Model Luminescence Signals

Description

This function models luminescence signals for quartz based on published physical models. It is possible to simulate TL, (CW-) OSL, RF measurements in a arbitrary sequence. This sequence is definded as a list of certain abrivations. Furthermore it is possible to load a sequence direct from the Riso Sequence Editor. The output is an RLum.Analysisobject and so the plots are done by the plot_RLum.Analysis function. If a SAR sequence is simulated the plot output can be disabled and SAR analyse functions can be used.

Usage

model_LuminescenceSignals(model, sequence, lab.dose_rate = 1,
  simulate_sample_history = FALSE, plot = TRUE, verbose = TRUE,
  show.structure = FALSE, ...)

Arguments

Details

Defining a sequence

Note: 100 % illumination power equates 20 mW/cm^2

Defining a SAR-sequence

Value

This function returns an RLum.Analysis object with all TL, (LM-) OSL and RF/RL steps in the sequence. Every entry is an RLum.Data.Curve object and can be plotted, analysed etc. with further RLum-functions.

Function version

0.1.0

Author(s)

Johannes Friedrich, University of Bayreuth (Germany), Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France)

References

Bailey, R.M., 2001. Towards a general kinetic model for optically and thermally stimulated luminescence of quartz. Radiation Measurements 33, 17-45.

Bailey, R.M., 2002. Simulations of variability in the luminescence characteristics of natural quartz and its implications for estimates of absorbed dose. Radiation Protection Dosimetry 100, 33-38.

Bailey, R.M., 2004. Paper I-simulation of dose absorption in quartz over geological timescales and it simplications for the precision and accuracy of optical dating. Radiation Measurements 38, 299-310.

Pagonis, V., Chen, R., Wintle, A.G., 2007: Modelling thermal transfer in optically stimulated luminescence of quartz. Journal of Physics D: Applied Physics 40, 998-1006.

Pagonis, V., Wintle, A.G., Chen, R., Wang, X.L., 2008. A theoretical model for a new dating protocol for quartz based on thermally transferred OSL (TT-OSL). Radiation Measurements 43, 704-708.

Soetaert, K., Cash, J., Mazzia, F., 2012. Solving differential equations in R. Springer Science & Business Media.

See Also

plot, RLum, read_SEQ2R

Examples

##================================================================##
## Example 1: Simulate sample history of Bailey2001
## (cf. Bailey, 2001, Fig. 1)
##================================================================##

##set sequence with the following steps
## (1) Irradiation at 20 deg. C with a dose of 10 Gy and a dose rate of 1 Gy/s
## (2) TL from 20-400 deg. C with a rate of 5 K/s

sequence <-
  list(
    IRR = c(20, 10, 1),
    TL = c(20, 400, 5)
  )

##model sequence
model.output <- model_LuminescenceSignals(
  sequence = sequence,
  model = "Bailey2001"
)

## Not run: 
##============================================================================##
## Example 2: Simulate sequence at labour without sample history
##============================================================================##

##set sequence with the following steps
## (1) Irraditation at 20 deg. C with a dose of 100 Gy and a dose rate of 1 Gy/s
## (2) Preheat to 200 deg. C and hold for 10 s
## (3) LM-OSL at 125 deg. C. for 100 s
## (4) Cutheat at 200 dec. C.
## (5) Irraditation at 20 deg. C with a dose of 10 Gy and a dose rate of 1 Gy/s
## (6) Pause at 200 de. C. for 100 s
## (7) OSL at 125 deg. C for 100 s with 90 % optical power
## (8) Pause at 200 deg. C for 100 s
## (9) TL from 20-400 deg. C with a heat rate of 5 K/s
## (10) Radiofluorescence at 20 deg. C with a dose of 200 Gy and a dose rate of 0.01 Gy/s

sequence <-
 list(
   IRR = c(20, 100, 1),
   PH = c(200, 10),
   LM_OSL = c(125, 100),
   CH = c(200),
   IRR = c(20, 10, 1),
   PAUSE = c(200, 100),
   OSL = c(125, 100, 90),
   PAUSE = c(200, 100),
   TL = c(20, 400, 5),
   RF = c(20, 200, 0.01)
)

