custom_priors {outbreaker2}

Customise priors for outbreaker

Description

Priors can be specified in several ways in outbreaker2 (see details and examples). The most flexible way to specify a prior is to provide a prior function directly. This function must take an argument 'param', which is a list which contains all the states of the parameters and augmented data. See the documentation of create_param for more information.

Usage

custom_priors(...)

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

Arguments

...

A list or a series of named, comma-separated functions implementing priors. Each function must have a single argument, which corresponds to a 'outbreaker_param' list.

x

an outbreaker_config object as returned by create_config.

Details

There are three ways a user can specify priors:

1) Default: this is what happens when the 'config' has default values of prior parameters.
2) Customized parameters: in this case, the prior functions are the default ones from the package, but will use custom parameters, specified by the user through create_config.

3) Customized functions: in this case, prior functions themselves are specified by the user, through the '...' argument of 'custom_priors'. The requirements is that such functions must have either hard-coded parameters or enclosed values. They will take a single argument which is a list containing all model parameters with the class 'outbreaker_param'. ALL PRIORS functions are expected to return values on a LOG SCALE.

Priors currently used for the model are:

• mu (mutation rate): default function is an exponential distribution implemented in outbreaker:::cpp_prior_mu. New prior functions should use x$mu to refer to the current value of mu, assuming their argument is called x.

• pi (reporting probability): default function is a beta distribution implemented in outbreaker:::cpp_prior_pi. New prior functions should use x$pi to refer to the current value of pi, assuming their argument is called x.

• eps (contact reporting coverage): default function is a beta distribution implemented in outbreaker:::cpp_prior_eps. New prior functions should use x$eps to refer to the current value of eps, assuming their argument is called x.

• lambda (non-infectious contact rate): default function is a beta distribution implemented in outbreaker:::cpp_prior_lambda. New prior functions should use x$lambda to refer to the current value of lambda, assuming their argument is called x.

Value

A list of custom functions with class custom_priors. Values set to NULL will be ignored and default functions will be used instead.

Author(s)

Thibaut Jombart ([e-mail]).

See Also

See customization vignette for detailed examples on how to customize priors.

Examples

## BASIC CONFIGURATION
custom_priors()


## SPECIFYING PRIOR PARAMETERS
## - this will need to be passed to outbreaker
default_config <- create_config()
new_config <- create_config(prior_mu = 1e-5,
                        prior_pi = c(2, 1))

## - to check the prior manually, default settings:
param <- list(mu = 0.001, pi = 0.9)
outbreaker2:::cpp_prior_mu(param, default_config)
outbreaker2:::cpp_prior_pi(param, default_config)

outbreaker2:::cpp_prior_mu(param, new_config)
outbreaker2:::cpp_prior_pi(param, new_config)

## these correspond to:
dexp(0.001, 0.01, log = TRUE)
dbeta(0.9, 2, 1, log = TRUE)


## SPECIFYING A PRIOR FUNCTION

## flat prior for pi between 0.5 and 1
f <- function(x) {ifelse(x$pi > 0.5, log(2), log(0))}
priors <- custom_priors(pi = f)
priors # this should be passed to outbreaker

## test the prior manually
priors$pi(list(pi=1))
priors$pi(list(pi=.6))
priors$pi(list(pi=.2))
priors$pi(list(pi=.49))