spectra-methods: Retrieves or sets the spectra of a 'Spectra*' objects.

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

Description

Either retrieves the spectra matrix from a Spectra* object, or creates a Spectra* object from a "data.frame" object different interfaces detailed below.

Usage

spectra(object, ...)
spectra(object) <- value

Arguments

object	a "data.frame" or an object inheriting from class Spectra
value	the wavelengths of the Spectra* object to create
...	Ignored

Details

When applied to a Spectra* object, this functions simply returns the spectra it is storing.

If applied on a "data.frame" object, it is an helper function to create a Spectra* object. Two kind of interfaces are then available. value can be:

a vector:

Similarly to wl, the wavelengths of the spectra can be passed by a "numeric" vector. Alternatively, the names of the columns that contain the spectra information can be passed as a "character" vector.

a formula:

This interface is specific to specstore. It follows a scheme where differents parts can be observed, the id column, the attributes columns, and the spectra columns, described by the wavelengths at which it has been measured:

• Placeholders:

  • ...:placeholder for all the columns of your data.frame object except those that have been already used in other parts of the formula. This can lead to errors. E.g. if object has data one every wavelength between 350 and 2500 nm, spectra(object) <- id_field ~ ... ~ 500:2500 will stores the columns corresponding to the wavelengths 350-499 nm in its data slot!

  • id:For the creation of a SpectraDataFrame, it is important to always specify an id field in the formula. If no id column is present, the id placeholder will create one for you.

• spectra(object) <- ~ 350:2500 will build a Spectra object from the wavelengths between 350 and 2500, based on the column names.

• spectra(object) <- ~ 350:2:2500 will build a Spectra object from the wavelengths in seq(350, 2500, by = 2).

• spectra(object) <- ~ 500:2350 will build a Spectra object from the wavelengths between 500 and 2350, even though other wavelengths are present (they will be dropped).

  In the three later cases, the id field has been dropped (it will be automatically created). If you want to use a column of "data.frame" as an id filed, you can still use the first part of the formula:

• spectra(object) <- id_field ~ 350:2500

• spectra(object) <- id_field ~ 350:5:2500

  Some data can also be added to the object, which will then be of SpectraDataFrame class:

• spectra(object) <- id_field ~ property1 ~ 500:2300 will create a SpectraDataFrame with ids from the id_field column, data from the property1 column, and spectral information between 500 and 2300 nm. That means that data property2, and all spectral information from bands < 500 nm or > 2300 nm will be dropped.

  You can also combine the placeholders:

• spectra(object) <- id_field ~ ... ~ 350:2500 will create a SpectraDataFrame object with ids from the id_field column, all spectral bands between 350 and 2500 nm. The data slot is given all the remaining columns.

Value

If applied on a "data.frame", either a Spectra or a SpectraDataFrame object. If applied on a Spectra* object, a vector.

Author(s)

Pierre Roudier [e-mail]

See Also

wl, Spectra-class, SpectraDataFrame-class

pierreroudier/specstore documentation built on May 25, 2019, 6:09 a.m.