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:
custom_moves(...) ## S3 method for class 'outbreaker_moves' print(x, ...)
A list or a series of named, comma-separated functions implementing movements of parameters or augmented data.
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
cpp_move_eps is used.
lambda: the movement of the non-infectious contact rate; the
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
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
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
config: a list of named items containing input data as returned by
likelihoods: a list of named custom likelihood functions as returned by
priors: a list of named custom prior functions as returned by
A list of movement functions with a single argument 'param', with
Thibaut Jombart (email@example.com).
See customization vignette for detailed examples on how to customise movement functions.
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