R/AAA-Classes.R

In inspectr: Storing, manipulating and analysis spectroscopy and associated data in R.

#' Class for spectra collections
#'
#' @slot wl object of class "\code{numeric}"; the wavelengths at which the spectra has been measured
#' @slot nir object of class "\code{matrix}"; the spectra, with as many columns as wavelengths, and as many rows as samples
#' @slot id object of class "\code{data.frame}" with one attribute; the identification strings for each sample in the collection
#' @slot units object of class "\code{character}"; units in which the wavelengths are expressed
#' @seealso \code{\link{spectra}}, \code{\link{wl}}, \code{\link{SpectraDataFrame-class}}
#' @author Pierre Roudier \email{pierre.roudier@@gmail.com}
#' @rdname Spectra-class
#' @exportClass Spectra
setClass(
  Class="Spectra",
  representation=representation(
    wl = 'numeric',
    nir = 'matrix',
    id = 'data.frame',
    units = "character"
  ),
  prototype = prototype(
    wl = numeric(),
    nir = matrix(),
    id = data.frame(NA),
    units = as.character(NA)
  ),
  validity = function(object) {
    # if the wl are given as an integer vector they are translated into a numeric vector
    # for clarity (only one type to manage)
    if (is(object@wl, "integer"))
      object@wl <- as.numeric(object@wl)
    if (!inherits(object@wl, "numeric"))
      stop("wl should be of class integer or numeric")
    if ((nrow(object@id) > 0) & (nrow(object@nir) != nrow(object@id)))
      stop("number of individuals and number of rows in the spectra matrix don't match")
    if ((length(object@wl > 1) & (ncol(object@nir) != length(object@wl))))
      stop("number of columns in the spectra matrix and number of observed wavelengths don't match")
    if (length(unique(object@id[,1])) != nrow(object@id))
      stop("The ids of the samples need to be unique")
    return(TRUE)
  }
)

#' Class for spectra collections with associated attributes
#'
#' @slot wl object of class "\code{numeric}"; the wavelengths at which the spectra has been measured
#' @slot nir object of class "\code{matrix}"; the spectra, with as many columns as wavelengths, and as many rows as samples
#' @slot id object of class "\code{data.frame}" with one attribute; the identification strings for each sample in the collection
#' @slot units object of class "\code{character}"; units in which the wavelengths are expressed
#' @slot data object of class data.frame containing the attribute data
#' @seealso \code{\link{spectra}}, \code{\link{wl}}, \code{\link{Spectra-class}}
#' @author Pierre Roudier \email{pierre.roudier@@gmail.com}
#' @rdname SpectraDataFrame-class
#' @exportClass SpectraDataFrame
setClass(
  Class='SpectraDataFrame',
  representation=representation(
    "Spectra",
    data='data.frame'
  ),
  prototype=prototype(
    wl = numeric(),
    nir = matrix(),
    id = data.frame(NA),
    units = as.character(NA),
    data = data.frame()
  ),
  validity = function(object) {
    if (ncol(object@data) == 0)
      stop("data.frame is empty: use Spectra() to create spectra-only object")
    if (nrow(object@data) != nrow(object@nir))
      stop("number of rows in data.frame and spectra don't match")
    return(TRUE)
  }
)

#' Class for spectra collections that have
#' associated spatial point locations
#'
setClass(
  Class='SpatialSpectra',
  representation=representation(
    'SpatialPoints',
    'Spectra'
  ),
  prototype=prototype(
    bbox = matrix(NA),
    proj4string = CRS(as.character(NA)),
    coords = matrix(NA),
    wl = numeric(),
    nir = matrix(),
    id = data.frame(NA),
    units = as.character(NA)
  )
)

#' Class for spectra collections that have
#' associated attributes and spatial point locations
#'
#' @slot wl object of class "\code{numeric}"; the wavelengths at which the spectra has been measured
#' @slot nir object of class "\code{matrix}"; the spectra, with as many columns as wavelengths, and as many rows as samples
#' @slot id object of class "\code{data.frame}" with one attribute; the identification strings for each sample in the collection
#' @slot units object of class "\code{character}"; units in which the wavelengths are expressed
#' @slot data object of class data.frame containing the attribute data (may or may not contain the coordinates in its columns)
#' @slot bbox object of class "matrix"; bounding box
#' @slot proj4string object of class "CRS"; projection string
#' @slot coords object of class "matrix"; the coordinates matrix (points are rows in the matrix)
#' @slot coords.nrs object of class logical; if TRUE, when the object was created the coordinates were retrieved from the data.frame, and hence stripped from it; after coercion to data.frame, e.g. by as.data.frame(x), coordinates will again be added (as first few columns) to the data.frame
#' @seealso \code{\link{spectra}}, \code{\link{wl}}, \code{\link{coordinates}}, \code{\link{SpectraDataFrame-class}}
#' @author Pierre Roudier \email{pierre.roudier@@gmail.com}
#' @rdname SpatialSpectraDataFrame-class
#' @exportClass SpatialSpectraDataFrame
#' @import sp
setClass(
  Class = 'SpatialSpectraDataFrame',
  representation = representation(
    'SpatialPoints',
    'SpectraDataFrame'
  ),
  prototype = prototype(
    bbox = matrix(NA),
    proj4string = CRS(as.character(NA)),
    coords = matrix(NA),
    coords.nrs = numeric(0),
    wl = numeric(),
    nir = matrix(),
    id = data.frame(NA),
    units = as.character(NA),
    data = data.frame()
  )
)