In situ gamma spectrometry is a useful technique used by the Luminescence and ESR dating community to improve the representativity of dose rate measurements in the context of gamma dose rate heterogeneities around dated material. This paper presents gamma, a new package and its graphical user interface gammaShiny, allowing a reliable and reproducible workflow for in situ gamma spectrometry data analysis in the context of luminescence and ESR dating.
2019 | Radiation Measurements
LumReader: Designing your luminescence experiment with R
by Strebler, David, Riedesel, Svenja, King, Georgina, Brill, Dominik, Brückner, Helmut
During the last decades, luminescence dating has entered a phase of diversification. This evolution is strongly linked to a series of technical advances, including but not limited to the improvement of EMCCD cameras and the use of violet and yellow LEDs. New measurement techniques have been developed, such as post infra-red infra-red stimulated luminescence (postIR-IRSL) measurement protocols and thermally-transferred OSL (TT-OSL), and the luminescence properties of new materials, such as gypsum and apatite, have been reinvestigated. The appropriate configuration of detection equipment is key to the design of new experimental investigations. The R-package LumReader has been designed to simulate both the detection properties of luminescence readers and the emission properties of materials. It allows optimisation of the experimental detection window for a given filter and detector (PMT or EMCCD camera) combination through comparison of the detection window, the stimulation signal and the luminescence emission of the studied material. With the development of a reference database and its flexibility for accommodating user defined functions, this package will allow the spectral information of any luminescence experiment to be simulated, also facilitating experimental design.
2019 | Ancient TL
‘RCarb’: Dose Rate Modelling of Carbonate-Rich Samples - an Implementation of Carb in R -
by Kreutzer, Sebastian, Mauz, Barbara, Martin, Loı̈c, Mercier, Norbert
Geochemical conditions (e.g., pH-value, tem- perature, availability of CO2) in carbonate-rich sedimentary environments lead to cementation processes, i.e., air or water in the pore space are substituted by mineral phases. Consequently, in such environments the conventional formalism of estimating the environmental dose rate from U, Th and K concentrations (pores are filling by air or water) cannot be overall correct. In 2008, Nathan & Mauz (2008) presented a model to account for dose-rate changes occurring when carbonate minerals replace air and water in the pore space between mineral grains. The underlying MATLAB⃝R code (Carb) was later published by Mauz & Hoffmann (2014). Here we present an implementation of this tool using the statistical programming environment R. Our implementation does not alter the under- lying model and its assumption but comes with an updated code basis published as R package under GPL-3 licence conditions.
2017 | Quaternary Geochronology
Using R for TL dating
by Strebler, David, Burow, Christoph, Brill, Dominik, Br ckner, Helmut
Whilst optically stimulated luminescence (OSL) is commonly more suitable for sediment dating because of faster signal resetting, thermoluminescence (TL) remains important for dating burnt material, e.g. in archaeological contexts, or for studying the luminescence properties of different materials. A lack of user-optimized analysis software for TL data has exacerbated the decline of TL dating in comparison to OSL. However, exciting developments in TL dating of flint and calcite indicate a rise in application of this underused method. R is a programming language and environment for statistical computing and graphics. It provides a wide variety of statistical and graphical techniques and is highly extendable. A package specifically designed for luminescence data analysis is available. However, it mainly includes functions for the analysis of OSL data. The TLdating package is a new R package specifically dedicated to TL dating. This package is designed to be fully compatible with the existing Luminescence package and is user-friendly. It includes functions for TL data pretreatment and palaeodose estimation using the MAAD and the SAR protocols. The functionality of the TLdating package is evaluated using heated flints from Taibeh, Jordan.
2017 | Ancient TL
Software in the context of luminescence dating: status, concepts and suggestions exemplified by the R package “Luminescence”
by Kreutzer, Sebastian, Burow, Christoph, Dietze, Michael, Fuchs, Margret C, Fischer, Manfred, Schmidt, Christoph
The relevance of luminescence dating is reflected by the steadily growing quantity of published data. At the same time, the amount of data available for analysis has increased due to technological and methodological advances. Routinely, luminescence data are analysed using a mixture of commercially available software, self-written tools and specific solutions. Based on a luminescence dating literature screening we show how rarely articles report on the software used for the data analysis and we discuss potential problems arising from this. We explore the growing importance of the statistical programming language R in general and especially its reflection in recent software developments in the context of luminescence dating. Specifically, for the R package “Luminescence” we show how the transparency, flexibility and reliability of tools used for the data analysis have been improved. We finally advocate for more transparency if unvalidated software solutions are used and we emphasise that more attention should be paid to the tools used for analysing the data.
2016 | Ancient TL
Bayesian statistics in luminescence dating: The ’baSAR’-model and its implementation in the R package ’Luminescence’
Kinetic models of quartz luminescence have gained an important role for predicting experimental results and for understanding charge transfers in (natural) quartz. Here we present and discuss the new R package “RLumModel”, offering an easy-to-use tool for simulating quartz luminescence signals (TL, OSL, LM-OSL and RF) based on five integrated and published parameter sets. Simulation commands can be created (a) using the Risø Sequence Editor, (b) a built-in SAR sequence generator or (c) self-explanatory keywords for customised sequences. Results can be analysed seamlessly using the R package “Luminescence” along with a visualisation of concentrations of electrons and holes in every trap/centre as well as in the valence and conduction band during all stages of the simulation. Examples of simulated luminescence phenomena and dating protocols are given, and the presented code snippets are available in the supplementary material. Package and source code are provided under the General Public Licence (GPL-3) conditions.
