Package: carbondate 1.0.1

carbondate: Calibration and Summarisation of Radiocarbon Dates

Performs Bayesian non-parametric calibration of multiple related radiocarbon determinations, and summarises the calendar age information to plot their joint calendar age density (see Heaton (2022) <doi:10.1111/rssc.12599>). Also models the occurrence of radiocarbon samples as a variable-rate (inhomogeneous) Poisson process, plotting the posterior estimate for the occurrence rate of the samples over calendar time, and providing information about potential change points.

Authors:Timothy J Heaton [aut, cre, cph], Sara Al-assam [aut, cph]

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carbondate.pdf |carbondate.html✨
carbondate/json (API)
NEWS

# Install 'carbondate' in R:
install.packages('carbondate', repos = c('https://tjheaton.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/tjheaton/carbondate/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • 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
  • intcal04 - IntCal04 calibration curve
  • intcal09 - IntCal09 calibration curve
  • intcal13 - IntCal13 calibration curve
  • intcal20 - IntCal20 calibration curve
  • intcal98 - IntCal98 calibration curve
  • 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
  • shcal04 - SHCal04 calibration curve
  • shcal13 - SHCal13 calibration curve
  • shcal20 - SHCal20 calibration curve
  • two_normals - Example artificial data - Mixture of Normal Phases

On CRAN:

6.18 score 5 stars 20 scripts 148 downloads 19 exports 1 dependencies

Last updated 9 months agofrom:070f528972. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-win-x86_64OKOct 31 2024
R-4.5-linux-x86_64OKOct 31 2024
R-4.4-win-x86_64OKOct 31 2024
R-4.4-mac-x86_64OKOct 31 2024
R-4.4-mac-aarch64OKOct 31 2024
R-4.3-win-x86_64OKOct 31 2024
R-4.3-mac-x86_64OKOct 31 2024
R-4.3-mac-aarch64OKOct 31 2024

Exports:CalibrateSingleDeterminationFindPosteriorMeanRateFindPredictiveCalendarAgeDensityFindSummedProbabilityDistributionGenerateOxcalCodeInterpolateCalibrationCurvePlotCalendarAgeDensityIndividualSamplePlotConvergenceDataPlotGelmanRubinDiagnosticMultiChainPlotGelmanRubinDiagnosticSingleChainPlotNumberOfClustersPlotNumberOfInternalChangesPlotPosteriorChangePointsPlotPosteriorHeightsPlotPosteriorMeanRatePlotPredictiveCalendarAgeDensityPolyaUrnBivarDirichletPPcalibrateWalkerBivarDirichlet

Dependencies:cpp11

Determining Convergence

Rendered fromdetermining-convergence.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-01-31
Started: 2023-06-15

Independent Single Sample Calibration

Rendered fromIndependent_calibration.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-01-29
Started: 2024-01-24

Introduction to carbondate

Rendered fromcarbondate.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-01-29
Started: 2024-01-17

Non-Parametric Joint Density Estimation

Rendered fromNon-parametric-summed-density.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-01-29
Started: 2024-01-17

Poisson Process Modelling

Rendered fromPoisson-process-modelling.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-01-29
Started: 2024-01-17

Why Not to Use SPDs

Rendered fromAgainst_SPDs.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-01-31
Started: 2024-01-24

Readme and manuals

Help Manual

Help pageTopics
Example real-life data - Alces in Yukon and Alaskaalces
Example real-life data - Population Decline in Iron Age Irelandarmit
Example real-life data - Bison in Yukon and Alaskabison
Example real-life data - Palaeo-Indian demographybuchanan
Calibrate a Single Radiocarbon DeterminationCalibrateSingleDetermination
Example real-life data - Cervus in Yukon and Alaskacervus
Example real-life data - Equus in Yukon and Alaskaequus
Find Posterior Mean Rate of Sample Occurrence for Poisson Process ModelFindPosteriorMeanRate
Find Predictive Estimate of Shared Calendar Age Density from Bayesian Non-Parametric DPMM OutputFindPredictiveCalendarAgeDensity
Find the summed probability distribution (SPD) for a set of radiocarbon observationsFindSummedProbabilityDistribution
Outputs code suitable for running in OxCal from a series of radiocarbon determinationsGenerateOxcalCode
Example real-life data - Humans in Yukon and Alaskahuman
IntCal04 calibration curveintcal04
IntCal09 calibration curveintcal09
IntCal13 calibration curveintcal13
IntCal20 calibration curveintcal20
IntCal98 calibration curveintcal98
Interpolate a calibration curve at a set of calendar agesInterpolateCalibrationCurve
Example real-life data - Irish Rathkerr
Example real-life data - Mammuthus in Yukon and Alaskamammuthus
Plot Posterior Calendar Age Estimate for an Individual Determination after Joint CalibrationPlotCalendarAgeDensityIndividualSample
Plot KL Divergence of Predictive Density to Assess Convergence of Bayesian Non-Parametric DPMM SamplerPlotConvergenceData
Plot Histogram of the Gelman-Rubin Convergence Diagnostic for Multiple Independent MCMC ChainsPlotGelmanRubinDiagnosticMultiChain
Plot Histogram of the Gelman-Rubin Convergence Diagnostic for a Single MCMC ChainPlotGelmanRubinDiagnosticSingleChain
Plot Number of Calendar Age Clusters Estimated in Bayesian Non-Parametric DPMM OutputPlotNumberOfClusters
Plot Number of Changepoints in Rate of Sample Occurrence for Poisson Process ModelPlotNumberOfInternalChanges
Plot Calendar Ages of Changes in Rate of Sample Occurrence for Poisson Process ModelPlotPosteriorChangePoints
Plot Heights of Segments in Rate of Sample Occurrence for Poisson Process ModelPlotPosteriorHeights
Plot Posterior Mean Rate of Sample Occurrence for Poisson Process ModelPlotPosteriorMeanRate
Plot Predictive Estimate of Shared Calendar Age Density from Bayesian Non-Parametric DPMM OutputPlotPredictiveCalendarAgeDensity
Calibrate and Summarise Multiple Radiocarbon Samples via a Bayesian Non-Parametric DPMM (with Polya Urn Updating)PolyaUrnBivarDirichlet
Example artificial data - Uniform Phasepp_uniform_phase
Model Occurrence of Multiple Radiocarbon Samples as a Variable-Rate Poisson ProcessPPcalibrate
SHCal04 calibration curveshcal04
SHCal13 calibration curveshcal13
SHCal20 calibration curveshcal20
Example artificial data - Mixture of Normal Phasestwo_normals
Calibrate and Summarise Multiple Radiocarbon Samples via a Bayesian Non-Parametric DPMM (with Walker Updating)WalkerBivarDirichlet