genTempCalibExp: Generate temperature recording experiment

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

Generate temperature recording experiment

Description

Generate the folder structure for a new experiment and populate it with the metadata suggested for recording then the temperature calibration-spectra used e.g. in the aquagram (see argument aqg.TCalib and aqg.Texp in calc_aqg_args).

Usage

genTempCalibExp(Tcenter = NULL, Tdelta = 5, stepBy = 1, repls = 4)

Arguments

Tcenter	Numeric length one. The temperature at which usually the measurements are performed. The final temperature will range from Tcenter-Tdelta to Tcenter+Tdelta, in steps given by argument 'stepsBy'.
Tdelta	Numeric length one, defaults to 5. The temperature range below and above 'Tcenter'.
stepBy	Numeric length one, defaults to 1. The temperature step between each single temperature in the range from Tcenter-Tdelta to Tcenter+Tdelta.
repls	Numeric length one. How many replicates of each single temperature to record. Defaults to 4.

Details

This generates the folder structure for a standard experiment and is adapting the metadata to record spectra at various temperatures in each 3 consecutive scans. For a possible workflow please see examples.

Important

When exporting the sample list via esl, make sure to export it non randomized - please see examples.

Warning

Do not change the name of the columns in the sample list before importing the dataset; if the numerical column smpTemp is not present, the temperature calibration data can not be used.

See Also

tempCalib_procedures, genFolderStr, genNoiseRecExp

Other Temperature procedures: tempCalib_procedures

Other Helper Functions: ap2_settings_setup(), ap2dme(), export_ap2_ToXlsx(), export_header_toXls(), genFolderStr(), genNoiseRecExp(), getcd(), getcm(), getstn(), printStdColnames(), reColor(), saveAQdata(), siWlg(), updateSettings()

Examples

## Not run: 
genTempCalibExp(Tcenter=30) # generate the folder structure in the current 
working directory
esl(rnd=FALSE) # export a *non* randomized sample list
#### now record the temperature-spectra #### (move sample list to folder 'sl_in')
gfd <- gfd() # imports temperature raw-data and saves an R-data file in the 
# R-data folder, from where you take it and move it into your 
# AQUAP2SH folder

## End(Not run)

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