analyseBINdata: BIN data analysis

In numOSL: Numeric Routines for Optically Stimulated Luminescence Dating

Description

Analysing signal data records extracted from a BIN file.

Usage

analyseBINdata(obj_pickBIN, nfchn, nlchn, bg = "late", 
               me = 2.0, distp = "p", kph = NULL, 
               kdc = NULL, dcr = NULL, FR.fchn = NULL, 
               FR.mchn = NULL, FR.lchn = NULL, 
               signal.type = "LxTx", outfile = NULL)

Arguments

obj_pickBIN	list(required): an object of S3 class "pickBIN" produced by function pickBINdata
nfchn	integer(required): number of the first few channels from the initial part of a decay curve. Number of counts summed over channels (Delay+1L):(Delay+nfchn) is calculated as the fast-component plus backgroud signal
nlchn	integer(required): number of the last few channels from the latter part of a decay curve. If bg="late", number of counts averaged over channels (Delay+On-nlchn+1L):(Delay+On) will be calculated as the backgroud signal, if bg="early", number of counts averaged over channels (Delay+nfchn+1L):(Delay+nfchn+nlchn) will be calculated as the backgroud signal. Delay and On are obtained internally from the BIN file.
bg	character(with default): background subtraction method, i.e., bg="early" or bg="late"
me	numeric(with default): measurement error of Lx (or Tx) in percent
distp	character(with default): distribution of photon counts, distp="p" denotes Poisson distribution, distp="op" denotes Over Poisson distribution
kph	numeric(optional): correction factor for photon counts
kdc	numeric(optional): correction factor for dark counts
dcr	numeric(optional): dark count rate
FR.fchn	vector(optional): fast-component signal channels, note that those channels are extracted internally from the "ON" channels, i.e., FR.fchn=((Delay+1):(Delay+On))[FR.fchn]. Example: FR.fchn=1:5
FR.mchn	vector(optional): medium-component signal channels, note that those channels are extracted internally from the "ON" channels, i.e., FR.mchn=((Delay+1):(Delay+On))[FR.mchn]. Example: FR.mchn=31:60
FR.lchn	vector(optional): background signal channels, note that those channels are extracted internally from the "ON" channels, i.e., FR.lchn=((Delay+1):(Delay+On))[FR.lchn]. Example: FR.lchn=201:250
signal.type	character(with default): type of signal, "LxTx", "Lx", or "Tx"
outfile	character(optional): if specified, analysis results (i.e., NO, Position, Grain, SAR.Cycle, Dose, Init, BG, Lx, seLx, TInit, TBG, Tx, seTx, LxTx, seLxTx) will be written to a CSV file named "outfile" and saved to the current work directory

Details

Function analyseBINdata is used for signal (i.e., Lx, Tx, and Lx/Tx) calculation. It provides two protocols for background subtraction (i.e., the early and late background subtraction methods).

Standard error of signals are assessed using two methods: if photon counts are assummed to follow Poisson distributions, Eqn.(3) of Galbraith (2002) will be applied; if photon counts are over-dispersed, Eqn.(10) of Bluszcz et al. (2015) will be applied.

If arguments FR.fchn, FR.mchn, and FR.lchn are provided, fast ratio will be calculated according to Madsen et al. (2009).

Value

Return an invisible list of S3 class object "analyseBIN" containing the following elements:

SARdata	a data.frame containing calculated SAR data sets
criteria	values used as rejection criteria (0-1 values indicating if Tn is more than 3 sigma above BG or not, ratio of initial Tn signal to BG and associated standard error, relative standard error of Tn in percent, fast ratio of Tn and associated standard error), NA is produced if the value can not be calculated. Note that in this function rejection criteria are calculated but not applied
Tn	values of Tn and associated standard errors
LnTn.curve	decay curves for Ln and Tn for different aliquots (grains)
TxTn	ratios of Tx to Tn for various SAR cycles
agID	aliquot or grain ID (i.e., NO, Position, and Grain)

SARdata is a data.frame containing the following elements if signal.type="LxTx":

Element	Description
NO	aliquot (grain) number
SAR.Cycle	SAR cycle (N, R1, R2, R3, ...)
Dose	regenerative dose
LxTx	sensitivity-corrected regenerative-dose signal
seLxTx	standard error of LxTx

SARdata contains the following elements if signal.type="Lx":

Element	Description
NO	aliquot (grain) number
SAR.Cycle	SAR cycle (N, R1, R2, R3, ...)
Dose	regenerative dose
Lx	regenerative-dose signal
seLx	standard error of Lx

SARdata contains the following elements if signal.type="Tx":

Element	Description
NO	aliquot (grain) number
SAR.Cycle	SAR cycle (N, R1, R2, R3, ...)
Dose	regenerative dose
Tx	test-dose signal
seTx	standard error of Tx

Note

Though function analyseBINdata is originally designed to analyze CW-OSL data sets, IRSL data sets obtained from the SAR protocol can also be analyzed.