# call function "model_LuminescenceSignals", set sequence = sequence,
# model = "Pagonis2008" (palaeodose = 200 Gy) and simulate_sample_history = FALSE (default),
# because the sample history is not part of the sequence

model.output <- model_LuminescenceSignals(
   sequence = sequence,
   model = "Pagonis2008"
   )



##============================================================================##
## Example 3: Simulate SAR sequence
##============================================================================##

##set SAR sequence with the following steps
## (1) RegDose: set regenerative dose [Gy] as vector
## (2) TestDose: set test dose [Gy]
## (3) PH: set preheat temperature in deg. C
## (4) CH: Set cutheat temperature in deg. C
## (5) OSL_temp: set OSL reading temperature in deg. C
## (6) OSL_duration: set OSL reading duration in s

sequence <- list(
 RegDose = c(0,10,20,50,90,0,10),
 TestDose = 5,
 PH = 240,
 CH = 200,
 OSL_temp = 125,
 OSL_duration = 70)

# call function "model_LuminescenceSignals", set sequence = sequence,
# model = "Pagonis2007" (palaeodose = 20 Gy) and simulate_sample_history = FALSE (default),
# because the sample history is not part of the sequence

 model.output <- model_LuminescenceSignals(

 sequence = sequence,
 model = "Pagonis2007",
 plot = FALSE
 )

# in environment is a new object "model.output" with the results of
# every step of the given sequence.
# Plots are done at OSL and TL steps and the growth curve

# call "analyse_SAR.CWOSL" from RLum package
 results <- analyse_SAR.CWOSL(model.output,
                            signal.integral.min = 1,
                            signal.integral.max = 15,
                            background.integral.min = 601,
                            background.integral.max = 701,
                            fit.method = "EXP",
                            dose.points = c(0,10,20,50,90,0,10))


##============================================================================##
## Example 4: generate sequence from *.seq file and run SAR simulation
##============================================================================##

# load example *.SEQ file and construct a sequence.
# call function "model_LuminescenceSignals", load created sequence for sequence,
# set model = "Bailey2002" (palaeodose = 10 Gy)
# and simulate_sample_history = FALSE (default),
# because the sample history is not part of the sequence

path <- system.file("extdata", "example_SAR_cycle.SEQ", package="RLumModel")

sequence <- read_SEQ2R(file = path)

model.output <- model_LuminescenceSignals(
  sequence = sequence,
  model = "Bailey2001",
  plot = FALSE
)


## call RLum package function "analyse_SAR.CWOSL" to analyse the simulated SAR cycle

results <- analyse_SAR.CWOSL(model.output,
                             signal.integral.min = 1,
                             signal.integral.max = 10,
                             background.integral.min = 301,
                             background.integral.max = 401,
                             dose.points = c(0,8,14,26,32,0,8),
                             fit.method = "EXP")

print(get_RLum(results))


##============================================================================##
## Example 5: compare different optical powers of stimulation light
##============================================================================##

# call function "model_LuminescenceSignals", model = "Bailey2004"
# and simulate_sample_history = FALSE (default),
# because the sample history is not part of the sequence
# the optical_power of the LED is varied and then compared.

optical_power <- seq(from = 0,to = 100,by = 20)

model.output <- lapply(1:length(optical_power), function(x){

 sequence <- list(IRR = c(20, 50, 1),
                  PH = c(220, 10, 5),
                  OSL = c(125, 50, optical_power[x])
                  )

 data <- model_LuminescenceSignals(
           sequence = sequence,
           model = "Bailey2004",
           plot = FALSE
           )

 return(get_RLum(data, recordType = "OSL$", drop = FALSE))
})

##combine output curves
model.output.merged <- merge_RLum(model.output)

##plot
plot_RLum(
 object = model.output.merged,
 xlab = "Illumination time [s]",
 ylab = "OSL signal [a.u.]",
 main = "OSL signal dependency on optical power of stimulation light",
 legend.text = paste("Optical power density", 20*optical_power/100, "mW/cm^2"),
 combine = TRUE)


## End(Not run)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(RLumModel)
Loading required package: Luminescence
Welcome to the R package Luminescence version 0.6.0 [Built: 2016-05-30 16:47:30 UTC]
The NSA: 'O'zapft is.'

