Description Usage Arguments Details Value Function version How to cite Note Author(s) References Examples
View source: R/calc_Huntley2006.R
A function to calculate the expected sample specific fraction of saturation based on the model of Huntley (2006) using the approach as implemented in Kars et al. (2008) or Guralnik et al. (2015).
1 2 3 4 5 6 7 8 9 10 11 12 13 
data 
data.frame (required):
A
(optional)  dose (s) LxTx  LxTx error   [ ,1]  [ ,2] [ ,3]   [1, ] 0  LnTn  LnTn error  (optional, see arg 'LnTn') [2, ] R1  L1T1  L1T1 error  ...  ...  ...  ...  [x, ] Rx  LxTx  LxTx error  NOTE: The function assumes the first row of the function to be the

LnTn 
data.frame (optional):
This argument should only be used to provide more than one  LnTn  LnTn error   [ ,1]  [ ,2]   [1, ] LnTn_1  LnTn_1 error  [2, ] LnTn_2  LnTn_2 error  ...  ...  ...  [x, ] LnTn_x  LnTn_x error  The function will calculate a mean NOTE: If you provide 
rhop 
numeric (required):
The density of recombination centres (ρ') and its error (see Huntley 2006),
given as numeric vector of length two. Note that ρ' must not be
provided as the common logarithm. Example: 
ddot 
numeric (required):
Environmental dose rate and its error, given as a numeric vector of length two.
Expected unit: Gy/ka. Example: 
readerDdot 
numeric (required):
Dose rate of the irradiation source of the OSL reader and its error,
given as a numeric vector of length two.
Expected unit: Gy/s. Example: 
normalise 
logical (with default):
If 
fit.method 
character (with default):
Fit function of the dose response curve. Can either be 
lower.bounds 
numeric (with default):
Only applicable for 
summary 
logical (with default):
If 
plot 
logical (with default): enables/disables plot output. 
... 
Further parameters:
All other arguments are passed to plot and plot_GrowthCurve. 
This function applies the approach described in Kars et al. (2008) or Guralnik et al. (2015),
which are both developed from the model of Huntley (2006) to calculate the expected sample
specific fraction of saturation of a feldspar and also to calculate fading
corrected age using this model. ρ' (rhop
), the density of recombination
centres, is a crucial parameter of this model and must be determined
separately from a fading measurement. The function analyse_FadingMeasurement
can be used to calculate the sample specific ρ' value.
Kars et al. (2008)  Single saturating exponential
To apply the approach after Kars et al. (2008) use fit.method = "EXP"
.
Firstly, the unfaded D0 value is determined through applying equation 5 of Kars et al. (2008) to the measured LxTx data as a function of irradiation time, and fitting the data with a single saturating exponential of the form:
LxTx(t*) = A x φ(t*) x (1  exp((t* / D0)))
where
φ(t*) = exp(ρ' x ln(1.8 x s_tilde x t*)^3)
after King et al. (2016) where A
is a preexponential factor,
t*
(s) is the irradiation time, starting at the midpoint of
irradiation (Auclair et al. 2003) and s_tilde
(3x10^15 s^1) is the athermal
frequency factor after Huntley (2006).
Using fit parameters A
and D0
, the function then computes a natural dose
response curve using the environmental dose rate, D_dot
(Gy/s) and equations
[1]
and [2]
. Computed LxTx values are then fitted using the
plot_GrowthCurve function and the laboratory measured LnTn can then
be interpolated onto this curve to determine the fading corrected
De value, from which the fading corrected age is calculated.
Guralnik et al. (2015)  Generalorder kinetics
To apply the approach after Guralnik et al. (2015) use fit.method = "GOK"
.
The approach of Guralnik et al. (2015) is very similar to that of Kars et al. (2008), but instead of using a single saturating exponential the model fits a generalorder kinetics function of the form:
LxTx(t*) = A x φ(t*) x (1(1+(1/D0) x t* x c)^(1/c))
where A
, φ, t*
and D0
are the same as above and c
is a
dimensionless kinetic order modifier (cf. equation 10 in
Guralnik et al., 2015).
Level of saturation
The calc_Huntley2006
function also calculates the level of saturation (n/N)
and the field saturation (i.e. athermal steady state, (n/N)_SS) value for
the sample under investigation using the sample specific ρ',
unfaded D0
and D_dot
values, following the approach of Kars et al. (2008).
