R/aggregate_spectra.R

In pierreroudier/specstore: Stores and eases the manipulation of spectra and associated data

#' Aggregates the spectral information of a Spectra object using
#' an aggregation function chosen by the user.
#'
#' Aggregates the spectral information of a Spectra object using
#' an aggregation function chosen by the user.If some data is also
#' present, it is aggregated using the same function.
#'
#' @param obj an object inheriting from class Spectra
#' @param fun an aggregation function
#' @param ... expressions evaluated in the context of \code{fun}
#' @return An object of the same class as \code{obj}
#' @export
#' @author Pierre Roudier \url{pierre.roudier@@gmail.com}
#' @import plyr

if (!isGeneric("aggregate_spectra"))
  setGeneric("aggregate_spectra", function(obj, fun = mean, ...)
    standardGeneric("aggregate_spectra"))

setMethod("aggregate_spectra", "Spectra",
  function(obj, fun = mean, ...){
    # making up an id name from the aggregation function
    id <- as.character(substitute(fun))[1]

    # applying the function to the spectra
    nir <- aaply(.data = spectra(obj), .margins = 2, .fun = fun, ...)

    res <- Spectra(wl=wl(obj), nir=nir, id=id, units=units(obj))

    # if there is some data
    if ("data" %in% slotNames(obj)) {
#     if (is(obj, 'SpectraDataFrame')) {
      data <- aaply(.data = data(obj), .margins = 2, .fun = fun, ...)
      res <- SpectraDataFrame(res, data=data.frame(matrix(data, nrow=1, dimnames=list(id, names(data)))))
    }

    res
  }
)