R/age_calc.R

In agdamsbo/daDoctoR: Functions For Health Research

#' Calculating age from date of birth
#'
#' For age calculations.
#' @param dob Date of birth. Data format follows standard POSIX layout. Format is yyyy-mm-dd.
#' @param enddate Date to calculate age at. Format is yyyy-mm-dd.
#' @param units Default is "years". Can be changed to "days".
#' @param precise Default is TRUE. Flag set whether to include calculations of spring years. Only of matter if using units = "days".
#' @keywords age
#' @export
#' @examples
#'   ##Kim Larsen (cpr is known from album)
#'   dob<-daDoctoR::dob_extract_cpr("231045-0637")
#'   date<-as.Date("2018-09-30")
#'   trunc(age_calc(dob,date))

age_calc<-function (dob, enddate = Sys.Date(), units = "years", precise = TRUE)
## Build upon the work of Jason P. Becker, as part of the eeptools
## Alternative is to just use lubridate::time_length
  {

  if (!inherits(dob, "Date") | !inherits(enddate, "Date")) {
    stop("Both dob and enddate must be Date class objects")
  }

  if (length(dob)==1 && enddate < dob) {
    stop("End date must be a date after date of birth")
  }

  if (length(dob)>1 && any(enddate < dob)) {
    stop("End date must be a date after date of birth")
  }

  start <- as.POSIXlt(dob)
  end <- as.POSIXlt(enddate)

  if (precise) {
    start_is_leap <- ifelse(start$year%%400 == 0, TRUE, ifelse(start$year%%100 ==
                                                                 0, FALSE, ifelse(start$year%%4 == 0, TRUE, FALSE)))
    end_is_leap <- ifelse(end$year%%400 == 0, TRUE, ifelse(end$year%%100 ==
                                                             0, FALSE, ifelse(end$year%%4 == 0, TRUE, FALSE)))
  }
  if (units == "days") {
    result <- difftime(end, start, units = "days")
  }
  else if (units == "months") {
    months <- sapply(mapply(seq, as.POSIXct(start), as.POSIXct(end),
                            by = "months", SIMPLIFY = FALSE), length) - 1
    if (precise) {
      month_length_end <- ifelse(end$mon == 1 & end_is_leap,
                                 29, ifelse(end$mon == 1, 28, ifelse(end$mon %in%
                                                                       c(3, 5, 8, 10), 30, 31)))
      month_length_prior <- ifelse((end$mon - 1) == 1 &
                                     start_is_leap, 29, ifelse((end$mon - 1) == 1,
                                                               28, ifelse((end$mon - 1) %in% c(3, 5, 8, 10),
                                                                          30, 31)))
      month_frac <- ifelse(end$mday > start$mday, (end$mday -
                                                     start$mday)/month_length_end, ifelse(end$mday <
                                                                                            start$mday, (month_length_prior - start$mday)/month_length_prior +
                                                                                            end$mday/month_length_end, 0))
      result <- months + month_frac
    }
    else {
      result <- months
    }
  }
  else if (units == "years") {
    years <- sapply(mapply(seq, as.POSIXct(start), as.POSIXct(end),
                           by = "years", SIMPLIFY = FALSE), length) - 1
    if (precise) {
      start_length <- ifelse(start_is_leap, 366, 365)
      end_length <- ifelse(end_is_leap, 366, 365)
      start_day <- ifelse(start_is_leap & start$yday >=
                            60, start$yday - 1, start$yday)
      end_day <- ifelse(end_is_leap & end$yday >= 60, end$yday -
                          1, end$yday)
      year_frac <- ifelse(start_day < end_day, (end_day -
                                                  start_day)/end_length, ifelse(start_day > end_day,
                                                                                (start_length - start_day)/start_length + end_day/end_length,
                                                                                0))
      result <- years + year_frac
    }
    else {
      result <- years
    }
  }

  else {
    stop("Unrecognized units. Please choose years, months, or days.")
  }
  return(result)
}