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Trapped Charge Data Analysis: Task View

Sebastian Kreutzer (last update: 2024-02-19)

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: 43

Age calculation

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 [1.8]       
    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 [0.3.1]       
    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] [01.02.19]       
    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 exchange

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 calculation

  • μRate [ 2022.5.3]      
    Online dose rate calculator for trapped charge dating
     https://miu-rate.polsl.pl/miu-rate/
    Tudyka, K., Koruszowic, M., Osadnik, R., Adamiec, G., Moska, P., Szymak, A., Bluszcz, A., Zhang, J., Kolb, T., Poręba, G., 2022. μRate: An online dose rate calculator for trapped charge dating. Archaeometry, 65(2), 423-443.

Dose rate modelling

Dosimetry

ESR data analysis

Gamma-ray spectrometry

Luminescence data analysis

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 [0.1.9]       
    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] [27.01.17]       
    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

Legend

Icon Meaning
[0.1] Indicates the latest available version, here 0.1
This software is open source
Type of software (here: R package)

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