Trapped Charge Data Analysis: Task View
Sebastian Kreutzer (last update: 2022-06-10)
About
In analogy of the CRAN task view lists, this list provides an overview of freely available tools for trapped charge (dating) data analysis (e.g., luminescence and ESR data). Tasks, software tools and data repositories are ordered alphabetically. URLs are automatically tested every time this list is updated, information from R packages are extracted and updated automatically from CRAN (version, description).
Not listed are:
- Single scripts (e.g., functions or XLS-sheets usually without a dedicated name)
- Software not accessible free of charge through the internet
If your software is missing or you did spot a mistake, please let me know via https://github.com/RLumSK/luminescence-tv/issues.
Mission tasks
Total number of listed tools: 40
Age calculation
- AGE [2009-11-14]
Program for the calculation of luminescence ages estimates
http://ancienttl.org/ATL_27-2_2009/ATL_27-2_Grun_supplement.zip
http://ancienttl.org/ATL_27-2_2009/ATL_27-2_Grun_p45-46.pdf
- DRAC [1.2]
Online dose rate and luminescence age calculator
http://www.aber.ac.uk/en/dges/research/quaternary/luminescence-research-laboratory/dose-rate-calculator/
Durcan, J.A., King, G.E., Duller, G.A.T., 2015. DRAC: Dose Rate and Age Calculator for trapped charge dating. Quaternary Geochronology 28, 54–61. doi: https://doi.org/10.1016/j.quageo.2015.03.012
- DRc
Dose Rate Calculator for luminescence and ESR Dating (Java application)
https://www.dropbox.com/s/nvn6n68lt4to8ur/DRcalculator.exe?dl=0
Tsakalos, E., Christodoulakis, J., Charalambous, L., 2015. The Dose Rate Calculator (DRc) for Luminescence and ESR Dating-a Java Application for Dose Rate and Age Determination. Archaeometry 58, 347–352. doi: https://doi.org/10.1111/arcm.12162
- eM-Age [version.1.1] [Mon, 14 Dec 2020 10:33:38 GMT]
Application for luminescence age calculation based on Dose Rate and Age Calculator (DRAC) and Analyst
https://github.com/yomismovk/eM-Age-program | Source code: https://github.com/yomismovk/eM-Age-program
Pérez-Garrido, C., 2020. eM-Age (excel Macro for Age calculation), a new application for luminescence age calculation based on Dose Rate and Age Calculator (DRAC) and Analyst. Ancient TL 38, 21–24.
Chronological modelling
- ArchaeoChron [0.1]
Provides a list of functions for the Bayesian modeling of archaeological chronologies. The Bayesian models are implemented in ‘JAGS’ (‘JAGS’ stands for Just Another Gibbs Sampler. It is a program for the analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation. See http://mcmc-jags.sourceforge.net/ and “JAGS Version 4.3.0 user manual”, Martin Plummer (2017) https://sourceforge.net/projects/mcmc-jags/files/Manuals/.). The inputs are measurements with their associated standard deviations and the study period. The output is the MCMC sample of the posterior distribution of the event date with or without radiocarbon calibration.
https://CRAN.R-project.org/package=ArchaeoChron
- ArchaeoPhases [1.6]
Provides a list of functions for the statistical analysis of archaeological dates and groups of dates. It is based on the post-processing of the Markov Chains whose stationary distribution is the posterior distribution of a series of dates. Such output can be simulated by different applications as for instance ‘ChronoModel’ (see https://chronomodel.com/), ‘Oxcal’ (see https://c14.arch.ox.ac.uk/oxcal.html) or ‘BCal’ (see https://bcal.shef.ac.uk/). The only requirement is to have a csv file containing a sample from the posterior distribution. Note that this package interacts with data available through the ‘ArchaeoPhases.dataset’ package which is available in a separate repository. The size of the ‘ArchaeoPhases.dataset’ package is approximately 4 MB.
https://CRAN.R-project.org/package=ArchaeoPhases
Philippe, A., Vibet, M.-A., 2018. Analysis of Archaeological Phases using the CRAN Package ArchaeoPhases. Journal of Statistical Software 1–26. doi: https://doi.org/10.18637/jss.v000.i00
- BayLum [0.2.1]
Bayesian analysis of luminescence data and C-14 age estimates. Bayesian models are based on the following publications: Combes, B. & Philippe, A. (2017) doi:10.1016/j.quageo.2017.02.003 and Combes et al (2015) doi:10.1016/j.quageo.2015.04.001. This includes, amongst others, data import, export, application of age models and palaeodose model.
