Package index • carbondate

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.

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)

PolyaUrnBivarDirichlet(): Calibrate and Summarise Multiple Radiocarbon Samples via a Bayesian Non-Parametric DPMM (with Polya Urn Updating)
WalkerBivarDirichlet(): Calibrate and Summarise Multiple Radiocarbon Samples via a Bayesian Non-Parametric DPMM (with Walker Updating)
FindPredictiveCalendarAgeDensity(): Find Predictive Estimate of Shared Calendar Age Density from Bayesian Non-Parametric DPMM Output
PlotPredictiveCalendarAgeDensity(): Plot Predictive Estimate of Shared Calendar Age Density from Bayesian Non-Parametric DPMM Output
PlotNumberOfClusters(): Plot Number of Calendar Age Clusters Estimated in Bayesian Non-Parametric DPMM Output
PlotCalendarAgeDensityIndividualSample(): Plot Posterior Calendar Age Estimate for an Individual Determination after Joint Calibration
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.

PPcalibrate(): Model Occurrence of Multiple Radiocarbon Samples as a Variable-Rate Poisson Process
PPcalibrateMixedCurves(): Model Occurrence of Multiple Radiocarbon Samples as a Variable-Rate Poisson Process when the Samples Come from a Variety of Environments and Multiple Calibration Curves are Needed
FindPosteriorMeanRate(): Find Posterior Mean Rate of Sample Occurrence for Poisson Process Model
PlotPosteriorMeanRate(): Plot Posterior Mean Rate of Sample Occurrence for Poisson Process Model
PlotNumberOfInternalChanges(): Plot Number of Changepoints in Rate of Sample Occurrence for Poisson Process Model
PlotPosteriorChangePoints(): Plot Calendar Ages of Changes in Rate of Sample Occurrence for Poisson Process Model
PlotPosteriorHeights(): Plot Heights of Segments in Rate of Sample Occurrence for Poisson Process Model
PlotCalendarAgeDensityIndividualSample(): Plot Posterior Calendar Age Estimate for an Individual Determination after Joint Calibration
PlotRateIndividualRealisation(): Plot Individual Realisations of Posterior Rate of Sample Occurrence for Poisson Process Model

Annotating the Summary Plots

Functions that can be used to annotate the various summary plots.

AddTextPlot(): Add Text Annotation to Various Summary Plots
AddLinePlot(): Add Straight Lines to Various Summary Plots
AddShadingPlot(): Add Shading to Various Summary Plots

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.

PlotGelmanRubinDiagnosticSingleChain(): Plot Histogram of the Gelman-Rubin Convergence Diagnostic for a Single MCMC Chain
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).

FindSummedProbabilityDistribution(): Find the summed probability distribution (SPD) for a set of radiocarbon observations
InterpolateCalibrationCurve(): Interpolate a calibration curve at a set of calendar ages
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.

alces: Example real-life data - Alces in Yukon and Alaska
armit: Example real-life data - Population Decline in Iron Age Ireland
bison: Example real-life data - Bison in Yukon and Alaska
buchanan: Example real-life data - Palaeo-Indian demography
cervus: Example real-life data - Cervus in Yukon and Alaska
equus: Example real-life data - Equus in Yukon and Alaska
human: Example real-life data - Humans in Yukon and Alaska
kerr: Example real-life data - Irish Rath
mammuthus: Example real-life data - Mammuthus in Yukon and Alaska
pp_uniform_phase: Example artificial data - Uniform Phase
pp_uniform_phase_marine: Example artificial marine data - Uniform Phase
pp_uniform_phase_mixed: Example artificial data requiring multiple calibration curves - Uniform Phase
two_normals: Example artificial data - Mixture of Normal Phases
two_normals_marine: Example artificial data - Mixture of Normal Phases Using Marine20 calibration curve

Calibration curves

intcal04: IntCal04 calibration curve
intcal09: IntCal09 calibration curve
intcal13: IntCal13 calibration curve
intcal20: IntCal20 calibration curve
intcal98: IntCal98 calibration curve
shcal04: SHCal04 calibration curve
shcal13: SHCal13 calibration curve
shcal20: SHCal20 calibration curve
marine04: Marine04 calibration curve
marine09: Marine09 calibration curve
marine13: Marine13 calibration curve
marine20: Marine20 calibration curve