analyseBINdata: BIN data analysis

Description Usage Arguments Details Value Note References See Also Examples

View source: R/analyseBINdata.R

Description

Analysing signal data records extracted from a BIN file.

Usage

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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

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   ### 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

numOSL documentation built on July 26, 2018, 9 a.m.