hyperSpec: initialize – R documentation

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initialize

Creating a hyperSpec Object

Description

Like other S4 objects, a hyperSpec object can be created by new. The hyperSpec object is then initialized using the given parameters.

Usage

## S4 method for signature 'hyperSpec'
initialize(.Object, spc = NULL, data = NULL, wavelength = NULL, labels = NULL)

Arguments

`.Object`	the new `hyperSpec` object.
`spc`	the spectra matrix. `spc` does not need to be a matrix, it is converted explicitly by `I (as.matrix (spc))`.
`data`	`data.frame`, possibly with the spectra in `data$spc`, and further variates in more columns. A matrix can be entered as one column of a data frame by: `data.frame (spc = I (as.matrix (spc)))`. However, it will usually be more convenient if the spectra are given in `spc`
`wavelength`	The wavelengths corresponding to the columns of `data`. If no wavelengths are given, an appropriate vector is derived from the column names of `data$spc`. If this is not possible, `1 : ncol (data$spc)` is used instead.
`labels`	A `list` containing the labels for the columns of the `data` slot of the `hyperSpec` object and for the wavelength (in `label$.wavelength`). The labels should be given in a form ready for the text-drawing functions (see `plotmath`). If `label` is not given, a list containing `NULL` for each of the columns of`data` and `wavelength` is used.

Details

If option gc is TRUE, the initialization will have frequent calls to gc () which can help to avoid swapping or running out of memory.

Author(s)

C.Beleites

Examples

new ("hyperSpec")

spc <- matrix (rnorm (12), ncol = 4)
new ("hyperSpec", spc = spc)
new ("hyperSpec", data = data.frame (x = letters[1:3]),
     spc = spc)

colnames (spc) <- 600:603
new ("hyperSpec", spc = spc)  # wavelength taken from colnames (spc)

# given wavelengths precede over colnames of spc
new ("hyperSpec", spc = spc, wavelength = 700:703)

# specifying labels
h <- new ("hyperSpec", spc = spc, data = data.frame (pos = 1 : 3),
          label = list (spc = "I / a.u.",
                        .wavelength = expression (tilde (nu) / cm^-1),
                        pos = expression ("/" (x, mu*m)))
)

plot (h)
plotc (h, spc ~ pos)

hyperSpec

Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)

v0.100.0

GPL (>= 3)

Authors

Claudia Beleites [aut, cre, dtc] (<https://orcid.org/0000-0003-1626-154X>), Valter Sergo [aut], Alois Bonifacio [ctb, dtc], Marcel Dahms [ctb], Björn Egert [ctb], Simon Fuller [ctb], Vilmantas Gegzna [ctb], Rustam Guliev [ctb], Bryan A. Hanson [ctb], Michael Hermes [ctb], Martin Kammer [dtc], Roman Kiselev [ctb], Sebastian Mellor [ctb]

Initial release

2021-09-13