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.

custom_priors(...)

# S3 method for 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.

Value

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

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.

See also

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

Examples

## BASIC CONFIGURATION custom_priors()
#> #> #> ///// outbreaker custom priors /// #> #> class: custom_priors list #> number of items: 4 #> #> /// custom priors set to NULL (default used) // #> $mu #> NULL #> #> $pi #> NULL #> #> $eps #> NULL #> #> $lambda #> NULL #>
## SPECIFYING PRIOR PARAMETERS ## - this will need to be passed to outbreaker default_config <- create_config() new_config <- create_config(prior_mu = 1e-5, prior_pi = c(2, 1)) ## - to check the prior manually, default settings: param <- list(mu = 0.001, pi = 0.9) outbreaker2:::cpp_prior_mu(param, default_config)
#> [1] -0.001
outbreaker2:::cpp_prior_pi(param, default_config)
#> [1] 1.35434
outbreaker2:::cpp_prior_mu(param, new_config)
#> [1] -11.51293
outbreaker2:::cpp_prior_pi(param, new_config)
#> [1] 0.5877867
## these correspond to: dexp(0.001, 0.01, log = TRUE)
#> [1] -4.60518
dbeta(0.9, 2, 1, log = TRUE)
#> [1] 0.5877867
## SPECIFYING A PRIOR FUNCTION ## flat prior for pi between 0.5 and 1 f <- function(x) {ifelse(x$pi > 0.5, log(2), log(0))} priors <- custom_priors(pi = f) priors # this should be passed to outbreaker
#> #> #> ///// outbreaker custom priors /// #> #> class: custom_priors list #> number of items: 4 #> #> /// custom priors set to NULL (default used) // #> $mu #> NULL #> #> $eps #> NULL #> #> $lambda #> NULL #> #> /// custom priors // #> $pi #> function(x) {ifelse(x$pi > 0.5, log(2), log(0))} #> <environment: 0x2abe580> #>
## test the prior manually priors$pi(list(pi=1))
#> [1] 0.6931472
priors$pi(list(pi=.6))
#> [1] 0.6931472
priors$pi(list(pi=.2))
#> [1] -Inf
priors$pi(list(pi=.49))
#> [1] -Inf