Attaching package: 'RLumModel'

The following object is masked from 'package:Luminescence':

    model_LuminescenceSignals

> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/RLumModel/model_LuminescenceSignals.Rd_%03d_medium.png", width=480, height=480)
> ### Name: model_LuminescenceSignals
> ### Title: Model Luminescence Signals
> ### Aliases: model_LuminescenceSignals
> 
> ### ** Examples
> 
> 
> 
> ##================================================================##
> ## Example 1: Simulate sample history of Bailey2001
> ## (cf. Bailey, 2001, Fig. 1)
> ##================================================================##
> 
> ##set sequence with the following steps
> ## (1) Irradiation at 20 deg. C with a dose of 10 Gy and a dose rate of 1 Gy/s
> ## (2) TL from 20-400 deg. C with a rate of 5 K/s
> 
> sequence <-
+   list(
+     IRR = c(20, 10, 1),
+     TL = c(20, 400, 5)
+   )
> 
> ##model sequence
> model.output <- model_LuminescenceSignals(
+   sequence = sequence,
+   model = "Bailey2001"
+ )

[.translate_Sequence()] 
	>> Simulate sequence 
   |                                                                               |                                                                      |   0%   |                                                                               |===================================                                   |  50%   |                                                                               |======================================================================| 100%
> 
> ## Not run: 
> ##D ##============================================================================##
> ##D ## Example 2: Simulate sequence at labour without sample history
> ##D ##============================================================================##
> ##D 
> ##D ##set sequence with the following steps
> ##D ## (1) Irraditation at 20 deg. C with a dose of 100 Gy and a dose rate of 1 Gy/s
> ##D ## (2) Preheat to 200 deg. C and hold for 10 s
> ##D ## (3) LM-OSL at 125 deg. C. for 100 s
> ##D ## (4) Cutheat at 200 dec. C.
> ##D ## (5) Irraditation at 20 deg. C with a dose of 10 Gy and a dose rate of 1 Gy/s
> ##D ## (6) Pause at 200 de. C. for 100 s
> ##D ## (7) OSL at 125 deg. C for 100 s with 90 % optical power
> ##D ## (8) Pause at 200 deg. C for 100 s
> ##D ## (9) TL from 20-400 deg. C with a heat rate of 5 K/s
> ##D ## (10) Radiofluorescence at 20 deg. C with a dose of 200 Gy and a dose rate of 0.01 Gy/s
> ##D 
> ##D sequence <-
> ##D  list(
> ##D    IRR = c(20, 100, 1),
> ##D    PH = c(200, 10),
> ##D    LM_OSL = c(125, 100),
> ##D    CH = c(200),
> ##D    IRR = c(20, 10, 1),
> ##D    PAUSE = c(200, 100),
> ##D    OSL = c(125, 100, 90),
> ##D    PAUSE = c(200, 100),
> ##D    TL = c(20, 400, 5),
> ##D    RF = c(20, 200, 0.01)
> ##D )
> ##D 
> ##D # call function "model_LuminescenceSignals", set sequence = sequence,
> ##D # model = "Pagonis2008" (palaeodose = 200 Gy) and simulate_sample_history = FALSE (default),
> ##D # because the sample history is not part of the sequence
> ##D 
> ##D model.output <- model_LuminescenceSignals(
> ##D    sequence = sequence,
> ##D    model = "Pagonis2008"
> ##D    )
> ##D 
> ##D 
> ##D 
> ##D ##============================================================================##
> ##D ## Example 3: Simulate SAR sequence
> ##D ##============================================================================##
> ##D 
> ##D ##set SAR sequence with the following steps
> ##D ## (1) RegDose: set regenerative dose [Gy] as vector
> ##D ## (2) TestDose: set test dose [Gy]
> ##D ## (3) PH: set preheat temperature in deg. C
> ##D ## (4) CH: Set cutheat temperature in deg. C
> ##D ## (5) OSL_temp: set OSL reading temperature in deg. C
> ##D ## (6) OSL_duration: set OSL reading duration in s
> ##D 
> ##D sequence <- list(
> ##D  RegDose = c(0,10,20,50,90,0,10),
> ##D  TestDose = 5,
> ##D  PH = 240,
> ##D  CH = 200,
> ##D  OSL_temp = 125,
> ##D  OSL_duration = 70)
> ##D 
> ##D # call function "model_LuminescenceSignals", set sequence = sequence,
