gdmm: *** Generate Datasets and make Models ***

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

*** Generate Datasets and make Models ***

Description

Generate several datasets by splitting up the original dataset according to the variables and values as specified in the analysis procedure in the 'split dataset' section and then calculate the models as specified in the 'statistics' section on all of the datasets. By providing additional arguments to the function getap (what is the default way to get the analysis procedure 'ap') you can override any value in the analysis procedure. Please see examples and getap and anproc_file for further information.

Usage

gdmm(dataset, ap = getap(), noiseFile = "def", tempFile = "def")

Arguments

dataset	An object of class 'aquap_data' as generated by gfd
ap	The analysis procedure, an object of class 'aquap_ap'
noiseFile	Character length one. The name of the corresponding noise data file residing in the AQUAP2SH folder. Leave at the default 'def' to read in the value from the settings.r file (parameter noi_noiseDataFilename), or provide the name of an existing R-data file in your specified AQUAP2SH folder to use this as source for the noise data. If a value other than "def" is provided, this is overriding the value of "noiseFileName" in the metadata file. Please see noise_procedures for more information.
tempFile	Character length one. The name of the corresponding temperature calibration data file residing in the AQUAP2SH folder. Leave at the default 'def' to read in the value from the settings.r file (parameter aqg_tempCalib_Filename), or provide the name of an existing R-data file in your specified AQUAP2SH folder to use this as source for the temperature calibration data. If a value other than "def" is provided, this is overriding the value of "tempCalibFileName" in the metadata file. Please see tempCalib_procedures for more information.

Details

Split-combinations that yield no result will automatically be omitted. It is recommended to first make the analysis procedure file as complete and accurate as possible, and then to override only a few parameters if necessary.

Value

An object of class aquap_cube containing all the statistical models / calculations that were performed on the split-variations of the dataset.

See Also

getap, getmd

Other Core functions: exportSampleList(), getFullData(), plot,aquap_cube,missing-method, plot,aquap_data,missing-method

Examples

## Not run: 
dataset <- gfd() # will load or import data
cube <- gdmm(dataset) # split up the dataset and make models, execute the 
# analysis procedure as specified in its .r file
cube <- gdmm(dataset, getap(spl.var="C_Group")) # split the dataset by "C_Group"
cube <- gdmm(dataset, getap(spl.var=c("C_Group", "C_Temp"))) # split the dataset 
# by "C_Group", then by "C_Temp"
cube <- gdmm(dataset, getap(spl.wl="1300-to-1600")) # override 'spl.wl' in the 
# analysis procedure
cube <- gdmm(dataset, getap(aqg.bootCI=FALSE)) # override the value in 
# 'aqg.bootCI' of the analysis procedure with 'FALSE'. 
cube <- gdmm(dataset, getap(do.sim=FALSE, pls.regOn="Y_Temp"))
cube <- gdmm(dataset, getap(spl.do.noise=TRUE), noiseFile="FooBarNoise") # to
# use the noise-data file 'FooBarNoise' instead of the default noise data file

## End(Not run)

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