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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{mu}: movement of the mutation rate; by default, the function
#' \code{cpp_move_mu} is used.
#'
#' \item \code{pi}: movement of the reporting probability; by default, the function
#' \code{cpp_move_pi} is used.
#'
#' \item \code{eps}: movement of the contact reporting coverage; by default, the
#' function \code{cpp_move_eps} is used.
#'
#' \item \code{lambda}: the movement of the non-infectious contact rate; the
#' function \code{cpp_move_lambda} 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{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 Thibaut Jombart (\email{thibautjombart@@gmail.com}).
#'
#' @seealso See \href{http://www.repidemicsconsortium.org/outbreaker2/articles/customisation.html#customising-movements}{customization vignette} for detailed examples on how to customise movement functions.
#'
#' @export
#'
#' @param ... A list or a series of named, comma-separated functions
#' implementing movements of parameters or augmented data.
#'
#' @return A 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(mu = cpp_move_mu,
pi = cpp_move_pi,
eps = cpp_move_eps,
lambda = cpp_move_lambda,
alpha = cpp_move_alpha,
swap_cases = cpp_move_swap_cases,
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)
}
#' @rdname custom_moves
#'
#' @export
#'
#' @aliases print.outbreaker_moves
#'
#' @param x an \code{outbreaker_moves} object as returned by \code{create_moves}.
#'
print.outbreaker_moves <- function(x, ...) {
cat("\n\n ///// outbreaker movement functions ///\n")
cat("\nclass:", class(x))
cat("\nnumber of items:", length(x))
cat("\n\n/// movement functions //\n")
print(x[])
## is_custom <- !vapply(x, is.null, FALSE)
## names_default <- names(x)[!is_custom]
## if (length(names_default) > 0) {
## cat("/// custom priors set to NULL (default used) //\n")
## print(x[!is_custom])
## }
## names_custom <- names(x)[is_custom]
## if (length(names_custom) > 0) {
## cat("/// custom priors //\n")
## print(x[is_custom])
## }
return(invisible(NULL))
}
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