custom_priors: Customise priors for outbreaker

Description Usage Arguments Details Value Author(s) Examples

View source: R/custom_priors.R

Description

Priors can be specified in several ways in o2geosocial (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

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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:

Value

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

Author(s)

Initial version by Thibaut Jombart, rewritten by Alexis Robert (alexis.robert@lshtm.ac.uk)

Examples

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## SPECIFYING PRIOR PARAMETERS
## Default values: pi follows a beta distribution (parameters 10, 1), 
## a and b follow a uniform distribution (parameters 0, 5)
default_config <- create_config()
## Use the variables prior_a, prior_b and prior_pi to change the parameters
## of the prior distributions can be 
new_config <- create_config(prior_a = c(0,5), prior_b = c(0,5),
                        prior_pi = c(2, 1))


## SPECIFYING A NEW PRIOR FUNCTION
## Example: flat prior for pi between 0.5 and 1
f <- function(x) {ifelse(x$pi > 0.5, log(2), log(0))}
priors <- custom_priors(pi = f)
## test the new prior distribution
priors$pi(list(pi=1))
priors$pi(list(pi=.6))
priors$pi(list(pi=.2))
priors$pi(list(pi=.49))

o2geosocial documentation built on Sept. 11, 2021, 9:07 a.m.