RadialPlotter: Statistical age model optimization (with a Maximum Likelihood...

Description Usage Arguments Details Value Note References See Also Examples

View source: R/RadialPlotter.R

Description

Depending on the specified number of components, this function performs statistical age models analysis reviewed in Galbraith and Roberts (2012) dynamically using a Maximum Likelihood Estimation method. Age models that can be applied include: central age model (CAM), minimum age model (MAM), and finite mixture age model (FMM).

Usage

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RadialPlotter(EDdata, ncomp = 0, addsigma = 0, 
              maxcomp = 6, algorithm = c("port","lbfgsb"),
              plot = TRUE, pcolor = "blue", psize = 1.5, 
              kratio = 0.3, zscale = NULL)

Arguments

EDdata

matrix(required): a two-column matrix (i.e., equivalent dose values and
associated standard errors)

ncomp

integer(with default): number of components, -1=MAM3, -2=MAM4, 1=CAM,
0 means fitting FMM automatically, and >=1 means fitting FMM
with a given number of components

addsigma

numeric(with default): additional uncertainty

maxcomp

integer(with default): maximum number of components in FMM

algorithm

character(with default): algorithm used for optimizing MAM,
default algorithm="port"

plot

logical(with default): draw a radial plot or not

pcolor

character(with default): color of a data point, input colors() to see more available colors

psize

numeric(with default): size of a data point

kratio

numeric(with default): argument controlling the shape of zscale

zscale

vector(optional): argument controlling the scale of z-axis.
Example: zscale=seq(min(EDdata),max(EDdata),by=3L)

Details

Both CAM and FMM are fitted using a iterative Maximum Likelihood Estimation procedure outlined by Galbraith (1988), while MAM can be estimated using either the "L-BFGS-B" algorithm (R function optim in package stats) or the "port" algorithm (R function nlminb in package stats).

Value

Return an object of S3 class "RadialPlotter" that contains the following elements:

pars

optimizaed parameters

bic

calculated Bayesian Information Criterion (BIC) value

maxlik

optimized maximum logged likelihood value

Note

Function RadialPlotter was given the same name as the Java package RadialPlotter written by Pieter Vermeesch (Vermeesch, 2009). Note that this function fits a model in log-scale, hence any minus equivalent dose value is not allowed, and that the procedure will return an error if any standard error of a parameter cannot be estimated by numerical difference-approximation.

The original S code for drawing a radial plot was written by Rex Galbraith and was transformed to R by Sebastian Kreutzer. The code for drawing radial plot in this function was modified from package Luminescence written by Kreutzer et al. (2012). We thank Dr Rex Galbraith for his permission to modify and bundle the code to this function. We also thank Dr Silke Schmidt, Dr Helena Rodnight, Dr Xian-Jiao Ou, and Dr Amanda Keen-Zebert for providing published OSL data sets to test this routine.

References

Galbraith RF, 1988. Graphical display of estimates having differing standard errors. Technometrics, 30(3): 271-281.

Galbraith RF, 1990. The radial plot: Graphical assessment of spread in ages. International Journal of Radiation Applications and Instrumentation. Part D. Nuclear Tracks and Radiation Measurements, 17(3): 207-214.

Galbraith RF, Green P, 1990. Estimating the component ages in a finite mixture. International Journal of Radiation Applications and Instrumentation. Part D. Nuclear Tracks and Radiation Measurements, 17: 197-206.

Galbraith RF, Laslett GM, 1993. Statistical models for mixed fission track ages. Nuclear Tracks And Radiation Measurements, 21(4): 459-470.

Galbraith RF, 1994. Some applications of radial plots. Journal of the American Statistical Association, 89(428): 1232-1242.

Galbraith RF, Roberts RG, Laslett GM, Yoshida H, Olley JM, 1999. Optical dating of single grains of quartz from Jinmium rock shelter, northern Australia. Part I: experimental design and statistical models. Archaeometry, 41(2): 339-364.

Galbraith RF, 2005. Statistics for fission track analysis. Chapman & Hall/CRC Press.

Galbraith RF, 2010. On plotting OSL equivalent doses. Ancient TL, 28(1): 1-10.

Galbraith RF, Roberts RG, 2012. Statistical aspects of equivalent dose and error calculation and display in OSL dating: an overview and some recommendations. Quaternary Geochronology, 11: 1-27.

Further reading

Duller GAT, 2008. Single-grain optical dating of Quaternary sediments: why aliquot size matters in luminescence dating. Boreas, 37(4): 589-612.

Kreutzer S, Schmidt C, Fuchs MC, Dietze M, Fischer M, Fuchs M, 2012. Introducing an R package for luminescence dating analysis. Ancient TL, 30(1): 1-8. Software is freely available at https://CRAN.R-project.org/package=Luminescence.

Rodnight H, 2008. How many equivalent dose values are needed to obtain a reproducible distribution? Ancient TL, 26(1): 3-10.

Rodnight H, Duller GAT, Wintle AG, Tooth S, 2006. Assessing the reproducibility and accuracy of optical dating of fluvial deposits. Quaternary Geochronology, 1(2): 109-120.

Schmidt S, Tsukamoto S, Salomon E, Frechen M, Hetzel R, 2012. Optical dating of alluvial deposits at the orogenic front of the andean precordillera (Mendoza, Argentina). Geochronometria, 39(1): 62-75.

Vermeesch P, 2009. RadialPlotter: a Java application for fission track, luminescence and other radial plots. Radiation Measurements, 44: 409-410. Software is freely available at http://www.ucl.ac.uk/~ucfbpve/radialplotter/.

See Also

mcMAM; mcFMM;
dbED; psRadialPlot; EDdata

Examples

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  data(EDdata)
  # Find out the appropriate number of components 
  # in FMM and fit automatically.
  RadialPlotter(EDdata$al3,zscale=seq(24,93,7))

  # Fit MAM3 (not run). 
  # RadialPlotter(EDdata$gl11,ncomp=-1,zscale=seq(20,37,3))

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