> ##D # model = "Pagonis2007" (palaeodose = 20 Gy) and simulate_sample_history = FALSE (default),
> ##D # because the sample history is not part of the sequence
> ##D 
> ##D  model.output <- model_LuminescenceSignals(
> ##D 
> ##D  sequence = sequence,
> ##D  model = "Pagonis2007",
> ##D  plot = FALSE
> ##D  )
> ##D 
> ##D # in environment is a new object "model.output" with the results of
> ##D # every step of the given sequence.
> ##D # Plots are done at OSL and TL steps and the growth curve
> ##D 
> ##D # call "analyse_SAR.CWOSL" from RLum package
> ##D  results <- analyse_SAR.CWOSL(model.output,
> ##D                             signal.integral.min = 1,
> ##D                             signal.integral.max = 15,
> ##D                             background.integral.min = 601,
> ##D                             background.integral.max = 701,
> ##D                             fit.method = "EXP",
> ##D                             dose.points = c(0,10,20,50,90,0,10))
> ##D 
> ##D 
> ##D ##============================================================================##
> ##D ## Example 4: generate sequence from *.seq file and run SAR simulation
> ##D ##============================================================================##
> ##D 
> ##D # load example *.SEQ file and construct a sequence.
> ##D # call function "model_LuminescenceSignals", load created sequence for sequence,
> ##D # set model = "Bailey2002" (palaeodose = 10 Gy)
> ##D # and simulate_sample_history = FALSE (default),
> ##D # because the sample history is not part of the sequence
> ##D 
> ##D path <- system.file("extdata", "example_SAR_cycle.SEQ", package="RLumModel")
> ##D 
> ##D sequence <- read_SEQ2R(file = path)
> ##D 
> ##D model.output <- model_LuminescenceSignals(
> ##D   sequence = sequence,
> ##D   model = "Bailey2001",
> ##D   plot = FALSE
> ##D )
> ##D 
> ##D 
> ##D ## call RLum package function "analyse_SAR.CWOSL" to analyse the simulated SAR cycle
> ##D 
> ##D results <- analyse_SAR.CWOSL(model.output,
> ##D                              signal.integral.min = 1,
> ##D                              signal.integral.max = 10,
> ##D                              background.integral.min = 301,
> ##D                              background.integral.max = 401,
> ##D                              dose.points = c(0,8,14,26,32,0,8),
> ##D                              fit.method = "EXP")
> ##D 
> ##D print(get_RLum(results))
> ##D 
> ##D 
> ##D ##============================================================================##
> ##D ## Example 5: compare different optical powers of stimulation light
> ##D ##============================================================================##
> ##D 
> ##D # call function "model_LuminescenceSignals", model = "Bailey2004"
> ##D # and simulate_sample_history = FALSE (default),
> ##D # because the sample history is not part of the sequence
> ##D # the optical_power of the LED is varied and then compared.
> ##D 
> ##D optical_power <- seq(from = 0,to = 100,by = 20)
> ##D 
> ##D model.output <- lapply(1:length(optical_power), function(x){
> ##D 
> ##D  sequence <- list(IRR = c(20, 50, 1),
> ##D                   PH = c(220, 10, 5),
> ##D                   OSL = c(125, 50, optical_power[x])
> ##D                   )
> ##D 
> ##D  data <- model_LuminescenceSignals(
> ##D            sequence = sequence,
> ##D            model = "Bailey2004",
> ##D            plot = FALSE
> ##D            )
> ##D 
> ##D  return(get_RLum(data, recordType = "OSL$", drop = FALSE))
> ##D })
> ##D 
> ##D ##combine output curves
> ##D model.output.merged <- merge_RLum(model.output)
> ##D 
> ##D ##plot
> ##D plot_RLum(
> ##D  object = model.output.merged,
> ##D  xlab = "Illumination time [s]",
> ##D  ylab = "OSL signal [a.u.]",
> ##D  main = "OSL signal dependency on optical power of stimulation light",
> ##D  legend.text = paste("Optical power density", 20*optical_power/100, "mW/cm^2"),
> ##D  combine = TRUE)
> ##D 
> ## End(Not run)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>