#' Access internal C++ rountines used in outbreaker2

#'

#' This function returns an environment containing all C++ functions (bound to R

#' using Rcpp) used for priors, likelihoods, and movements of parameters in

#' outbreaker2.

#'

#' @export

#'

#' @author Thibaut Jombart (\email{thibautjombart@@gmail.com}).

#'

#' @return

#'

#' An environment containing Rcpp bindings to C++ functions used internally in

#' outbreaker2. All functions are named as cpp_[type]_[component], where 'type'

#' can be:

#'

#' \itemize{

#'

#' \item 'prior': prior computation.

#'

#' \item 'll':  likelihood computation.

#'

#' \item 'move': movement of parameters or augmented data.

#'

#' }

#'

#' And where 'component' can be:

#'

#' \itemize{

#'

#' \item 'mu': (parameter) mutation rate.

#'

#' \item 'pi': (parameter) reporting probability.

#'

#' \item 'lambda': (parameter) non-infectious contact rate.

#'

#' \item 'eps': (parameter) contact reporting coverage.

#' 

#' \item 'alpha': (augmented data) ancestries of the cases.

#'

#' \item 'kappa': (augmented data) generation between cases on transmission

#' chains.

#'

#' \item 't_inf': (augmented data) dates of infections.

#'

#' \item 'timing_infections': (likelihood component) timing between infectors and

#' infectees.

#'

#' \item 'timing_sampling': (likelihood component) timing between infection and

#' reporting / isolation.

#'

#' \item 'timing': (likelihood component) sum of the two timing components.

#' 

#' \item 'genetic': (likelihood component) genetic diversity accumulated along

#' transmission chains.

#' 

#' \item 'reporting': (likelihood component) reporting of cases.

#' 

#' \item 'all': (likelihood component) sum of all likelihood components.

#'

#' \item '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 (\code{vignette("Rcpp_API", package = "outbreaker2")}).

#'

#' 

#' @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)

#' 

get_cpp_api <- function() {

    pkg_env <- asNamespace("outbreaker2")

    regxp <- "^cpp_(ll|prior|move)"

    names_cpp_functions <- sort(ls(envir = pkg_env, pattern = regxp))

    out_env <- new.env()

    for (e in names_cpp_functions) {

        f <- get(e, envir = pkg_env)

        assign(e, f, envir = out_env)

    }

    return(out_env)

}