R/AggregateDiurnalFlux.R

In bmcnellis/sapflux: Analyze Sapflux Traces

#' Aggregates sub-daily sapflow measurements to diurnal means
#'
#' @description
#' Subdaily sapflow measurements are difficult to visualize over long time
#' spans. Diurnal means smooth out the data without losing information on
#' total daily transpiration.
#'
#' @param flux    'flux' class object
#' @export
#' @examples
#' myflux <- AggregateDiurnalFlux(flux = myflux)
AggregateDiurnalFlux <- function(flux) {
  validObject(flux)
  data <- slot(flux, name = "data")
  time <- slot(flux, name = "time")
  time <- as.Date(time)
  days <- unique(time)
  diurnal.return <- matrix(data = NA, ncol = ncol(data), nrow = length(days))
  meanNA <- function(x) {
    mean(x, na.rm = TRUE)
  }
  for (i in 1:ncol(data)) {
    diurnal.return[, i] <- tapply(X = data[, i], INDEX = time, FUN = meanNA)
  }
  slot(flux, name = "data") <- diurnal.return
  slot(flux, name = "time") <- .POSIXct(NULL)
  slot(flux, name = "date") <- days
  return(flux)
}