custom_likelihoods: Customise likelihood functions for outbreaker

In thibautjombart/outbreaker2: Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

Customise likelihood functions for outbreaker

Description

This function is used to specify customised likelihood functions for outbreaker. Custom functions are specified as a named list or series of comma-separated, named arguments, indicating which log-likelihood component they compute. Values currently available are:

Usage

custom_likelihoods(...)

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

Arguments

...	a named list of functions, each computing a log-likelihood component.
x	an outbreaker_config object as returned by create_config.

Details

• genetic: the genetic likelihood; by default, the function cpp_ll_genetic is used.

• timing_sampling: the likelihood of sampling times; by default, the function cpp_ll_timing_sampling is used.

• timing_infections: the likelihood of infection times; by default, the function cpp_ll_timing_infections is used.

• reporting: the likelihood of the reporting process; by default, the function cpp_ll_reporting is used.

• contact: the likelihood of the contact tracing data; by default, the function cpp_ll_contact is used.

All log-likelihood functions should have the following arguments, in this order:

• data: a list of named items containing input data as returned by outbreaker_data

• param: a list of parameters with the class create_param

Value

A named list of list(function, arity) pairs with the class custom_likelihood, each function implementing a customised log-likelihood component of outbreaker. Functions which are not customised will result in a list(NULL, 0) component. Any function with arity 3 must have the third parameter default to NULL.

a list of named functions

Author(s)

Thibaut Jombart ([e-mail])

See Also

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

Examples

## specify a null model by disabling all likelihood components
f_null <- function(data, param) {
  return(0.0)
}

null_model <- custom_likelihoods(genetic = f_null,
                                timing_sampling = f_null,
                                timing_infections = f_null,
                                reporting = f_null,
                                contact = f_null)

null_config <- list(find_import = FALSE,
                    n_iter = 100,
                    sample_every = 1)

## load data
x <- fake_outbreak
data <- outbreaker_data(dates = x$sample, dna = x$dna, w_dens = x$w)

res_null <- outbreaker(data = data,
                       config = null_config,
                       likelihoods = null_model)

## visualise ancestries to see if all transmission trees have been explored
plot(res_null, type = "alpha")

thibautjombart/outbreaker2 documentation built on July 6, 2022, 11:10 p.m.