| get_cpp_api {outbreaker2} | R Documentation |
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 (thibautjombart@gmail.com)
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)