get_cpp_api: Access internal C++ rountines used in outbreaker2

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

Access internal C++ rountines used in outbreaker2

Description

This function returns an environment containing all C++ functions (bound to R using Rcpp) used for priors, likelihoods, and movements of parameters in outbreaker2.

Usage

get_cpp_api()

Value

An environment containing Rcpp bindings to C++ functions used internally in outbreaker2. All functions are named as cpp_[type]_[component], where 'type' can be:

• 'prior': prior computation

• 'll': likelihood computation

• 'move': movement of parameters or augmented data

And where 'component' can be:

• 'mu': (parameter) mutation rate

• 'pi': (parameter) reporting probability

• 'lambda': (parameter) non-infectious contact rate

• 'eps': (parameter) contact reporting coverage

• 'alpha': (augmented data) ancestries of the cases

• 'kappa': (augmented data) generation between cases on transmission chains

• 't_inf': (augmented data) dates of infections

• 'timing_infections': (likelihood component) timing between infectors and infectees

• 'timing_sampling': (likelihood component) timing between infection and reporting / isolation

• 'timing': (likelihood component) sum of the two timing components

• 'genetic': (likelihood component) genetic diversity accumulated along transmission chains

• 'reporting': (likelihood component) reporting of cases

• 'all': (likelihood component) sum of all likelihood components

• 'swap_cases': (type of movement) swap infectors and infectees on a transmission tree

For a description of the arguments of these functions, see the Rcpp_API vignette (vignette("Rcpp_API", package = "outbreaker2")).

Author(s)

Thibaut Jombart ([e-mail])

Examples

## get functions in an environment
api <- get_cpp_api()
api

## check content of the environment
ls(api)

## test the prior for mu
args(api$cpp_prior_mu)

config <- create_config()

api$cpp_prior_mu(list(mu = 0.00123), config)

dexp(0.00123, rate = config$prior_mu, log = TRUE)

outbreaker2 documentation built on May 23, 2022, 5:06 p.m.