R/custom_moves.R

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

#' 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))
}