2016 | Quaternary Geochronology
The abanico plot: visualising chronometric data with individual standard errors
by Dietze, M., Kreutzer, S., Burow, C., Fuchs, M. C, Fischer, M., Schmidt, C.
Numerical dating methods in Quaternary science are faced with the need to adequately visualise data consisting of estimates that have differing standard errors. Recent approaches either focus on the display of age frequency distributions that ignore the standard errors or on radial plots, that support comparisons between estimates allowing for their differing precisions, but without giving an explicit picture of the age frequency distribution. Hence, visualising both aspects requires at least two plots. Here, an alternative is introduced: The abanico plot. It combines both aspects and therefore allows comprehensive presentation of chronometric data with individual standard errors. It extends the radial plot by a kernel density estimate plot, histogram or dot plot and contains elements that link both plot types. As part of the R package "Luminescence"" (version >= 0.4.5), the abanico plot is designed as the final part of a comprehensive analysis chain of luminescence data but is open to a wide range of other Quaternary dating communities, as illustrated by several examples.
2016 | Ancient TL
RLumShiny - A graphical user interface for the R Package ’Luminescence’
by Burow, Christoph, Kreutzer, Sebastian, Dietze, Michael, Fuchs, Margret C, Fischer, Manfred, Schmidt, Christoph, Brückner, Helmut
Since the release of the R package ’Luminescence’ in 2012 the functionality of the package has been greatly enhanced by implementing further functions for measurement data processing, statistical analysis and graphical output. Along with the accompanying increase in complexity of the package, working with the command-line interface of R can be tedious, especially for users without previous experience in programming languages. Here, we present a collection of interactive web applications that provide a user-friendly graphical user interface for the ’Luminescence’ package. These applications can be accessed over the internet or used on a local computer using the R package ’RLumShiny’. A short installation and usage guide is accompanied by the presentation of two exemplary applications.
2015 | Ancient TL
A new R function for the Internal External Uncertainty (IEU) model
A new function (calc IEU) is now available in the latest version of the R Luminescence package (version 0.4.2). The calc IEU function can be used to calculate an equivalent dose (De) value for a given dose distribution using the Internal External Uncertainty (IEU) model. The IEU model is used in luminescence dating to determine a De value for a partially-bleached sample by calculating the weighted mean from the well bleached part of a partially-bleached population. The new calc IEU function au- tomates the calculation of the IEU model so that the results are produced rapidly and reproducibly. This is advantageous as the user can easily perform sensitivity tests of the model in response to changing input parameters.
2015 | Quaternary International
Data processing in luminescence dating analysis: An exemplary workflow using the R package ‘Luminescence’
by Fuchs, M. C., Kreutzer, S., Burow, C., Dietze, M., Fischer, M., Schmidt, C., Fuchs, M.
The first version of the R package “Luminescence” was released and published in 2012. Since then, the package has been continuously improved by implementing further measurement protocols, adding age models, and extending functions. In geoscientific applications, luminescence dating requires a series of data processing procedures. A comprehensive and replicate analysis of luminescence data using the R package “Luminescence”, therefore, suggests combining selected functions. With this contribution, we provide a practical example of a workﬂow from reading measurement data to age modelling. The exemplary data processing routine is applied to an OSL data set of a ﬂuvial sediment sample from the Pamir Mountains.
2013 | Ancient TL
A practical guide to the R package Luminescence
by Dietze, Michael, Kreutzer, Sebastian, Fuchs, Margret C, Burow, Christoph, Fischer, Manfred, Schmidt, Christoph
A practical guide for the R package “Luminescence” is provided. An introduction on data types in R is given first, followed by a guideline on how to import, analyse and visualise typical SAR- OSL measurement data.
2012 | Ancient TL
Introducing an R package for luminescence dating analysis
by Kreutzer, S., Schmidt, C., Fuchs, M. C., Dietze, M., Fischer, M., Fuchs, M.
For routine luminescence dating applications the commonly used Risø readers are bundled with analysis software, such as Viewer or Analyst. These software solutions are appropriate for most of the regular dating and publication jobs and enable assessment of luminescence characteristics and provide basic statistical data treatment. However, for further statistical analysis and data treatments, this software may reach its limits. In such cases, open programming languages are a more appropriate approach. Here, we present the R package “Luminescence” for a more flexible handling of luminescence data and related plotting purposes using the statistical programming language R. The R language as well as the package and the source code are provided under the General Public License (GPL) conditions and are available for free. The basic functionality of the package is described along with three application examples. This package is not an alternative to the existing software (Analyst, Viewer) but may provide a collection of additional tools to analyse luminescence data and serve as a platform for further contributions.