fit_CWCurve: Nonlinear Least Squares Fit for CW-OSL curves -beta version-

In Luminescence: Comprehensive Luminescence Dating Data Analysis

Nonlinear Least Squares Fit for CW-OSL curves -beta version-

Description

The function determines the weighted least-squares estimates of the component parameters of a CW-OSL signal for a given maximum number of components and returns various component parameters. The fitting procedure uses the nls function with the port algorithm.

Usage

fit_CWCurve(
  values,
  n.components.max,
  fit.failure_threshold = 5,
  fit.method = "port",
  fit.trace = FALSE,
  fit.calcError = FALSE,
  LED.power = 36,
  LED.wavelength = 470,
  cex.global = 0.6,
  sample_code = "Default",
  output.path,
  output.terminal = TRUE,
  output.terminalAdvanced = TRUE,
  plot = TRUE,
  ...
)

Arguments

values	RLum.Data.Curve or data.frame (required): x, y data of measured values (time and counts). See examples.
n.components.max	vector (optional): maximum number of components that are to be used for fitting. The upper limit is 7.
fit.failure_threshold	vector (with default): limits the failed fitting attempts.
fit.method	character (with default): select fit method, allowed values: 'port' and 'LM'. 'port' uses the 'port' routine from the function nls 'LM' utilises the function nlsLM from the package minpack.lm and with that the Levenberg-Marquardt algorithm.
fit.trace	logical (with default): traces the fitting process on the terminal.
fit.calcError	logical (with default): calculate 1-sigma error range of components using stats::confint
LED.power	numeric (with default): LED power (max.) used for intensity ramping in mW/cm^2. Note: The value is used for the calculation of the absolute photoionisation cross section.
LED.wavelength	numeric (with default): LED wavelength used for stimulation in nm. Note: The value is used for the calculation of the absolute photoionisation cross section.
cex.global	numeric (with default): global scaling factor.
sample_code	character (optional): sample code used for the plot and the optional output table (mtext).
output.path	character (optional): output path for table output containing the results of the fit. The file name is set automatically. If the file already exists in the directory, the values are appended.
output.terminal	logical (with default): terminal output with fitting results.
output.terminalAdvanced	logical (with default): enhanced terminal output. Requires output.terminal = TRUE. If output.terminal = FALSE no advanced output is possible.
plot	logical (with default): returns a plot of the fitted curves.
...	further arguments and graphical parameters passed to plot.

Details

Fitting function

The function for the CW-OSL fitting has the general form:

y = I0_{1}*\lambda_{1}*exp(-\lambda_1*x) + ,\ldots, + I0_{i}*\lambda_{i}*exp(-\lambda_i*x)

where 0 < i < 8

and \lambda is the decay constant
and I0 the initial number of trapped electrons.

(for the used equation cf. Boetter-Jensen et al., 2003, Eq. 2.31)

Start values

Start values are estimated automatically by fitting a linear function to the logarithmized input data set. Currently, there is no option to manually provide start parameters.

Goodness of fit

The goodness of the fit is given as pseudoR^2 value (pseudo coefficient of determination). According to Lave (1970), the value is calculated as:

pseudoR^2 = 1 - RSS/TSS

where RSS = Residual~Sum~of~Squares
and TSS = Total~Sum~of~Squares

Error of fitted component parameters

The 1-sigma error for the components is calculated using the function stats::confint. Due to considerable calculation time, this option is deactivated by default. In addition, the error for the components can be estimated by using internal R functions like summary. See the nls help page for more information.

For details on the nonlinear regression in R, see Ritz & Streibig (2008).

Value

plot (optional)

the fitted CW-OSL curves are returned as plot.

table (optional)

an output table (⁠*.csv⁠) with parameters of the fitted components is provided if the output.path is set.

RLum.Results

Beside the plot and table output options, an RLum.Results object is returned.

fit: an nls object (⁠$fit⁠) for which generic R functions are provided, e.g. summary, stats::confint, profile. For more details, see nls.

output.table: a data.frame containing the summarised parameters including the error

component.contribution.matrix: matrix containing the values for the component to sum contribution plot (⁠$component.contribution.matrix⁠).

Matrix structure:
Column 1 and 2: time and rev(time) values
Additional columns are used for the components, two for each component, containing I0 and n0. The last columns cont. provide information on the relative component contribution for each time interval including the row sum for this values.

object

beside the plot and table output options, an RLum.Results object is returned.

fit: an nls object (⁠$fit⁠) for which generic R functions are provided, e.g. summary, confint, profile. For more details, see nls.

output.table: a data.frame containing the summarised parameters including the error
component.contribution.matrix: matrix containing the values for the component to sum contribution plot (⁠$component.contribution.matrix⁠).

Matrix structure:
Column 1 and 2: time and rev(time) values
Additional columns are used for the components, two for each component, containing I0 and n0. The last columns cont. provide information on the relative component contribution for each time interval including the row sum for this values.

Function version

0.5.2

How to cite

Kreutzer, S., 2023. fit_CWCurve(): Nonlinear Least Squares Fit for CW-OSL curves -beta version-. Function version 0.5.2. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J., Mercier, N., Philippe, A., Riedesel, S., Autzen, M., Mittelstrass, D., Gray, H.J., Galharret, J., 2023. Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.9.23. https://CRAN.R-project.org/package=Luminescence

Note

Beta version - This function has not been properly tested yet and should therefore not be used for publication purposes!

The pseudo-R^2 may not be the best parameter to describe the goodness of the fit. The trade off between the n.components and the pseudo-R^2 value is currently not considered.

The function does not ensure that the fitting procedure has reached a global minimum rather than a local minimum!

Author(s)

Sebastian Kreutzer, Institute of Geography, Heidelberg University (Germany) , RLum Developer Team

References

Boetter-Jensen, L., McKeever, S.W.S., Wintle, A.G., 2003. Optically Stimulated Luminescence Dosimetry. Elsevier Science B.V.

Lave, C.A.T., 1970. The Demand for Urban Mass Transportation. The Review of Economics and Statistics, 52 (3), 320-323.

Ritz, C. & Streibig, J.C., 2008. Nonlinear Regression with R. In: R. Gentleman, K. Hornik, G. Parmigiani, eds., Springer, p. 150.

See Also

fit_LMCurve, plot,nls, RLum.Data.Curve, RLum.Results, get_RLum, minpack.lm::nlsLM

Examples

##load data
data(ExampleData.CW_OSL_Curve, envir = environment())

##fit data
fit <- fit_CWCurve(values = ExampleData.CW_OSL_Curve,
                   main = "CW Curve Fit",
                   n.components.max = 4,
                   log = "x")

Luminescence documentation built on Nov. 3, 2023, 5:09 p.m.