(DEPRECATED) LOESS smoothing interpolation for spectra

Source: R/DEPRECATED-spc_loess.R

These hyperSpec functions are deprecated and not maintained any more. You should not use these. Currently they are present due to back-compatibility reasons and will be removed in the next release of the package. Please, use the suggested alternative functions instead.

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Spectra smoothing and interpolation on a new wavelength axis using stats::loess().

spc.loess(spc, newx, enp.target = nwl(spc)/4, surface = "direct", ...)

Arguments

spc

The hyperSpec object.
newx

Wavelength axis to interpolate on.
enp.target, surface, ...

Further parameters for stats::loess() and stats::loess.control().

Value

A new hyperSpec object.

Details

Applying stats::loess() to each of the spectra, an interpolation onto a new wavelength axis is performed. At the same time, the spectra are smoothed in order to increase the signal to noise ratio. See stats::loess() and stats::loess.control() on the parameters that control the amount of smoothing.

See also

stats::loess(), stats::loess.control()

Author

C. Beleites

Examples

data(flu, package = "hyperSpec")
nwl(flu)

#> [1] 181

smoothed_flu <- spc.loess(flu, seq(420, 470, 5))

#> Warning: Function 'spc.loess' is deprecated. 
#> Use function 'spc_loess' instead.
#> Warning: Function '.fix_spc_colnames' is deprecated. 
nwl(smoothed_flu)

#> [1] 11

plot(flu, col = "darkgray")

plot(smoothed_flu, add = TRUE, col = "red")



flu_na <- flu
flu_na[[3, ]] <- NA_real_
flu_na_smoothed <- spc.loess(flu_na, seq(420, 470, 5))

#> Warning: Function 'spc.loess' is deprecated. 
#> Use function 'spc_loess' instead.
#> Warning: NAs were generated. Probably `newx` was outside the spectral range covered by `spc`.
#> Warning: Function '.fix_spc_colnames' is deprecated. 
flu_na_smoothed[[]]

#>            420       425       430      435      440      445      450      455
#> [1,]  69.37812  80.30948  91.84728 100.2360 104.5292 104.9064 105.7577 104.8149
#> [2,] 139.77571 164.01308 186.70646 202.3563 210.6401 213.3784 213.4778 211.8374
#> [3,]        NA        NA        NA       NA       NA       NA       NA       NA
#> [4,] 294.90432 342.15512 392.92353 425.2415 440.4607 445.2538 447.5044 440.8911
#> [5,] 362.00455 427.75670 487.47455 529.7585 550.0944 556.9861 554.9146 548.4495
#> [6,] 442.89661 519.84822 593.45501 644.1054 669.0614 674.8410 672.3328 666.8127
#>            460      465       470
#> [1,]  99.62751  92.9669  84.80506
#> [2,] 201.97621 187.6462 169.38644
#> [3,]        NA       NA        NA
#> [4,] 421.76483 391.7258 354.35753
#> [5,] 524.96452 487.5104 441.95012
#> [6,] 639.70144 594.3875 539.25115

plot(flu, col = "darkgray")

plot(flu_na_smoothed, add = TRUE, col = "blue")