R/age.window.R

In goranbrostrom/eha2: Event History Analysis

#' Age cut of survival data
#'
#' For a given age interval, each spell is cut to fit into the
#' given age interval.
#'
#' @param dat Input data frame. Must contain survival data.
#' @param window Vector of length two: The age interval.
#' @param surv Vector of length three giving tha names of the central
#'    variables (a Surv object) in the dataframe 'dat'.
#' @return A dataframe of the same form as the input, but 'cut' as
#'    desired. Intervals exceeding \code{window[2]} are cut there and
#'    given event = 0 (censoring).
#'
#' @author Göran Broström
#' @seealso \code{\link{cal.window}}.
#' @examples
#' dat <- data.frame(enter = 0, exit = 5.731, event = 1, x = 2)
#' window <- c(2, 5.3)
#' dat.trim <- age.window(dat, window)
#'
#' @export
age.window <- function(dat, window,
                       surv = c("enter", "exit", "event")){

    if (!is.data.frame(dat))stop("dat must be a data frame")
    if (length(surv) != 3) stop("surv must have length 3")
    fixed.names <- names(dat)
    surv.indices <- match(surv, fixed.names)
    if (length(which(is.na(surv.indices)))){
        x <- which(is.na(surv.indices))
        stop(paste(surv[x], " is not a name in the data frame."))
    }

    enter <- dat[[surv.indices[1]]]
    exit <- dat[[surv.indices[2]]]
    event <- dat[[surv.indices[3]]]

    who <- (exit > window[1]) & (enter < window[2])
    if (sum(who) > 0.5){ # Not empty selection!
        enter <- enter[who]
        exit <- exit[who]
        event <- event[who]
        ##event <- ifelse(exit > window[2], 0, event)
        event[exit > window[2]] <- 0
        ##exit <- pmin(exit, window[2])
        exit[exit > window[2]] <- window[2]
        ##enter <- pmax(enter[who], window[1])
        enter[enter < window[1]] <- window[1]

        dat <- dat[who, ]
        dat[surv.indices[1]] <- enter
        dat[surv.indices[2]] <- exit
        dat[surv.indices[3]] <- event
    }else{ # Empty selection...
        warning(paste("The age interval", window[1], "-", window[2],
                      "is empty."))
        dat <- NULL
    }
    dat
}