_moves(...)

...

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

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