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Last data update: 2014.03.03

R: Calculate De value based on the gSGC by Li et al., 2015

calc_gSGC

R Documentation

Calculate De value based on the gSGC by Li et al., 2015

Description

Function returns De value and De value error using the global standardised growth curve (gSGC) assumption proposed by Li et al., 2015 for OSL dating of sedimentary quartz

Usage

calc_gSGC(data, gSGC.type = "0-250", gSGC.parameters, n.MC = 100,
  verbose = TRUE, plot = TRUE, ...)

Arguments

`data`	`data.frame` (required): input data of providing the following columns: 'LnTn', 'LnTn.error', Lr1Tr1', 'Lr1Tr1.error', 'Dr1' Note: column names are not required. The function expect the input data in the given order
`gSGC.type`	`character` (with default): define the function parameters that should be used for the iteration procedure: Li et al., 2015 (Table 2) presented function parameters for two dose ranges: `"0-450"` and `"0-250"`
`gSGC.parameters`	`list` (optional): option to provide own function parameters used for #' fitting as named list. Nomenclature follows Li et al., 2015, i.e. `list(A,A.error,D0,D0.error,c,c.error,Y0,Y0.error,range)`, range requires a vector for the range the function is considered as valid, e.g. `range = c(0,250)` Using this option overwrites the default parameter list of the gSGC, meaning the argument `gSGC.type` will be without effect
`n.MC`	`integer` (with default): number of Monte Carlo simulation runs for error estimation, s. details.
`verbose`	`logical`: enable or disable terminal output
`plot`	`logical`: enable or disable graphical feedback as plot
`...`	parameters will be passed to the plot output

Details

The error of the De value is determined using a Monte Carlo simulation approach. Solving of the equation is realised using uniroot. Large values for n.MC will significantly increase the computation time.

Value

Returns an S4 object of type RLum.Results.

@data
$ De.value (data.frame)
.. $ De
.. $ De.error
.. $ Eta
$ De.MC (list) contains the matricies from the error estimation.
$ uniroot (list) contains the uniroot outputs of the De estimations

@info
$ call (call) the original function call

Function version

0.1.1 (2016-05-03 12:29:30)

Author(s)

Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montagine (France)

R Luminescence Package Team

References

Li, B., Roberts, R.G., Jacobs, Z., Li, S.-H., 2015. Potential of establishing a 'global standardised growth curve' (gSGC) for optical dating of quartz from sediments. Quaternary Geochronology 27, 94-104. doi:10.1016/j.quageo.2015.02.011

Examples

results <- calc_gSGC(data = data.frame(
LnTn =  2.361, LnTn.error = 0.087,
Lr1Tr1 = 2.744, Lr1Tr1.error = 0.091,
Dr1 = 34.4))

get_RLum(results, data.object = "De")

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(Luminescence)
Welcome to the R package Luminescence version 0.6.0 [Built: 2016-05-30 16:47:30 UTC]
A trapped electron to a yellow LED: 'Well, that's all?'
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/Luminescence/calc_gSGC.Rd_%03d_medium.png", width=480, height=480)
> ### Name: calc_gSGC
> ### Title: Calculate De value based on the gSGC by Li et al., 2015
> ### Aliases: calc_gSGC
> ### Keywords: datagen
> 
> ### ** Examples
> 
> results <- calc_gSGC(data = data.frame(
+ LnTn =  2.361, LnTn.error = 0.087,
+ Lr1Tr1 = 2.744, Lr1Tr1.error = 0.091,
+ Dr1 = 34.4))

[calc_gSGC()]
	 Corresponding De based on the gSGC

	 Ln/Tn:		 2.361 <U+00B1> 0.087
	 Lr1/Tr1:	 2.744 <U+00B1> 0.091
	 Dr1:		 34.4
	 f(D):		 0.787 * (1 - exp(-D /73.9)) + c * D + 0.01791
	 n.MC:		 100
	 ------------------------------ 
	 De:		28.43 <U+00B1> 1.98
	 ------------------------------ 
> 
> get_RLum(results, data.object = "De")
        DE DE.ERROR       ETA
1 28.42881 1.984767 0.1325632
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>