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Read and Process Spectral Data of Time Dependent CW EPR Experiments

Source: R/readEPR_Exp_Specs_kin.R
readEPR_Exp_Specs_kin.Rd

Reading the continuous wave (CW) EPR time series spectral data (recorded by e.g. 2D_Field_Delay experiment in "Xenon" acquisition/processing software). Function (based on readEPR_Exp_Specs) includes automatic time correction for CW EPR time.series experiments (see also correct_time_Exp_Specs).

Usage

readEPR_Exp_Specs_kin(
  name.root,
  dir_ASC,
  dir_dsc_par,
  time.unit = "s",
  time.delta.slice.s = NULL,
  col.names = c("index", "B_G", "time_s", "dIepr_over_dB"),
  x.id = 2,
  x.unit = "G",
  Intensity.id = 4,
  time.series.id = 3,
  convertB.unit = TRUE,
  qValue = NULL,
  norm.vec.add = NULL,
  origin = "xenon",
  ...
)

Arguments

name.root

Character string, corresponding to entire file name without extension.

dir_ASC

Character string, path (can be also defined by the file.path) to directory where the ASCII spectral data is stored.

dir_dsc_par

Character string, path (can be also defined by the file.path) to directory where the .DSC/.dsc or .par parameter file is stored (in order to calculate \(g\)-value and/or normalize intensities).

time.unit

Character string, specifying the "s","min", "h" or time.unit = "unitless" (if time.delta.slice.s is different from NULL). Default: time.unit = "s"

time.delta.slice.s

Numeric, time interval in seconds between slices, in the case if origin = "winepr". Default: time.delta.slice = NULL (actually, corresponding to 1 s).

col.names

Character/String vector inherited from fread, corresponding to column/variable names. A safe rule of thumb is to use column names incl. physical quantity notation with its units, Quantity_Unit like "B_G", "RF_MHz", "Bsim_mT" (e.g. pointing to simulated EPR spectrum \(x\)-axis)...etc, default: col.names = c("index","B_G","dIepr_over_dB").

x.id

Numeric index related to col.names vector pointing to independent variable, which corresponds to \(x\)-axis in the spectra or other plots. Default: x.id = 2 (for Xenon).

x.unit

Character string, corresponding to original x variable/column unit, such as "G", "mT" or "MHz".

Intensity.id

Numeric index related to col.names vector, pointing to general intensity, like derivative intensity (dIepr_over_dB), integral one (e.g. single_Integ), double or sigmoid integral (e.g. Area)...etc. This corresponds to column/vector which should be presented like \(y\)-axis in the EPR spectra or other plots. Default: Intensity.id = 3 (for Xenon).

time.series.id

Numeric index related to col.names pointing to time column for time series EPR spectra changing upon time. If data contains simple relationship like \(Area\) vs \(time\) use x and x.unit parameters/arguments instead. This parameter/argument is dedicated to kinetic-like experiments. Default: time.series.id = 3.

convertB.unit

Logical (default: convertB.unit = TRUE), whether upon reading, an automatic conversion between G and mT should be performed. If default is chosen, a new column/variable \(B\) in mT/G is created.

qValue

Numeric, Q value (quality factor, number) displayed at specific dB by spectrometer. In case of "Xenon" software the parameter is included in .DSC file, therefore default: qValue = NULL (actually corresponding to value 1). If EPR spectra were acquired by the "Winepr" software, the Q value must be defined like qValue = 3400.

norm.vec.add

Numeric vector, additional normalization constant in the form of vector, involving all (in addition to qValue) normalization(s) such as concentration, powder sample weight, number of scans, ...etc (e.g. norm.vec.add = c(2000,0.5,2)). Default: norm.vec.add = NULL (actually corresponding to value 1).

origin

Character string, corresponding to origin of the ASCII data, like from the most common spectrometers (from which the data are loaded automatically using the default parameters). Options are summarized in the following table (any other specific origin may be added later) =>

StringDescription
"xenon"default automatically loads data from the "Xenon" software with the default parameters.
"winepr"automatically loads data from the "WinEpr" software.
"magnettech"automatically loads data from the new "Magnettech" software (ESR5000 [11-0422]).
"other" (arbitrary string, e.g. "csv")general, loads any other original data like csv, txt, asc incl. also data from other instrumental/spectrometer software. In such case, all the arguments for readEPR_Exp_Specs have to be set up accordingly.
...

additional arguments specified, see also the readEPR_Exp_Specs and fread.

Value

List of EPR spectrum data (including time) in tidy long table format (df) + corrected time vector (time). For the origon = "winepr" "time" slices/indices must be already converted into time domain by time.delta.slice.s (see arguments and examples).

See also

Other Data Reading: readEPR_Exp_Specs(), readEPR_Exp_Specs_multif(), readEPR_Sim_Spec(), readEPR_param_slct(), readEPR_params_slct_kin(), readEPR_params_slct_quant(), readEPR_params_slct_sim(), readEPR_params_tabs(), readEPR_solvent_props(), readMAT_params_file()

Examples

## loading the built-in package example to demonstrate
## the reading of time series EPR spectra/kinetics:
triarylam.decay.series.dsc.path <-
  load_data_example(file = "Triarylamine_radCat_decay_series.DSC")
triarylam.decay.series.asc.path <-
  load_data_example(file = "Triarylamine_radCat_decay_series.zip")
unzip(triarylam.decay.series.asc.path,exdir = tempdir())
#
## loading the kinetics:
triarylam.decay.series.data <-
  readEPR_Exp_Specs_kin(name.root = "Triarylamine_radCat_decay_series",
                        dir_ASC = tempdir(),
                        dir_dsc_par =
                          system.file("extdata",
                                      package = "eprscope")
                       )
#
## data preview
head(triarylam.decay.series.data$df)
#>    index       B_G time_s  dIepr_over_dB      B_mT
#>    <int>     <num>  <num>          <num>     <num>
#> 1:     1 3390.0000      6  1.3629316e-05 339.00000
#> 2:     2 3390.0833      6 -1.0134169e-06 339.00833
#> 3:     3 3390.1667      6 -1.9794802e-05 339.01667
#> 4:     4 3390.2500      6 -2.9826537e-05 339.02500
#> 5:     5 3390.3333      6 -1.6870754e-05 339.03333
#> 6:     6 3390.4167      6  2.5629187e-06 339.04167
#
## preview of corrected time vector
## (the uncorrected one actually starts from `0`)
triarylam.decay.series.data$time
#>   [1]    6   21   36   51   66   81   95  110  125  140  155  170  184  199  214
#>  [16]  229  244  259  274  288  303  318  333  348  363  378  392  407  422  437
#>  [31]  452  467  482  496  511  526  541  556  571  586  600  615  630  645  660
#>  [46]  675  690  705  719  734  749  764  779  794  809  824  838  853  868  883
#>  [61]  898  913  927  942  957  972  987 1002 1016 1031 1046 1061 1076 1091 1106
#>  [76] 1120 1135 1150 1165 1180 1195 1210 1225 1239 1254 1269 1284 1299 1314 1329
#>  [91] 1344 1358 1373 1388 1403 1418 1433 1448 1463 1477
#
if (FALSE) { # \dontrun{
## reading by the "WinEPR" software
readEPR_Exp_Specs_kin("Sample_spectra_irradiation",
                      file.path(".","ASCII_data_dir"),
                      file.path(".","dsc_data_dir"),
                      time.unit = "s",
                      time.delta.slice.s = 24.1,
                      col.names = c("B_G",
                                    "Slice",
                                    "Intensity"),
                      x.unit = "G",
                      qValue = 2900,
                      origin = "winepr")

} # }