Luminescence (version 0.8.6)

# analyse_IRSAR.RF: Analyse IRSAR RF measurements

## Description

Function to analyse IRSAR RF measurements on K-feldspar samples, performed using the protocol according to Erfurt et al. (2003) and beyond.

## Usage

analyse_IRSAR.RF(object, sequence_structure = c("NATURAL",
"REGENERATED"), RF_nat.lim = NULL, RF_reg.lim = NULL,
method = "FIT", method.control = NULL, test_parameters = NULL,
n.MC = 10, txtProgressBar = TRUE, plot = TRUE,
plot_reduced = FALSE, ...)

## Arguments

object

'>RLum.Analysis or a list of '>RLum.Analysis-objects (required): input object containing data for protocol analysis. The function expects to find at least two curves in the '>RLum.Analysis object: (1) RF_nat, (2) RF_reg. If a list is provided as input all other parameters can be provided as list as well to gain full control.

sequence_structure

vector character (with default): specifies the general sequence structure. Allowed steps are NATURAL, REGENERATED. In addition any other character is allowed in the sequence structure; such curves will be ignored during the analysis.

RF_nat.lim

vector (with default): set minimum and maximum channel range for natural signal fitting and sliding. If only one value is provided this will be treated as minimum value and the maximum limit will be added automatically.

RF_reg.lim

vector (with default): set minimum and maximum channel range for regenerated signal fitting and sliding. If only one value is provided this will be treated as minimum value and the maximum limit will be added automatically.

method

character (with default): setting method applied for the data analysis. Possible options are "FIT" or "SLIDE".

method.control

list (optional): parameters to control the method, that can be passed to the chosen method. These are for (1) method = "FIT": 'trace', 'maxiter', 'warnOnly', 'minFactor' and for (2) method = "SLIDE": 'correct_onset', 'show_density', 'show_fit', 'trace'. See details.

test_parameters

list (with default): set test parameters. Supported parameters are: curves_ratio, residuals_slope (only for method = "SLIDE"), curves_bounds, dynamic_ratio, lambda, beta and delta.phi. All input: numeric values, NA and NULL (s. Details)

(see Details for further information)

n.MC

numeric (with default): set number of Monte Carlo runs for start parameter estimation (method = "FIT") or error estimation (method = "SLIDE"). This value can be set to NULL to skip the MC runs. Note: Large values will significantly increase the computation time

txtProgressBar

logical (with default): enables TRUE or disables FALSE the progression bar during MC runs

plot

logical (with default): plot output (TRUE or FALSE)

plot_reduced

logical (optional): provides a reduced plot output if enabled to allow common R plot combinations, e.g., par(mfrow(...)). If TRUE no residual plot is returned; it has no effect if plot = FALSE

...

further arguments that will be passed to the plot output. Currently supported arguments are main, xlab, ylab, xlim, ylim, log, legend (TRUE/FALSE), legend.pos, legend.text (passes argument to x,y in graphics::legend), xaxt

## Value

The function returns numerical output and an (optional) plot.

----------------------------------- [ NUMERICAL OUTPUT ] -----------------------------------

RLum.Results-object

slot: @data

[.. $data : data.frame]  Column Type Description DE numeric the obtained equivalent dose DE.ERROR numeric (only method = "SLIDE") standard deviation obtained from MC runs DE.LOWER numeric 2.5% quantile for De values obtained by MC runs DE.UPPER numeric 97.5% quantile for De values obtained by MC runs DE.STATUS character test parameter status RF_NAT.LIM charcter used RF_nat curve limits RF_REG.LIM character used RF_reg curve limits POSITION integer (optional) position of the curves DATE character (optional) measurement date SEQUENCE_NAME character (optional) sequence name [..$De.MC : numeric]

A numeric vector with all the De values obtained by the MC runs.

