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#' Customise samplers for outbreaker
#'
#' This function is used to specify customised movement functions
#' (a.k.a. samplers) for outbreaker. Custom functions are specified as a named
#' list or series of comma-separated, named arguments, indicating which type of
#' movement they implement. Values currently available are:
#'
#' \itemize{
#'
#' \item \code{pi}: movement of the reporting probability; by default, the function
#' \code{cpp_move_pi} is used.
#'
#' \item \code{a}: movement of the first spatial parameter; by default, the function
#' \code{cpp_move_a} is used.
#'
#' \item \code{b}: movement of the second spatial parameter; by default, the function
#' \code{cpp_move_b} is used.
#'
#' \item \code{alpha}: movement of the transmission tree, by randomly proposing
#' infectors in the pool of cases infected before; by default, the function
#' \code{cpp_move_alpha} is used.
#'
#' \item \code{swap_cases}: movement of the transmission tree, by swapping
#' infectors and infected cases; by default, the function
#' \code{cpp_move_swap_cases} is used.
#'
#' \item \code{ancestors}: movement of the transmission tree, by changing
#' the ancestors of the different trees in a cluster; by default, the function
#' \code{cpp_move_ancestors} is used.
#'
#' \item \code{t_inf}: movement of the date of infection; by default, the
#' function \code{cpp_move_t_inf} is used.
#'
#' \item \code{kappa}: movement of the number generations between cases; by
#' default, the function \code{cpp_move_kappa} is used.
#'
#' }
#'
#'
#' Movement functions must have an argument \code{param}, which is a list of
#' parameters and augmented data of the class \code{\link{create_param}}.
#' Each movement function will be enclosed with its other arguments, so that the
#' resulting function will have a single argument 'param'. For non-standard
#' movements (i.e. none of the names specified above), the closure will contain:
#'
#' \itemize{
#'
#' \item \code{data}: a list of named items containing input data as returned by
#' \code{\link{outbreaker_data}}
#'
#' \item \code{config}: a list of named items containing input data as returned by
#' \code{\link{create_config}}
#'
#' \item \code{likelihoods}: a list of named custom likelihood functions as returned by
#' \code{\link{custom_likelihoods}}
#'
#' \item \code{priors}: a list of named custom prior functions as returned by
#' \code{\link{custom_priors}}
#'
#' }
#'
#' @author Initial version by Thibaut Jombart, rewritten by Alexis Robert (\email{alexis.robert@lshtm.ac.uk})
#'
#' @export
#'
#' @param ... A list or a series of named, comma-separated functions
#' implementing movements of parameters or augmented data.
#'
#' @return A named list of movement functions with a single argument 'param', with
#' class \code{outbreaker_moves}.
custom_moves <- function(...) {
move_functions <- list(...)
if (length(move_functions) == 1L && is.list(move_functions[[1]])) {
move_functions <- move_functions[[1]]
}
defaults <- list(pi = cpp_move_pi,
a = cpp_move_a,
b = cpp_move_b,
alpha = cpp_move_alpha,
swap_cases = cpp_move_swap_cases,
ancestors = cpp_move_ancestors,
t_inf = cpp_move_t_inf,
kappa = cpp_move_kappa
)
moves <- modify_defaults(defaults, move_functions, FALSE)
moves_names <- names(moves)
## check all moves are functions
function_or_null <- function(x) {
is.null(x) || is.function(x)
}
is_ok <- vapply(moves, function_or_null, logical(1))
if (!all(is_ok)) {
culprits <- moves_names[!is_ok]
msg <- paste0("The following moves are not functions: ",
paste(culprits, collapse = ", "))
stop(msg)
}
## check they all have a 'param' argument
param_is_arg <- function(x) {
if(is.function(x)) {
return ("param" %in% methods::formalArgs(x))
}
return(TRUE)
}
param_ok <- vapply(moves, param_is_arg, logical(1))
if (!all(param_ok)) {
culprits <- moves_names[!param_ok]
msg <- paste0("The following moves dont' have a 'param' argument: ",
paste(culprits, collapse = ", "))
stop(msg)
}
class(moves) <- c("outbreaker_moves", "list")
return(moves)
}
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