Uncertainties
Uncertainties are reported at 1 sigma and are assumed to be normally
distributed and are estimated using montecarlo resamples (n.MC = 1000
)
of ρ' and LxTx during dose response curve fitting, and of ρ'
in the derivation of (n/N) and (n/N)_SS.
*Age calculated from 2\emphD0 of the simulated natural DRC
In addition to the age calculated from the equivalent dose derived from
Ln/Tn
projected on the simulated natural dose response curve (DRC), this function
also calculates an age from twice the characteristic saturation dose (D0
)
of the simulated natural DRC. This can be a useful information for
(over)saturated samples (ie. no intersect of Ln/Tn
on the natural DRC)
to obtain at least a "minimum age" estimate of the sample. In the console
output this value is denoted by "Age @2D0 (ka):".
An RLum.Results object is returned:
Slot: @data
OBJECT  TYPE  COMMENT 
results  data.frame  results of the of Kars et al. 2008 model 
data  data.frame  original input data 
Ln  numeric  Ln and its error 
LxTx_tables  list  A list of data.frames containing data on dose,
LxTx and LxTx error for each of the dose response curves.
Note that these do not contain the natural Ln signal, which is provided separately. 
fits  list  A list of nls objects produced by minpack.lm::nlsLM when fitting the dose response curves 
Slot: @info
OBJECT  TYPE  COMMENT 
call  call  the original function call 
args  list  arguments of the original function call 
0.4.1
King, G.E., Burow, C., 2020. calc_Huntley2006(): Apply the Huntley (2006) model. Function version 0.4.1. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J., 2020. Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.9.7. https://CRAN.Rproject.org/package=Luminescence
This function has BETA status and should not be used for publication work!
Georgina E. King, University of Bern (Switzerland)
Christoph Burow, University of Cologne (Germany)
, RLum Developer Team
Kars, R.H., Wallinga, J., Cohen, K.M., 2008. A new approach towards anomalous fading correction for feldspar IRSL datingtests on samples in field saturation. Radiation Measurements 43, 786790. doi:10.1016/j.radmeas.2008.01.021
Guralnik, B., Li, B., Jain, M., Chen, R., Paris, R.B., Murray, A.S., Li, S.H., Pagonis, P., Herman, F., 2015. Radiationinduced growth and isothermal decay of infraredstimulated luminescence from feldspar. Radiation Measurements 81, 224231.
Huntley, D.J., 2006. An explanation of the powerlaw decay of luminescence. Journal of Physics: Condensed Matter 18, 13591365. doi:10.1088/09538984/18/4/020
King, G.E., Herman, F., Lambert, R., Valla, P.G., Guralnik, B., 2016. MultiOSLthermochronometry of feldspar. Quaternary Geochronology 33, 7687. doi:10.1016/j.quageo.2016.01.004
Further reading
Morthekai, P., Jain, M., Cunha, P.P., Azevedo, J.M., Singhvi, A.K., 2011. An attempt to correct for the fading in million year old basaltic rocks. Geochronometria 38(3), 223230.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44  ## Load example data (sample UNIL/NB123, see ?ExampleData.Fading)
data("ExampleData.Fading", envir = environment())
## (1) Set all relevant parameters
# a. fading measurement data (IR50)
fading_data < ExampleData.Fading$fading.data$IR50
# b. Dose response curve data
data < ExampleData.Fading$equivalentDose.data$IR50
## (2) Define required function parameters
ddot < c(7.00, 0.004)
readerDdot < c(0.134, 0.0067)
# Analyse fading measurement and get an estimate of rho'.
# Note that the RLum.Results object can be directly used for further processing.
# The number of MC runs is reduced for this example
rhop < analyse_FadingMeasurement(fading_data, plot = TRUE, verbose = FALSE, n.MC = 10)
## (3) Apply the Kars et al. (2008) model to the data
kars < calc_Huntley2006(data = data,
rhop = rhop,
ddot = ddot,
readerDdot = readerDdot,
n.MC = 25)
## Not run:
# You can also provide LnTn values separately via the 'LnTn' argument.
# Note, however, that the data frame for 'data' must then NOT contain
# a LnTn value. See argument descriptions!
LnTn < data.frame(LnTn = c(1.84833, 2.24833),
LnTn.error = c(0.17, 0.22))
LxTx < data[2:nrow(data), ]
kars < calc_Huntley2006(data = LxTx,
LnTn = LnTn,
rhop = rhop,
ddot = ddot,
readerDdot = readerDdot,
n.MC = 25)
## End(Not run)

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