[.. $test_parameters : data.frame]  Column Type Description POSITION numeric aliquot position PARAMETER character test parameter name THRESHOLD numeric set test parameter threshold value VALUE numeric the calculated test parameter value (to be compared with the threshold) STATUS character test parameter status either "OK" or "FAILED" SEQUENCE_NAME character name of the sequence, so far available [..$fit : data.frame]

An nls object produced by the fitting.

[.. \$slide : list]

A list with data produced during the sliding. Some elements are previously reported with the summary object data. List elements are:

 Element Type Description De numeric the final De obtained with the sliding approach De.MC numeric all De values obtained by the MC runs residuals numeric the obtained residuals for each channel of the curve trend.fit lm fitting results produced by the fitting of the residuals RF_nat.slided matrix the slided RF_nat curve t_n.id numeric the index of the t_n offset I_n numeric the vertical intensity offset if a vertical slide was applied algorithm_error numeric the vertical sliding suffers from a systematic effect induced by the used algorithm. The returned value is the standard deviation of all obtained De values while expanding the vertical sliding range. I can be added as systematic error to the final De error; so far wanted. vslide_range numeric the range used for the vertical sliding

slot: @info

The original function call (methods::language-class-object)

The output (data) should be accessed using the function get_RLum

------------------------ [ PLOT OUTPUT ] ------------------------

The slided IR-RF curves with the finally obtained De

## Function version

0.7.5 (2018-10-03 19:48:32)

## How to cite

Kreutzer, S. (2018). analyse_IRSAR.RF(): Analyse IRSAR RF measurements. Function version 0.7.5. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.6. https://CRAN.R-project.org/package=Luminescence

## Details

The function performs an IRSAR analysis described for K-feldspar samples by Erfurt et al. (2003) assuming a negligible sensitivity change of the RF signal.

General Sequence Structure (according to Erfurt et al., 2003)

1. Measuring IR-RF intensity of the natural dose for a few seconds ($$RF_{nat}$$)

2. Bleach the samples under solar conditions for at least 30 min without changing the geometry

3. Waiting for at least one hour

4. Regeneration of the IR-RF signal to at least the natural level (measuring ($$RF_{reg}$$)

5. Fitting data with a stretched exponential function

6. Calculate the the palaeodose $$D_{e}$$ using the parameters from the fitting

Actually two methods are supported to obtain the $$D_{e}$$: method = "FIT" and method = "SLIDE":

method = "FIT"

The principle is described above and follows the original suggestions by Erfurt et al., 2003. For the fitting the mean count value of the RF_nat curve is used.

Function used for the fitting (according to Erfurt et al. (2003)):

$$\phi(D) = \phi_{0}-\Delta\phi(1-exp(-\lambda*D))^\beta$$

with $$\phi(D)$$ the dose dependent IR-RF flux, $$\phi_{0}$$ the initial IR-RF flux, $$\Delta\phi$$ the dose dependent change of the IR-RF flux, $$\lambda$$ the exponential parameter, $$D$$ the dose and $$\beta$$ the dispersive factor.

To obtain the palaeodose $$D_{e}$$ the function is changed to:

$$D_{e} = ln(-(\phi(D) - \phi_{0})/(-\lambda*\phi)^{1/\beta}+1)/-\lambda$$

The fitting is done using the port algorithm of the nls function.

method = "SLIDE"

For this method, the natural curve is slid along the x-axis until congruence with the regenerated curve is reached. Instead of fitting this allows working with the original data without the need for any physical model. This approach was introduced for RF curves by Buylaert et al., 2012 and Lapp et al., 2012.

