hyperSpec (version 0.98-20140523)

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

Description

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

Usage

## S3 method for class 'hyperSpec':
initialize(.Object, spc = NULL,
    data = NULL, wavelength = NULL, labels = NULL,
    log = NULL, short = "initialize", user = NULL,
    date = NULL)

Arguments

.Object

the new hyperSpec object.

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

spc

the spectra matrix.

spc does not need to be a matrix, it is converted explicitly by I (as.matrix (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 inst

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-drawin

log

A list used to fill into the first entry of .Object@log. The elements log$short, log$long, log$date, and log$user are handed down to

short,user,date

passed to logentry

See Also

new for more information on creating and initializing S4 objects.

plotmath on expressions for math annotations as for slot label.

hy.setOptions

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)

# giving a log entry
new ("hyperSpec", log = list (short = "measurement parameters",
     long = list ("exposure / s" = 10, sample = "327a")))