aquap_data-methods: aquap_data methods

In bpollner/aquap2: Multivariate Data Analysis Tools for R including Aquaphotomics Methods

aquap_data methods

Description

Available methods for objects of class 'aquap_data', used for subtractions, subscripting etc. of datasets.

Usage

## S4 method for signature 'aquap_data'
x[i]

## S4 replacement method for signature 'aquap_mergeLabels'
x[i, j] <- value

## S4 replacement method for signature 'aquap_mergeLabels'
x$name <- value

## S4 method for signature 'aquap_data,aquap_data'
e1 - e2

## S4 method for signature 'aquap_data,aquap_data'
e1 / e2

Arguments

x	An object of class 'aquap_data'
i	Subsricpting indices for rows
j	Subsricpting indices for columns
value	An R object
name	A valid column name
e1	Object of class 'aquap_data'
e2	Object of class 'aquap_data'

Details

Subscripting via '[]'

For subscripting via '[]', only values for rownumbers are accepted.

Subtractions via '-'

Use the subtraction via '-' to subtract the NIR-data in datasets that have the same structure, i.e. the same header, and possibly same wavelengths in the NIR. You can either subtract two equally long datasets, i.e. two datasets having the exactly same number of rows, or you can subtract a dataset having exactly one row from a full dataset. The latter can be useful for e.g. subtracting the averaged spectra of a single class from the complete dataset - see examples. If parameter gen_calc_allowSubtrDiffWavels in the settings.r file is set to TRUE, it is also possible to subtract two datasets that do not have the same number of wavelengths. This can e.g. happen ater the usage of do_gapDer. In this case, the bigger dataset, i.e. the dataset having more wavelengths, is cut down to match exactly the wavelength-range of the smaller dataset. In other words, the return in this case is a dataset having only the number of wavelengths as 'dictated' by the smaller dataset.

Division via '/'

Use the division via '/' to divide a first, complete dataset by a dataset containing only a single wavelength in the NIR data. Please see siWl for generating such a dataset.

Subscripting of objects of class 'aquap_mergeLabels' via '[,j]'

Can be used to modify the values to be filled in the new variables when merging datasets. Only values for columns are accepted.

Subscripting of objects of class 'aquap_mergeLabels' via 'object$name'

Can be used do modify the values to be filled in the new variables when merging datasets.

Note

drop is always set to FALSE for subsrictping via '[]'.

See Also

Other Data pre-treatment functions: do_addNoise(), do_avg(), do_blowup(), do_detrend(), do_emsc(), do_gapDer(), do_msc(), do_resampleNIR(), do_sgolay(), dpt_modules, selectWls(), ssc()

Other dataset modification functions: calculateVariable(), combineVariable(), generateMergeLabels,aquap_data,aquap_data,character,character-method, mergeDatasets,aquap_data,aquap_data,missing-method

Examples

## Not run: 
 dataset <- gfd()
 ds <- dataset[1:5,]
 ds <- dataset[1:5] # the same as above
	dSub <- dataset - do_sgolay(dataset, n=71) # apply smoothing and subtract
 plot(dSub, pg.where="", pg.main=" | smoothed subtracted")
 plot(do_gapDer(ds,1,11,13,1) - do_gapDer(ds, 1, 13, 13, 1))
 ###
 plot(dataset)
 plot(dataset / siWl(dataset, 1450))

## End(Not run)

bpollner/aquap2 documentation built on March 29, 2024, 7:33 a.m.