#' Finalise TB treatment outcome
#'
#' Finalise TB outcome variable to align with WHO definitions
#'
#' This is a generic function. Methods for EpiInfo and Koch6 data have been defined
#' within this package. They are designed to standardise outcome factor levels
#' according to \href{https://www.who.int/tb/publications/definitions/en/}{WHO (2013) TB definitions}.
#'
#' If \code{bin_outcome} is \code{TRUE}, an additional simplified factor outcome variable is generated with
#' levels \code{Successful}, \code{Unsuccessful} and \code{Not evaluated}, corresponding to definitions
#' in the WHO document.
#'
#' The original data frame with generated variables appended is returned.
#'
#' Any original data not represented in the WHO definitions are converted to \code{NA}.
#'
#' @param x data frame containing outcome variables
#' @param bin_outcome create new binary factor variable simplifying treatment outcome
#' @param ... further arguments passed to or from other methods
#' @author Jay Achar
#' @importFrom assertthat assert_that is.flag
#' @seealso \code{\link{tbgeneratr}}
#' @export
finalise_outcome <- function(x,
bin_outcome = TRUE,
...) {
# check input
assert_that(is.data.frame(x),
is.flag(bin_outcome))
# apply correct method
UseMethod("finalise_outcome", x)
}
#' Finalise TB treatment outcome
#'
#' Finalise TB outcome variable to align with WHO definitions
#' @inheritParams finalise_outcome
#' @author Jay Achar
#' @seealso \code{\link{tbgeneratr}}
#' @export
finalise_outcome.default <- function(x,
bin_outcome = TRUE,
...) {
message("No adm object class detected: finalise_outcome() not applied.")
x
}
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