https://CRAN.R-project.org/package=BayLum | Source code: https://github.com/crp2a/BayLum
Philippe, A., Guérin, G., Kreutzer, S., 2019. BayLum - An R package for Bayesian analysis of OSL ages: An introduction. Quaternary Geochronology 49, 16–24. doi: https://doi.org/10.1016/j.quageo.2018.05.009
- ChronoModel [2.0.18] [2019-02-01]
Chronological Modelling of Archaeological Data using Bayesian Statistics with an advanced graphical user interface
https://chronomodel.com | Source code: https://github.com/Chronomodel/chronomodel
- mcmcSAM [Mon, 07 Jan 2019 14:17:22 GMT]
Analyzing statistical age models for equivalent dose and burial age determination using a Markov Chain Monte Carlo method
https://github.com/pengjunUCAS/mcmcSAM | Source code: https://github.com/pengjunUCAS/mcmcSAM 
Peng, J., 2020. Analyzing statistical age models to determine the equivalent dose and burial age using a Markov chain Monte Carlo method. Geochronometria 0, 1–14.
- RChronoModel [0.4]
Provides a list of functions for the statistical analysis and the post-processing of the Markov Chains simulated by ChronoModel (see http://www.chronomodel.fr for more information). ChronoModel is a friendly software to construct a chronological model in a Bayesian framework. Its output is a sampled Markov chain from the posterior distribution of dates component the chronology. The functions can also be applied to the analyse of mcmc output generated by Oxcal software.
https://CRAN.R-project.org/package=RChronoModel
Philippe, A., Vibet, M.-A., 2017. Analysis of Archaeological Phases using the CRAN Package RChronoModel. doi: https://doi.org/10.13140/RG.2.2.19659.59688
Data mining
- INQUA Dunes Atlas
Collection of luminescence ages from sand dunes world wide
http://www.dri.edu/inquadunesatlas
Lancaster, N., Wolfe, S., Thomas, D., Bristow, C., Bubenzer, O., Burrough, S., Duller, G., Halfen, A., Hesse, P., Roskin, J., Singhvi, A., Tsoar, H., Tripaldi, A., Yang, X., Zárate, M., 2015. The INQUA Dunes Atlas chronologic database. Quaternary International 410, 3–10. doi: https://doi.org/10.1016/j.quaint.2015.10.044
- OCTOPUS
Open cosmogenic nuclide and luminescence data database
https://earth.uow.edu.au
Codilean, A.T., Munack, H., Cohen, T.J., Saktura, W.M., Gray, A., Mudd, S.M., 2018. OCTOPUS: an open cosmogenic isotope and luminescence database. Earth Syst. Sci. Data 10, 2123–2139. doi: https://doi.org/10.5194/essd-10-2123-2018
Dose rate modelling
- DosiVox [2018-12-03]
A Geant 4-based software for dosimetry simulations relevant to luminescence and ESR dating techniques
http://www.iramat-crp2a.cnrs.fr/spip/spip.php?article144&lang=fr
Martin, L., Incerti, S., Mercier, N., 2015. DosiVox: Implementing Geant 4-based software for dosimetry simulations relevant to luminescence and ESR dating techniques. Ancient TL 33, 1–10. http://ancienttl.org/ATL_33-1_2015/ATL_33-1_Martin_p1-10.pdf
- DosiVox2D [2018-12-03]
A Geant 4-based software for dosimetry simulations relevant to luminescence and ESR dating techniques; simplified version in comparison to DosiVox
http://www.iramat-crp2a.cnrs.fr/spip/spip.php?article144&lang=fr
- RCarb [0.1.5]
Translation of the ‘MATLAB’ program ‘Carb’ (Nathan and Mauz 2008 doi:10.1016/j.radmeas.2007.12.012; Mauz and Hoffmann 2014) for dose rate modelling for carbonate-rich samples in the context of trapped charged dating (e.g., luminescence dating) applications.
https://CRAN.R-project.org/package=RCarb | Source code: https://github.com/R-Lum/Rcarb
Kreutzer, S., Mauz, B., Martin, L., Mercier, N., 2019. “RCarb”: Dose Rate Modelling of Carbonate-Rich Samples - an Implementation of Carb in R . Ancient TL 37, 1–8.