Here the sliding is done by searching for the minimum of the squared residuals. For the mathematical details of the implementation see Frouin et al., 2017

method.control

To keep the generic argument list as clear as possible, arguments to control the methods for De estimation are all preset with meaningful default parameters and can be handled using the argument method.control only, e.g., method.control = list(trace = TRUE). Supported arguments are:

 ARGUMENT METHOD DESCRIPTION trace FIT, SLIDE as in nls; shows sum of squared residuals trace_vslide SLIDE logical argument to enable or disable the tracing of the vertical sliding maxiter FIT as in nls warnOnly FIT as in nls minFactor FIT as in nls correct_onset SLIDE The logical argument shifts the curves along the x-axis by the first channel, as light is expected in the first channel. The default value is TRUE. show_density SLIDE logical (with default) enables or disables KDE plots for MC run results. If the distribution is too narrow nothing is shown. show_fit SLIDE logical (with default) enables or disables the plot of the fitted curve routinely obtained during the evaluation. n.MC SLIDE integer (with default): This controls the number of MC runs within the sliding (assessing the possible minimum values). The default n.MC = 1000. Note: This parameter is not the same as controlled by the function argument n.MC. vslide_range SLDE logical or numeric or character (with default): This argument sets the boundaries for a vertical curve sliding. The argument expects a vector with an absolute minimum and a maximum (e.g., c(-1000,1000)). Alternatively the values NULL and 'auto' are allowed. The automatic mode detects the reasonable vertical sliding range (recommended). NULL applies no vertical sliding. The default is NULL.

Error estimation

For method = "FIT" the asymmetric error range is obtained by using the 2.5 % (lower) and the 97.5 % (upper) quantiles of the $$RF_{nat}$$ curve for calculating the $$D_{e}$$ error range.

For method = "SLIDE" the error is obtained by bootstrapping the residuals of the slided curve to construct new natural curves for a Monte Carlo simulation. The error is returned in two ways: (a) the standard deviation of the herewith obtained $$D_{e}$$ from the MC runs and (b) the confidence interval using the 2.5 % (lower) and the 97.5 % (upper) quantiles. The results of the MC runs are returned with the function output.

Test parameters

The argument test_parameters allows to pass some thresholds for several test parameters, which will be evaluated during the function run. If a threshold is set and it will be exceeded the test parameter status will be set to "FAILED". Intentionally this parameter is not termed 'rejection criteria' as not all test parameters are evaluated for both methods and some parameters are calculated by not evaluated by default. Common for all parameters are the allowed argument options NA and NULL. If the parameter is set to NA the value is calculated but the result will not be evaluated, means it has no effect on the status ("OK" or "FAILED") of the parameter. Setting the parameter to NULL disables the parameter entirely and the parameter will be also removed from the function output. This might be useful in cases where a particular parameter asks for long computation times. Currently supported parameters are:

curves_ratio numeric (default: 1.001):

The ratio of $$RF_{nat}$$ over $$RF_{reg}$$ in the range of$$RF_{nat}$$ of is calculated and should not exceed the threshold value.

intersection_ratio numeric (default: NA):

Calculated as absolute difference from 1 of the ratio of the integral of the normalised RF-curves, This value indicates intersection of the RF-curves and should be close to 0 if the curves have a similar shape. For this calculation first the corresponding time-count pair value on the RF_reg curve is obtained using the maximum count value of the RF_nat curve and only this segment (fitting to the RF_nat curve) on the RF_reg curve is taken for further calculating this ratio. If nothing is found at all, Inf is returned.

residuals_slope numeric (default: NA; only for method = "SLIDE"):

A linear function is fitted on the residuals after sliding. The corresponding slope can be used to discard values as a high (positive, negative) slope may indicate that both curves are fundamentally different and the method cannot be applied at all. Per default the value of this parameter is calculated but not evaluated.

curves_bounds numeric (default: $$max(RF_{reg_counts})$$:

This measure uses the maximum time (x) value of the regenerated curve. The maximum time (x) value of the natural curve cannot be larger than this value. However, although this is not recommended the value can be changed or disabled.

dynamic_ratio numeric (default: NA):

The dynamic ratio of the regenerated curve is calculated as ratio of the minimum and maximum count values.

lambda, beta and delta.phi numeric (default: NA; method = "SLIDE"):

The stretched exponential function suggested by Erfurt et al. (2003) describing the decay of the RF signal, comprises several parameters that might be useful to evaluate the shape of the curves. For method = "FIT" this parameter is obtained during the fitting, for method = "SLIDE" a rather rough estimation is made using the function minpack.lm::nlsLM and the equation given above. Note: As this procedure requests more computation time, setting of one of these three parameters to NULL also prevents a calculation of the remaining two.

