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+++ b/man/get_cpp_api.Rd
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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/get_cpp_api.R
+\name{get_cpp_api}
+\alias{get_cpp_api}
+\title{Access internal C++ rountines used 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:
+
+\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")}).
+}
+\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.
+}
+\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)
+
+}
+\author{
+Thibaut Jombart (\email{thibautjombart@gmail.com})
+}