Generate_DataFile_MG {BayLum}R Documentation

Generates, from one (or several) BIN file(s) of Multi-grain OSL measurements, a list of luminescence data and information before statistical analysis

Description

This function is used to generate, from the BIN file(s), a list of values of:

Usage

Generate_DataFile_MG(
  Path,
  FolderNames,
  Nb_sample,
  Nb_binfile = length(FolderNames),
  BinPerSample = rep(1, Nb_sample),
  sepD = c(","),
  sepDE = c(","),
  sepDS = c(","),
  sepR = c("="),
  verbose = TRUE,
  ...
)

Arguments

Path

character (required): the path to the project folder, containing one or more subfolders in which the BIN files are located. If it is not equal to "", it must be terminated by "/".

FolderNames

character (required) vector: list of names of the sub-folders containing the BIN files

  • each subfolder must contain a BIN file and associated csv files. See details for more informations on associated csv files required in the subfolders. If there is more than one BIN file per sample, see the details section for instructions regarding how to correctly fill the FolderNames vector.

Nb_sample

integer (required): number of samples.

Nb_binfile

integer (with default): number of BIN files. It must be equal to, or greater than Nb_sample.

BinPerSample

integer vector (with default): vector with the number of BIN files per sample. The length of this vector must be equal to Nb_sample and the sum of entries of this vector must be equal to Nb_binfile. If there is more than one BIN file per sample, see the details section for instructions regarding how to correctly fill BinPerSample vector. Otherwise, this vector must contain a list of 1 values.

sepD

character (with default): column separator in the DiscPose.csv files.

sepDE

character (with default): column separator in the DoseEnv.csv files.

sepDS

character (with default): column separator in the DoseLab.csv files.

sepR

character (with default): column separator in the Rule.csv files.

verbose

logical (with default): enable/disable verbose mode

...

further arguments that can be passed to Luminescence::read_BIN2R.

Details

Multi-grain OSL intensities and associated uncertainties, regenerative doses, etc., which will be the input of the Bayesian models. To be easy-to-use, this function requires a rigorous organisation - all needed files should be arranged in one folder - of informations concerning each BIN file.
It is possible to process data for various samples simultaneously and to consider more than one BIN-file per sample.

With Path and FolderNames, this function goes to the subfolders containing the BIN files and associated information to compute the luminescence data.

** What are the required files in each subfolder? **

Each subfolder can be named, for example, as the sample name followed by a number; it must contain:

** How to fill the FolderNames vector? **

FolderNames is a vector of length Nb_binfile. FolderNames[i] is the name (e.g., Sample1-File1, or successive names separated by "/" signs, if BIN files are in subfolders, e.g. Sample1/File1) of the subfolder containing all informations on the BIN file of ID number i. The names in FolderNames are ordered following two rules:

** How to fill the BinPerSample vector? **

BinPerSample[i] correponds to the number of BIN files for the sample whose number ID is equal to i.
For example, let us consider a case with two samples (Sample1 and Sample2), with 2 BIN files for Sample1 and 1 for Sample2. In this case, Nb_binfile=3 and Nb_sample=2. The user may then set FolderNames=c("Sample1-File1", "Sample1-File2", "Sample2-File1"), in which case "Sample1-1" is the name of the subfolder containing the first BIN file for Sample1, "Sample1-File2" the name of the subfolder for the second BIN file of Sample1; eventually, "Sample2-1" is the name of the subfolder containing the BIN file for the second sample. In this case, BinPerSample=c(2,1).

For the general BIN-file structure, the reader is referred to the following website: http://www.nutech.dtu.dk/

The function read_BIN2R developped in Luminescence package is used to read the BIN files.

Value

A list containing the following objects:

** How to save this list **

You can save this list in a .RData object. To do this, you can use the fonction save. Then, to load this list you can use the function load (see example section fore more details).

How to cite

Christophe, C., Kreutzer, S., Philippe, A., 2020. Generate_DataFile_MG(): Generates, from one (or several) BIN file(s) of Multi-grain OSL measurements, a list of luminescence data and information before statistical analysis. In: Christophe, C., Philippe, A., Kreutzer, S., Guerin, G., 2020. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.2.0. https://CRAN.r-project.org/package=BayLum

Note

The function imports only BIN/BINX-file records which have been previously selected.

Author(s)

Claire Christophe, Sebastian Kreutzer, Anne Philippe, Guillaume Guérin

See Also

read_BIN2R, combine_DataFiles, LT_RegenDose Age_Computation, AgeS_Computation, Palaeodose_Computation

Examples

path <- system.file("extdata/FER1", "", package="BayLum")
folder <- ""
# give the number of sample
nbsample <- 1
DATA <- Generate_DataFile_MG(
 Path = path,
 FolderNames = folder,
 Nb_sample = nbsample)
str(DATA)

# to save information in RData object in folder containing bin file
#save(DATA,file=c(paste(path,folder,'DATA.RData',sep="")))
# to load information containing DATA.RData object
#load(file=c(paste(path,folder,"DATA.RData",sep="")))


[Package BayLum version 0.2.0 Index]