In reconhub/outbreaker2: Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

List of available functions

The C++ functions bound to R via Rcpp used in outbreaker2 for priors, likelihoods and movements are not visible to the user, as they are not exported by the package. However, advanced users can access these functions using get_cpp_api(), which returns an environment with all relevant functions:

library(outbreaker2) 

## get all functions in an environment
x <- get_cpp_api()
x

## check content
ls(x)

## all functions are Rcpp bindings to a C++ function
x$cpp_ll_all

Function signatures

These functions take the following arguments:

list_args <- lapply(x, args)[ls(x)]
list_args

Arguments are detailed in the next section.

Arguments

Arguments of the Rcpp-bound C++ functions are:

list_formals <- lapply(x, formals)
args <- sort(unique(unlist(lapply(list_formals, names))))
args

• alpha: a vector of integers of length 'N' (number of cases), indicating infectors of each case, with values from 1 to N; missing values should be NA

• config: a list containing configuration settings as returned by create_config

• custom_function: a R function for a custom prior, with a single argument, which must be a list of parameters and augmented data with the class outbreaker_param; returned values must be on the log scale

• custom_functions: a list of R functions obeying the rules of custom_function, named according to the priors; currently available names are:

temp <- sub("cpp_prior_", "", ls(x, pattern = "cpp_prior.*"))
setdiff(temp, "all") 

• custom_ll: a R function for a custom likelihood, taking two arguments: data (see data), and param (see param)

• custom_prior: same as custom_function

• data: a valid 'outbreaker_data' list

• i: an integer scalar indicating the index of a case, from 1 to N (number of cases)

• list_custom_ll: a list of R functions obeying the rules of custom_ll, named according to the computed likelihood component; available names are:

temp <- sub("cpp_ll_", "", ls(x, pattern = "cpp_ll.*"))
setdiff(temp, c("timing", "all"))       

• param: a list containing parameters and augmented data with the class outbreaker_param

• t_inf: a vector of integers of length N (number of cases), indicating infection dates of each case; missing values should be NA

• x: a vector of integers to be sampled from

reconhub/outbreaker2 documentation built on July 5, 2022, 12:25 p.m.