Dosimetry
ESR data analysis
Gamma-ray spectrometry
Luminescence data analysis
- Analyst [4.57]
The standard programme to analyse luminescence data
http://users.aber.ac.uk/ggd/
Duller, G.A.T., 2015. The Analyst software package for luminescence data: overview and recent improvements. Ancient TL 33, 35–42. http://ancienttl.org/ATL_33-1_2015/ATL_33-1_Duller_p35-42.pdf
- LDAC [v1.0.1] [Fri, 11 Feb 2022 12:46:30 GMT]
A Microsoft Excel Visual Basic for Application (VBA)-based package which can be used to assemble OSL age information and associated calculations. This platform applies statistical models to determine equivalent dose (De) values and render corresponding OSL age estimates. This software is fully applicable for De measurements by single grain and aliquot regeneration (SAR) and thermal transfer OSL (TT-OSL) protocols. It could also be used to calculate the dose rate and final buried age for geology/archaeology samples.
https://github.com/lesshsroc/LDAC/releases | Source code: https://github.com/Peng-Liang/LDAC
Liang, P., Forman, S.L., 2019. LDAC: An Excel-based program for luminescence equivalent dose and burial age calculations. Ancient TL 37, 21–40.
- Luminescence [0.9.19]
A collection of various R functions for the purpose of Luminescence dating data analysis. This includes, amongst others, data import, export, application of age models, curve deconvolution, sequence analysis and plotting of equivalent dose distributions.
https://CRAN.R-project.org/package=Luminescence | Source code: https://github.com/R-Lum/Luminescence
Kreutzer, S., Schmidt, C., Fuchs, M.C., Dietze, M., Fischer, M., Fuchs, M., 2012. Introducing an R package for luminescence dating analysis. Ancient TL 30, 1–8. http://ancienttl.org/ATL_30-1_2012/ATL_30-1_Kreutzer_p1-8.pdf
- numOSL [2.6]
Package for optimizing regular numeric problems in optically stimulated luminescence dating, such as: equivalent dose calculation, dose rate determination, growth curve fitting, decay curve decomposition, statistical age model optimization, and statistical plot visualization.
https://CRAN.R-project.org/package=numOSL
Peng, J., Dong, Z., Han, F., Long, H., Liu, X., 2013. R package numOSL: numeric routines for optically stimulated luminescence dating. Ancient TL 31, 41–48. http://ancienttl.org/ATL_31-2_2013/ATL_31-2_Peng_p41-48.pdf
- PTanalyse [1.51]
Proprietary software to analyse TR-OSL data
https://www.fysik.dtu.dk/english/research/radphys/research/radiation-instruments/tl_osl_reader/software
Lapp, T., Jain, M., Ankjærgaard, C., Pirtzel, L., 2009. Development of pulsed stimulation and Photon Timer attachments to the Risø TL/OSL reader. Radiation Measurements 44, 571–575. doi: https://doi.org/10.1016/j.radmeas.2009.01.012
- RLanalyse [1.3]
Proprietary software to analyse radiofluorescence data (BIN/BINX-file input required)
https://www.fysik.dtu.dk/english/research/radphys/research/radiation-instruments/tl_osl_reader/software
Lapp, T., Jain, M., Thomsen, K.J., Murray, A.S., Buylaert, J.P., 2012. New luminescence measurement facilities in retrospective dosimetry. Radiation Measurements 47, 803–808. doi: https://doi.org/10.1016/j.radmeas.2012.02.006
- tgcd [2.5]
Deconvolving thermoluminescence glow curves according to various kinetic models (first-order, second-order, general-order, and mixed-order) using a modified Levenberg-Marquardt algorithm (More, 1978) doi:10.1007/BFb0067700. It provides the possibility of setting constraints or fixing any of parameters. It offers an interactive way to initialize parameters by clicking with a mouse on a plot at positions where peak maxima should be located. The optimal estimate is obtained by “trial-and-error”. It also provides routines for simulating first-order, second-order, and general-order glow peaks.
