#' 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))

}