References

Ballarini M, Wallinga J, Wintle AG, Bos AJJ, 2007. A modified SAR protocol for optical dating of individual grains from young quartz samples. Radiation Measurements, 42(3): 360-369.

Bluszcz A, Adamiec G, Heer AJ, 2015. Estimation of equivalent dose and its uncertainty in the OSL SAR protocol when count numbers do not follow a Poisson distribution. Radiation Measurements, 81: 46-54.

Cunningham AC, Wallinga J, 2010. Selection of integration time intervals for quartz OSL decay curves. Quaternary Geochronology, 5(6): 657-666

Duller GAT, 2016. Analyst (v4.31.9), User Mannual.

Durcan JA, Duller GAT, 2011. The fast ratio: A rapid measure for testing the dominance of the fast component in the initial OSL signal from quartz. Radiation Measurements, 46(10): 1065-1072.

Galbraith R, 2002. A note on the variance of a backround-corrected OSL count. Ancient TL, 20(2): 49-51.

Madsen AT, Duller GAT, Donnelly JP, Roberts HM, Wintle AG, 2009. A chronology of hurricane landfalls at Little Sippewissett Marsh, Massachusetts, USA, using optical dating. Geomorphology, 109(1-2): 36-45.

See Also

loadBINdata; pickBINdata; pickSARdata;
calED; calSARED; calSGCED;
fitGrowth; lsNORM; BIN

Examples

   ### Example 1 (not run):
   # obj_loadBIN <- loadBINdata("foo.bin", view=TRUE)
   # obj_pickBIN <- pickBINdata(obj_loadBIN, Position=2, LType="OSL")
   # analyseBINdata(obj_pickBIN, nfchn=3, nlchn=20)

   ### Example 2:
   data(BIN)
   obj_pickBIN <- pickBINdata(BIN, Position=c(2,4,6,8,10), 
                              LType="OSL", view=FALSE)
   obj_analyseBIN <- analyseBINdata(obj_pickBIN, nfchn=3, nlchn=20) 
   obj_analyseBIN$SARdata

Example output

   NO SAR.Cycle Dose        LxTx     seLxTx
1   1         N    0 1.921073247 0.09179489
2   1        R1  100 0.812777449 0.04459350
3   1        R2  200 1.454780362 0.06928321
4   1        R3  300 2.101610474 0.09130081
5   1        R4  400 2.804353809 0.11757923
6   1        R5    0 0.083302134 0.01434214
7   1        R6  100 0.845985945 0.04085199
8   2         N    0 1.670973435 0.07561007
9   2        R1  100 0.861161394 0.04246102
10  2        R2  200 1.570534340 0.06748917
11  2        R3  300 2.171279067 0.08777730
12  2        R4  400 2.846830318 0.11138327
13  2        R5    0 0.074647439 0.01251014
14  2        R6  100 0.848536182 0.03728819
15  3         N    0 1.919166267 0.09983816
16  3        R1  100 0.823725482 0.04833874
17  3        R2  200 1.576494658 0.07769819
18  3        R3  300 2.058367673 0.09125201
19  3        R4  400 2.615502221 0.11153514
20  3        R5    0 0.064494809 0.01369670
21  3        R6  100 0.895383104 0.04401155
22  4         N    0 2.079613486 0.11156115
23  4        R1  100 0.841090673 0.05100312
24  4        R2  200 1.637400577 0.08528417
25  4        R3  300 2.220009466 0.10405905
26  4        R4  400 2.724750311 0.11804096
27  4        R5    0 0.003318827 0.01343621
28  4        R6  100 0.836889113 0.04218036
29  5         N    0 1.693591654 0.08101986
30  5        R1  100 0.803419099 0.04311559
31  5        R2  200 1.477827304 0.06617150
32  5        R3  300 2.181801373 0.09169783
33  5        R4  400 2.644890330 0.10509793
34  5        R5    0 0.058464760 0.01197581
35  5        R6  100 0.883006381 0.04054355

numOSL documentation built on May 1, 2019, 8:45 p.m.