custom_moves: Customise samplers for outbreaker

In reconhub/outbreaker2: Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

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(...)

## S3 method for class 'outbreaker_moves'
print(x, ...)

Arguments

...	A list or a series of named, comma-separated functions implementing movements of parameters or augmented data.
x	an outbreaker_moves object as returned by create_moves.

Details

• mu: movement of the mutation rate; by default, the function cpp_move_mu is used.

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

• eps: movement of the contact reporting coverage; by default, the function cpp_move_eps is used.

• lambda: the movement of the non-infectious contact rate; the function cpp_move_lambda 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.

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

Author(s)

Thibaut Jombart ([e-mail]).

See Also

See customization vignette for detailed examples on how to customise movement functions.

reconhub/outbreaker2 documentation built on Sept. 25, 2024, 5:45 p.m.