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.

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

Thibaut Jombart (thibautjombart@gmail.com)

Examples


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

#> <environment: 0x000000003a142060>

## check content of the environment
ls(api)

#>  [1] "cpp_ll_all"               "cpp_ll_contact"          
#>  [3] "cpp_ll_genetic"           "cpp_ll_reporting"        
#>  [5] "cpp_ll_timing"            "cpp_ll_timing_infections"
#>  [7] "cpp_ll_timing_sampling"   "cpp_move_alpha"          
#>  [9] "cpp_move_eps"             "cpp_move_kappa"          
#> [11] "cpp_move_lambda"          "cpp_move_mu"             
#> [13] "cpp_move_pi"              "cpp_move_swap_cases"     
#> [15] "cpp_move_t_inf"           "cpp_prior_all"           
#> [17] "cpp_prior_eps"            "cpp_prior_lambda"        
#> [19] "cpp_prior_mu"             "cpp_prior_pi"            

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

#> function (param, config, custom_function = NULL) 
#> NULL

config <- create_config()

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

#> [1] -0.00123

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

#> [1] -0.00123