tempCalib_procedures: Record and use temperature calibration data

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

Record and use temperature calibration data

Description

Record a special temperature dataset and use these data as a kind of calibration data for all of the aquagram calculations except the 'classic' and 'sfc' modes. In other words, you need the temperature dataset in order to be able to calculate Aquagrams of the 'auc' modes. It is strongly recommended that you do generate the temperature data and so can also use the advanced features of these AUC (area under curve) stabilized Aquagrams.

Details

For generating a new experiment with all the necessary defaults to record the temperature data, please use genTempCalibExp (see examples there). After having recorded the spectra in their resp. temperature, import the raw data (gfd) and move the resulting R-data file into your AQUAP2SH folder. Now in the metadata of any experiment (parameter tempCalibFileName) or in the corresponding parameter in the settings file (aqg_tempCalib_Filename) provide the name of the R-data object that you moved into the AQUAP2SH folder. Whenever now an Aquagram is calculated, first and only once per R-session this temperate data file is read in and used to calculate the necessary data enabling the calculation of 'auc' Aquagrams. These temperature-datafile specific objects are stored in aquap2_globalData on the search path (ls(aquap2_globalData, all.names=T)), starting with the name of the temperature data file followed by an '_' underscore.

Procedure

The procedure to work with a temperature-data file (or more of them of course) and use it to calculate area-under-curve 'auc' stabilized Aquagrams is as follows:

Record temperature spectra

Use the function genTempCalibExp to generate a folder structure for an experiment, export the sample list non randomized, then record the temperature-spectra. Finally, use gfd to import the raw-data and create the R-data file (in the folder 'R-data' in the working directory of the experiment).

Move R-data file

Move the resulting R-data file containing the temperature-data from the R-data folder into your AQUAP2SH folder, i.e. the folder also containing e.g. the settings.r file.

Specify temperature-data file

In your actual experiment, specify the name of the file (residing in the folder AQUAP2SH) containing the temperature-spectra either in the metadata or at the argument tempFile in the function gdmm - see examples.

Choose to calculate an Aquagram

In your actual experiment, choose to actually calculate an Aquagram and specify all the necessary parameters in the analysis procedure. You can override the values for the Aquagram-calculations via the ... argument in the function getap in gdmm - please see examples and calc_aqg_args.

See Also

genTempCalibExp

Other Temperature procedures: genTempCalibExp()

Other Aquagram documentation: calc_aqg_args, plot_aqg(), plot_aqg_args

Examples

## Not run: 
fd <- gfd()
cube <- gdmm(fd)
cube <- gdmm(fd, tempFile="def") # to use the default from the settings file, 
# same as above
cube <- gdmm(fd, tempFile="FooBar") # use the temperature-data file 'FooBar'
# residing in the AQUAP2SH folder
cube <- gdmm(fd, getap(do.aqg=TRUE))
cube <- gdmm(fd, getap(do.aqg=TRUE, aqg.bootCI=TRUE))
cube <- gdmm(fd, getap(aqg.mod="aucs.dce"))
cube <- gdmm(fd, getap(aqg.mod="aucs.dce-diff", aqg.minus="C_Cont"), tempFile="FooBar2") 

## End(Not run)

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