custom_moves.RdThis 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:
custom_moves(...) # S3 method for outbreaker_moves print(x, ...)
| ... | A list or a series of named, comma-separated functions implementing movements of parameters or augmented data. |
|---|---|
| x | an |
A list of movement functions with a single argument 'param', with
class outbreaker_moves.
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
See customization vignette for detailed examples on how to customise movement functions.
Thibaut Jombart (thibautjombart@gmail.com).