Spectra-classes: Spectra* classes

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

Description

The inspectr package provides the user with S4 classes that have been developped to store and manipulate spectroscopy data.

The Spectra class is storing the spectra matrix, along with the wavelengths at which those have been measured, the units in whioch those wavelengths are expressed, and a unique id for each sample in the collection.

The SpectraDataFrame class is extending the Spectra class by giving the opportunity to store attribute data along with the spectra - this is mostly the case when we want to predict physical or chemical properties from the spectra set.

The SpatialSpectra and SpatialSpectraDataFrame classes are extending the Spectra and SpectraDataFrame classes using the SpatialPoints class from package sp. This allows to store spatial information on the dataset: coordinates, coordinate reference system, bounding box, etc.

Common generic methods implemented for these classes include:

summary, show, nrow, length, plot, [, [[, $.

SpatialPoints methods from the sp package can be applied to SpatialSpectra and SpatialSpectraDataFrame objects are they inherit from this class.

Objects from the Class

Objects can be created by calls of the form new("Spectra", ...), with the constructor functions like Spectra(...), or with the helper functions such as wl and spectra.

Slots

• Slots for the Spectra class

  wl:

  object of class "numeric"; the wavelengths at which the spectra has been measured

  nir:

  object of class "matrix"; the spectra, with as many columns as wavelengths, and as many rows as samples

  id:

  object of class "data.frame" with one attribute; the identification strings for each sample in the collection

  units:

  object of class "character"; units in which the wavelengths are expressed

• Slots for the SpectraDataFrame class

  wl:

  object of class "numeric"; the wavelengths at which the spectra has been measured

  nir:

  object of class "matrix"; the spectra, with as many columns as wavelengths, and as many rows as samples

  id:

  object of class "data.frame" with one attribute; the identification strings for each sample in the collection

  units:

  object of class "character"; units in which the wavelengths are expressed

  data:

  object of class "data.frame" containing the attribute data

Author(s)

Pierre Roudier [e-mail]

Examples

showClass("Spectra")
showClass("SpectraDataFrame")

inspectr documentation built on May 2, 2019, 5:45 p.m.