R/detect_transitions.R

In dschoenig/IDENTcc: Catch and correct errors in IDENT datasets

#' Detect value transitions
#'
#' `detect_transitions` detects transitions between values in a vector.
#'
#' This function is intended to be a helper function to quickly detect
#' transitions in a sequence of values that are assumed to be erroneous. The
#' output may be coerced to a logical vector and used for indexing the original
#' sequence (see examples).
#'
#' @param x A vector in which transitions are to be detected.
#' @param transition A vector of length 2, specifying the first and second value
#'     of the transition.
#' @return An integer vector of the same length as `x`. The start (i.e. first
#'     value) of a transition is `1` all other entries are `0`.
#' @examples
#' # Example for a sequence of values where a tree turns "Alive" after having
#' # been measured "Dead"
#' x <- c("Alive", "Almost dead", "Dead", "Dead", "Dead", "Alive", "Dead",
#'             "Dead", "Alive", "Dead", "Cut and Resprout", "Dead", "Alive")
#' detect_transitions(x, c("Dead", "Alive"))
#'
#' # Extract starting points of the transition
#' trans <- as.logical(detect_transitions(x, c("Dead", "Alive")))
#' which(trans)
#' x[trans]
#' @export
detect_transitions <- function(x, transition) {
    if(length(transition) != 2) {
        stop("`transition` must be a vector of length 2.")
    }
    if(is.factor(x)) {
        x <- as.character(x)
    }

    x1 <- x
    x2 <- x
    x1[x == transition[1]] <- 1
    x1[x != transition[1]] <- 0
    x2[x == transition[2]] <- 1
    x2[x != transition[2]] <- 0

    x_detected <- as.integer(x1) * as.integer(x2[c(2:length(x2), length(x2))])
    return(x_detected)
}