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