Package index
Calibration of a Single Radiocarbon Sample
Function to independently calibrate a single radiocarbon determination against a given calibration curve. The rest of the library concerns calibration of multiple (related) radiocarbon samples.
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CalibrateSingleDetermination() - Calibrate a Single Radiocarbon Determination
Bayesian Non-Parametric Joint Density Estimation
Functions providing a rigorous Bayesian non-parametric alternative to summed probability distributions (SPDs). These functions enable the calibration and calendar age summarisation of multiple related radiocarbon samples (and provide plotting of the results)
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PolyaUrnBivarDirichlet() - Calibrate and Summarise Multiple Radiocarbon Samples via a Bayesian Non-Parametric DPMM (with Polya Urn Updating)
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WalkerBivarDirichlet() - Calibrate and Summarise Multiple Radiocarbon Samples via a Bayesian Non-Parametric DPMM (with Walker Updating)
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FindPredictiveCalendarAgeDensity() - Find Predictive Estimate of Shared Calendar Age Density from Bayesian Non-Parametric DPMM Output
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PlotPredictiveCalendarAgeDensity() - Plot Predictive Estimate of Shared Calendar Age Density from Bayesian Non-Parametric DPMM Output
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PlotNumberOfClusters() - Plot Number of Calendar Age Clusters Estimated in Bayesian Non-Parametric DPMM Output
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PlotCalendarAgeDensityIndividualSample() - Plot Posterior Calendar Age Estimate for an Individual Determination after Joint Calibration
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PlotConvergenceData() - Plot KL Divergence of Predictive Density to Assess Convergence of Bayesian Non-Parametric DPMM Sampler
Poisson Process Modelling
Functions for modelling the occurrence of radiocarbon samples as a variable-rate (inhomogeneous) Poisson process. This is a further (analogous) approach that enables the rigorous summarisation of calendar age information from multiple related radiocarbon samples.
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PPcalibrate() - Model Occurrence of Multiple Radiocarbon Samples as a Variable-Rate Poisson Process
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FindPosteriorMeanRate() - Find Posterior Mean Rate of Sample Occurrence for Poisson Process Model
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PlotPosteriorMeanRate() - Plot Posterior Mean Rate of Sample Occurrence for Poisson Process Model
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PlotNumberOfInternalChanges() - Plot Number of Changepoints in Rate of Sample Occurrence for Poisson Process Model
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PlotPosteriorChangePoints() - Plot Calendar Ages of Changes in Rate of Sample Occurrence for Poisson Process Model
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PlotPosteriorHeights() - Plot Heights of Segments in Rate of Sample Occurrence for Poisson Process Model
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PlotCalendarAgeDensityIndividualSample() - Plot Posterior Calendar Age Estimate for an Individual Determination after Joint Calibration
Common convergence plotting functions
Functions that can be used to plot information on convergence of the MCMC for both the Bayesian non-parametric DPMM and the Poisson process approaches to calibration and summarisation.
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PlotGelmanRubinDiagnosticSingleChain() - Plot Histogram of the Gelman-Rubin Convergence Diagnostic for a Single MCMC Chain
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PlotGelmanRubinDiagnosticMultiChain() - Plot Histogram of the Gelman-Rubin Convergence Diagnostic for Multiple Independent MCMC Chains
Helper functions
General functions that may be of use. However, please do not use SPDs in your inference (use either the Bayesian non-parametric or Poisson Process approaches described above).
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FindSummedProbabilityDistribution() - Find the summed probability distribution (SPD) for a set of radiocarbon observations
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InterpolateCalibrationCurve() - Interpolate a calibration curve at a set of calendar ages
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GenerateOxcalCode() - Outputs code suitable for running in OxCal from a series of radiocarbon determinations
Example datasets
Sets of radiocarbon determinations, either from real-life examples or artificially-generated, that can be used as examples with the calibration functions.
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alces - Example real-life data - Alces in Yukon and Alaska
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armit - Example real-life data - Population Decline in Iron Age Ireland
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bison - Example real-life data - Bison in Yukon and Alaska
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buchanan - Example real-life data - Palaeo-Indian demography
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cervus - Example real-life data - Cervus in Yukon and Alaska
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equus - Example real-life data - Equus in Yukon and Alaska
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human - Example real-life data - Humans in Yukon and Alaska
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kerr - Example real-life data - Irish Rath
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mammuthus - Example real-life data - Mammuthus in Yukon and Alaska
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pp_uniform_phase - Example artificial data - Uniform Phase
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two_normals - Example artificial data - Mixture of Normal Phases