calc_aqg_args: Calculate Aquagram - Arguments

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

Calculate Aquagram - Arguments

Description

The following parameters can be used in the ... argument in function getap, also within function gdmm, to override the values in the analysis procedure file and so to modify the calculation of Aquagrams - see examples.

getap(...)

gdmm(dataset, ap=getap(...))

Arguments

do.aqg	Logical. If used in getap, if Aquagrams should be calculated with a given dataset.
aqg.vars	NULL or character vector. Which class variables should be used for grouping the data for the Aquagram. Provide a character vector with the column names of one or more class variables for grouping data and generate an Aquagram for every one of them.
aqg.nrCorr	Character or Logical. If the number of observations in each spectral pattern should be corrected (if necessary by random sampling) so that all the spectral pattern are calculated out from the same number of observations. If left at the default "def", the default value from the settings will be used. Provide "TRUE" or "FALSE" to switch number correction manually on or off.
aqg.spectra	Logical or Character. If left at "FALSE" (the default) no additional spectra are calculated / prepared for plotting. Other possible values are one or more of: "raw" for the raw spectra "avg" for the averaged spectra of the data represented in the aquagram; "subtr" for subtractions in the averaged spectra (see "minus" below) "all" for all of the aforementioned
aqg.minus	Character length one, character vector or NULL. Which of the levels present in each of the class-variables provided in aqg.vars should be used for subtractions – the average of this 'minus' gets subtracted from all the other averages. aqg.minus is used for the subtractions in the raw spectra as well as for the subtractions within the Aquagram, should you choose any of the -diff modes. If a vector with the same length as the vector in aqg.vars is provided, each element of aqg.minus is used to perform the corresponding subtraction for each element in aqg.vars. If a character length one is provided and the input in aqg.vars is longer than one, the single value in aqg.minus gets recycled and is used in each element in aqg.vars for subtractions.
aqg.mod	Character. What mode, what kind of Aquagram should be calculated? Possible values are: 'classic', 'classic-diff', 'sfc', 'sfc-diff', 'aucs', 'aucs-diff', 'aucs.tn', 'aucs.tn-diff', 'aucs.tn.dce', 'aucs.tn.dce-diff', 'aucs.dce', 'aucs.dce-diff', and 'def' for reading in the default from settings.r. Please see calc_aqg_modes for an explanation of the different modes.
aqg.TCalib	Character, numeric or NULL. The default (leave at 'def') can be set in the settings. If 'NULL' the complete temperature range of the calibration data is used for calibration. Provide a numeric length two [c(x1, x2)] for manually determining the calibration range. Provide a character 'symm@x', with 'x' being the plus and minus delta in temperature from the temperature of the experiment for having a calibration range from Texp-x to Texp+x. The 'Factory' default is 'symm@2'. Applies to all modes except the 'classic' and 'sfc' modes. If, in any of the modes showing percentages, the numbers on the Aquagram are below 0 or above 100, then the calibration range has to be extended. To record your own temperature calibration spectra, please see genTempCalibExp.
aqg.Texp	Numeric length one. The temperature at which the spectra were taken. The default (leave at 'def') can be set in the settings. Please see also genTempCalibExp.
aqg.bootCI	Logical. If confidence intervalls for the selected wavelengths should be calculated within each group (using bootstrap). Leave at 'def' for getting the default from the settings.
aqg.R	Character or numeric. Given aqg.bootCI = TRUE, how many bootstrap replicates should be performed? Leave at 'def' for choossing the default from the settings, where the factory-default is "nrow@3" for for 3 x nrow(samples). By manually providing a character in the form of 'nrow@x' where x is any number, you can set the factor with which the number of rows get multiplicated, the result of this multiplication is then used for the number of bootstrap replicates. By providing a length one numeric you can directly set the number of bootstrap replicates.
aqg.smoothN	Only used in the 'classic' and 'sfc' modes. Numeric length 1. Must be odd. Smoothing points for the Sav. Golay smoothing that is applied before making the calculations. Change to NULL or anything not-numeric to switch off smoothing.
aqg.selWls	Only used in the 'classic' and 'sfc' modes. Numerical vector. If provided and in the mode "classic", classic-diff", "sfc" and "sfc-diff" these numbers will be used to determine the coordinates of the aquagram. Leave at 'def' to use the defaults from the settings file.
aqg.msc	Only used in the 'classic' and 'sfc' modes. Logical. If MSC should be performed.
aqg.reference	Only used in the 'classic' and 'sfc' modes. An optional numerical vector (loadings, etc..) used for MSC.

Details

For a list of all parameters that can be used in the ... argument in getap and in the plot functions please see anproc_file.

Important

As the AUC-mods of the Aquagram compare the actual data to your previously recoreded temperature calibration data (see genTempCalibExp and tempCalib_procedures), the application of some data-treatment functions (see e.g. do_gapDer) can lead to unexpected and distorted results in the Aquagram.

References

XXX hopefully a nice reference to the Aquagram paper!! XXX

See Also

gdmm

Other Calc. arguments: calc_NNET_args, calc_SVM_args, calc_discrimAnalysis_args, calc_pca_args, calc_pls_args, calc_randomForest_args, calc_sim_args, split_dataset

Other Aquagram documentation: plot_aqg(), plot_aqg_args, tempCalib_procedures

Examples

## Not run: 
 dataset <- gfd()
 cube <- gdmm(dataset, ap=getap())
 cube <- gdmm(dataset, ap=getap())

## End(Not run)

bpollner/aquap2 documentation built on June 29, 2024, 5:21 p.m.