do_detrend: Perform De-Trend

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

Perform De-Trend

Description

Perform de-trending of the given dataset. For each observation, the linear model lm(absorbance ~ wavelength) is calculated. The coefficients of the resulting model are then used to modify the absorbance values after the formula newAbsorbance = absorbance - intercept - k*wavelength. It is possible to separately specify the source and the target of the de-trend operation.

Usage

do_detrend(dataset, src = NULL, trg = "src", exportModel = FALSE)

Arguments

dataset	An object of class 'aquap_data' as produced e.g. by gfd.
src	'source'; the wavelength-range from where the values for de-trend should be calculated (i.e. the linear models). Leave at the default NULL to use the full range of wavelengths in the provided dataset, or provide a numeric length two to use this wavelength range for calculating the values for de-trend.
trg	'target'; character length one or numeric length two. The wavelengths where the de-trend should be applied. If left at the default 'src' the same wavelength as specified in src is used. Possible values are: src Apply the de-trend to the same wavelength-range as specified in argument src (the default). all Apply the de-trend to all the wavelengths in the provided dataset. Numeric length two Provide a numeric length two to the argument trg to apply the de-trend only to this wavelength range.
exportModel	Logical. If a possible model should be stored in the set, (leave at FALSE).

Details

Via the arguments src ('source') and trg ('target') it is possible to specify separately from which wavelength-range the values for the de-trend should be taken resp. to which wavelength-range the resulting de-trend should be applied. Please see documentation for the arguments src and trg for further details. If the target wavelengths are only a part of the whole wavelength-range in the dataset, the de-trend will be applied only to this wavelengths, and the rest of the wavelengths will remain unchanged. Abrupt steps in the resulting spectra can be the result of this. If both arguments src and trg are left at their defaults, the full range of wavelengths in the dataset is used for calculating the de-trend values, i.e. the linear models, and the resulting de-trend is also applied to the full range of wavelengths present in the dataset.

Value

The transformed dataset

See Also

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

Other dpt modules documentation: do_emsc(), do_gapDer(), do_msc(), do_sgolay(), do_snv(), dpt_modules

Examples

## Not run: 
fd <- gfd()
fdDT <- do_detrend(fd) # use the whole wavelength range of 'fd' as source and
# target for the de-trend
plot(fd)
plot(fdDT)
###
fdc <- selectWls(fd, 1300, 1600)
plot(fdc)
plot(do_detrend(fdc)) # whole range as source and target
plot(do_detrend(fdc, src=c(1400, 1500))) # same target as soruce
plot(do_detrend(fdc, src=c(1400, 1500), trg="all")) # apply to full range
plot(do_detrend(fdc, src=c(1400, 1500), trg=c(1300, 1600))) # same as above 
plot(do_detrend(fdc, src=c(1300, 1400), trg=c(1380, 1580))) 

## End(Not run)

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