https://CRAN.R-project.org/package=tgcd
Peng, J., Dong, Z., Han, F., 2016. tgcd: An R package for analyzing thermoluminescence glow curves. SoftwareX 1–9. doi: https://doi.org/10.1016/j.softx.2016.06.001
- TLdating [0.1.3] [2016-08-31]
https://CRAN.R-project.org/package=TLdating | Source code: https://github.com/dstreble/Tldating
Strebler, D., Burow, C., Brill, D., Brückner, H., 2017. Using R for TL dating. Quaternary Geochronology 37, 97–107. doi: https://doi.org/10.1016/j.quageo.2016.09.001
Luminescence data visualisation
Miscellaneous
Modelling
- KMS [Wed, 11 Jul 2018 01:41:12 GMT]
Collection of functions to simulate kinetic models for quartz luminescence production
https://github.com/pengjunUCAS/KMS | Source code: https://github.com/pengjunUCAS/KMS
Peng, J., Pagonis, V., 2016. Simulating comprehensive kinetic models for quartz luminescence using the R program KMS. Radiation Measurements 86, 63–70. doi: https://doi.org/10.1016/j.radmeas.2016.01.022
- RLumCarlo [0.1.8]
A collection of functions to simulate luminescence production in dosimetric materials using Monte Carlo methods. Implemented are models for delocalised transitions (e.g., Chen and McKeever (1997) doi:10.1142/2781), localised transitions (e.g., Pagonis et al. (2019) doi:10.1016/j.jlumin.2018.11.024) and tunnelling transitions (Jain et al. (2012) doi:10.1088/0953-8984/24/38/385402 and Pagonis et al. (2019) doi:10.1016/j.jlumin.2018.11.024). Supported stimulation methods are thermal luminescence (TL), continuous-wave optically stimulated luminescence (CW-OSL), linearly-modulated optically stimulated luminescence (LM-OSL), linearly-modulated infrared stimulated luminescence (LM-IRSL), and isothermal luminescence (ITL or ISO-TL).
https://CRAN.R-project.org/package=RLumCarlo | Source code: https://github.com/R-Lum/RLumCarlo
- RLumModel [0.2.10]
A collection of functions to simulate luminescence signals in quartz and Al2O3 based on published models.
https://CRAN.R-project.org/package=RLumModel | Source code: https://github.com/R-Lum/RLumModel
Friedrich, J., Kreutzer, S., Schmidt, C., 2016. Solving ordinary differential equations to understand luminescence: “RLumModel” an advanced research tool for simulating luminescence in quartz using R. Quaternary Geochronology 35, 88–100. doi: https://doi.org/10.1016/j.quageo.2016.05.004
- sandbox [0.2.1]
A flexible framework for definition and application of time/depth- based rules for sets of parameters for single grains that can be used to create artificial sediment profiles. Such profiles can be used for virtual sample preparation and synthetic, for instance, luminescence measurements.
https://CRAN.R-project.org/package=sandbox | Source code: https://github.com/coffeemuggler/sandbox
Plotting
- RLumShiny [0.2.3]
A collection of ‘shiny’ applications for the R package ‘Luminescence’. These mainly, but not exclusively, include applications for plotting chronometric data from e.g. luminescence or radiocarbon dating. It further provides access to bootstraps tooltip and popover functionality and contains the ‘jscolor.js’ library with a custom ‘shiny’ output binding.
https://CRAN.R-project.org/package=RLumShiny | Source code: https://github.com/tzerk/RLumShiny
Burow, C., Kreutzer, S., Dietze, M., Fuchs, M.C., Fischer, M., Schmidt, C., Brückner, H., 2016. RLumShiny - A graphical user interface for the R Package ’Luminescence’. Ancient TL 34, 22–32. http://ancienttl.org/ATL_34-2_2016/ATL_34-2_Burow_p22-32.pdf
Teaching
- LumReader [0.1.0] [2017-01-27]
A series of functions to estimate the detection windows of a luminescence reader based on the filters and the photomultiplier (PMT) selected. These functions also allow to simulate a luminescence experiment based on the thermoluminesce (TL) or the optically stimulated luminescence (OSL) properties of a material
https://CRAN.R-project.org/package=LumReader | Source code: https://github.com/dstreble/LumReader
Visualisation
- DensityPlotter [8.5]
Java application for Kernel Density Estimation plots
https://www.ucl.ac.uk/~ucfbpve/densityplotter/
Vermeesch, P., 2012. On the visualisation of detrital age distributions. Chemical Geology, 312-313, 190-194, doi: https://doi.org/10.1016/j.chemgeo.2012.04.021
- RadialPlotter [9.5]
Java software to create radial plots
https://www.ucl.ac.uk/~ucfbpve/radialplotter/
Vermeesch, P., 2009, RadialPlotter: a Java application for fission track, luminescence and other radial plots, Radiation Measurements, 44 (4), 409-410. doi: https://doi.org/10.1016/j.radmeas.2009.05.003
Legend
| [0.1] |
Indicates the latest available version, here 0.1 |
|
This software is open source |
|
Type of software (here: R package) |
Some of the badges are created using https://shields.io.
https://www.sciencedirect.com/science/article/pii/S1871101417300626?via%3Dihub