## References

Buylaert, J.P., Jain, M., Murray, A.S., Thomsen, K.J., Lapp, T., 2012. IR-RF dating of sand-sized K-feldspar extracts: A test of accuracy. Radiation Measurements 44 (5-6), 560-565. doi: 10.1016/j.radmeas.2012.06.021

Erfurt, G., Krbetschek, M.R., 2003. IRSAR - A single-aliquot regenerative-dose dating protocol applied to the infrared radiofluorescence (IR-RF) of coarse- grain K-feldspar. Ancient TL 21, 35-42.

Erfurt, G., 2003. Infrared luminescence of Pb+ centres in potassium-rich feldspars. physica status solidi (a) 200, 429-438.

Erfurt, G., Krbetschek, M.R., 2003. Studies on the physics of the infrared radioluminescence of potassium feldspar and on the methodology of its application to sediment dating. Radiation Measurements 37, 505-510.

Erfurt, G., Krbetschek, M.R., Bortolot, V.J., Preusser, F., 2003. A fully automated multi-spectral radioluminescence reading system for geochronometry and dosimetry. Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms 207, 487-499.

Frouin, M., Huot, S., Kreutzer, S., Lahaye, C., Lamothe, M., Philippe, A., Mercier, N., 2017. An improved radiofluorescence single-aliquot regenerative dose protocol for K-feldspars. Quaternary Geochronology 38, 13-24. doi:10.1016/j.quageo.2016.11.004

Lapp, T., Jain, M., Thomsen, K.J., Murray, A.S., Buylaert, J.P., 2012. New luminescence measurement facilities in retrospective dosimetry. Radiation Measurements 47, 803-808. doi:10.1016/j.radmeas.2012.02.006

Trautmann, T., 2000. A study of radioluminescence kinetics of natural feldspar dosimeters: experiments and simulations. Journal of Physics D: Applied Physics 33, 2304-2310.

Trautmann, T., Krbetschek, M.R., Dietrich, A., Stolz, W., 1998. Investigations of feldspar radioluminescence: potential for a new dating technique. Radiation Measurements 29, 421-425.

Trautmann, T., Krbetschek, M.R., Dietrich, A., Stolz, W., 1999. Feldspar radioluminescence: a new dating method and its physical background. Journal of Luminescence 85, 45-58.

Trautmann, T., Krbetschek, M.R., Stolz, W., 2000. A systematic study of the radioluminescence properties of single feldspar grains. Radiation Measurements 32, 685-690.

'>RLum.Analysis, '>RLum.Results, get_RLum, nls, minpack.lm::nlsLM, parallel::mclapply

## Examples

# NOT RUN {
data(ExampleData.RLum.Analysis, envir = environment())

##(1) perform analysis using the method 'FIT'
results <- analyse_IRSAR.RF(object = IRSAR.RF.Data)

##show De results and test paramter results
get_RLum(results, data.object = "data")
get_RLum(results, data.object = "test_parameters")

##(2) perform analysis using the method 'SLIDE'
results <- analyse_IRSAR.RF(object = IRSAR.RF.Data, method = "SLIDE", n.MC = 1)

# }
# NOT RUN {
##(3) perform analysis using the method 'SLIDE' and method control option
## 'trace
results <- analyse_IRSAR.RF(
object = IRSAR.RF.Data,
method = "SLIDE",
method.control = list(trace = TRUE))

# }
# NOT RUN {
# }