Package: ArchaeoPhases 2.0

Anne Philippe

ArchaeoPhases: Post-Processing of Markov Chain Monte Carlo Simulations for Chronological Modelling

Statistical analysis of archaeological dates and groups of dates. This package allows to post-process Markov Chain Monte Carlo (MCMC) simulations from 'ChronoModel' <https://chronomodel.com/>, 'Oxcal' <https://c14.arch.ox.ac.uk/oxcal.html> or 'BCal' <https://bcal.shef.ac.uk/>. It provides functions for the study of rhythms of the long term from the posterior distribution of a series of dates (tempo and activity plot). It also allows the estimation and visualization of time ranges from the posterior distribution of groups of dates (e.g. duration, transition and hiatus between successive phases) as described in Philippe and Vibet (2020) <doi:10.18637/jss.v093.c01>.

Authors:Anne Philippe [aut, cre], Marie-Anne Vibet [aut], Thomas S. Dye [ctb], Nicolas Frerebeau [aut]

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ArchaeoPhases.pdf |ArchaeoPhases.html
ArchaeoPhases/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/archaeostat/archaeophases/issues

Datasets:

On CRAN:

archaeologybayesian-statisticsgeochronologymarkov-chainradiocarbon-dates

6.81 score 9 stars 60 scripts 690 downloads 1 mentions 96 exports 2 dependencies

Last updated 8 months agofrom:76add93b49 (on v2.0). Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 05 2024
R-4.5-winNOTENov 05 2024
R-4.5-linuxNOTENov 05 2024
R-4.4-winOKNov 05 2024
R-4.4-macOKNov 05 2024
R-4.3-winOKNov 05 2024
R-4.3-macOKNov 05 2024

Exports:activityADAgeDepthallen_analyzeallen_complementallen_compositionallen_converseallen_illustrateallen_intersectallen_joint_concurrencyallen_observeallen_observe_frequencyallen_relationallen_relation_codeallen_relation_concurrentallen_relation_distinctallen_relation_stringallen_unionas_codaas_eventsas_phasesas.data.frameb2kBCBCEboundariesBPburycalendarcbind2CECreateMinMaxGroupcredible_intervalCredibleIntervaldates_hiatusDatesHiatusdurationelapseestimate_rangehiatusinterpolateinterval_credibleinterval_hdris_originalmarginal_plotmarginal_statisticsMarginalPlotMarginalProbaMarginalStatisticsmulti_credible_intervalmulti_dates_plotmulti_hpdmulti_marginal_plotmulti_marginal_statisticsMultiCredibleIntervalMultiDatesPlotMultiHPDMultiMarginalPlotMultiPhasePlotMultiPhasesGapMultiPhasesTransitionMultiPhaseTimeRangeMultiSuccessionPlotoccurrenceoccurrence_plotOccurrencePlotolderPhaseDurationPlotPhasePlotphasesphases_gapPhasesGapPhaseStatisticsPhasesTransitionPhaseTimeRangeplotpredictread_bcalread_chronomodel_eventsread_chronomodel_phasesread_oxcalsensitivitysortsort.liststartSuccessionPlotsummarytempotempo_activity_plottempo_plotTempoActivityPlotTempoPlottimetransitionundated_sampleyear_axis

Dependencies:aionarkhe

Allen's interval algebra

Rendered fromallen.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2024-03-04
Started: 2023-06-02

Bibliography

Rendered frombibliography.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2024-03-04
Started: 2023-06-02

Import MCMC Samples

Rendered fromimport.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2024-03-04
Started: 2023-06-02

Introduction to ArchaeoPhases

Rendered fromArchaeoPhases.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2024-03-04
Started: 2023-06-02

Readme and manuals

Help Manual

Help pageTopics
Activity Plotactivity activity,CumulativeEvents-method activity,EventsMCMC-method activity-method plot,ActivityEvents,missing-method
Analyze Composite Allen Relationsallen_analyze
Complement of an Allen Relationallen_complement allen_complement,character-method allen_complement,matrix-method allen_complement-method
Composition of Allen Relationsallen_composition allen_composition,character,character-method allen_composition-method
Converse of an Allen Relationallen_converse allen_converse,character-method allen_converse,matrix-method allen_converse-method
Illustrate Basic and Composite Allen Relationsallen_illustrate
Intersection of Allen Relationsallen_intersect allen_intersect,character,character-method allen_intersect-method
Joint Concurrence of Two or More Observed Intervalsallen_joint_concurrency allen_joint_concurrency,EventsMCMC,list-method allen_joint_concurrency-method
Observe the Relation Between two Phasesallen_observe allen_observe,EventsMCMC,list-method allen_observe,PhasesMCMC,missing-method allen_observe-method
Observed Frequency of an Allen Setallen_observe_frequency allen_observe_frequency,EventsMCMC,list-method allen_observe_frequency,PhasesMCMC,missing-method allen_observe_frequency-method
Allen Relation Between Definite Intervalsallen_relation allen_relation,ANY,missing-method allen_relation,numeric,numeric-method allen_relation-method
The Basic Allen Relation Setallen_relation_code allen_relation_concurrent allen_relation_distinct allen_relation_string
Union of Allen Relationsallen_union allen_union,character,character-method allen_union-method
Coerce to Codaas_coda as_coda,MCMC-method as_coda-method
Coerce to Eventsas_events as_events,data.frame-method as_events,matrix-method as_events-method
Coerce to Phasesas_phases as_phases,data.frame-method as_phases,matrix-method as_phases-method
Combine two MCMC Objectsbind cbind2,MCMC,MCMC-method
Phase Time Rangeboundaries boundaries,numeric,numeric-method boundaries,PhasesMCMC,missing-method boundaries-method
Age-Depth Modelingbury bury,AgeDepthModel-method bury,EventsMCMC,numeric-method bury,EventsMCMC-method bury-method plot,AgeDepthModel,missing-method predict,AgeDepthModel-method
Check for an Original MCMC Filecheck is_original is_original,ActivityEvents-method is_original,CumulativeEvents-method is_original,MCMC-method is_original,OccurrenceEvents-method is_original,PhasesMCMC-method is_original-method
Coerce to a Data Frameas.data.frame,ActivityEvents-method as.data.frame,CumulativeEvents-method as.data.frame,OccurrenceEvents-method as.data.frame,TimeRange-method data.frame
Phase Durationduration duration,numeric,numeric-method duration,PhasesMCMC,missing-method duration-method
Elapsed Time Scaleelapse elapse,MCMC-method elapse-method
Hiatus Between Two Dateshiatus hiatus,EventsMCMC,missing-method hiatus,EventsMCMC-method hiatus,numeric,numeric-method hiatus,PhasesMCMC,missing-method hiatus-method
Interpolate Between Two Datesinterpolate interpolate,EventsMCMC,missing-method interpolate,numeric,numeric-method interpolate-method
Bayesian Credible Intervalinterval_credible interval_credible,MCMC-method interval_credible-method
Bayesian HPD Regionsinterval_hdr interval_hdr,MCMC,missing-method interval_hdr-method
Eventsmcmc_events
Phasesmcmc_phases
The Names of an Objectnames names,MCMC-method names,PhasesMCMC-method names<-,MCMC-method names<-,PhasesMCMC-method
Occurrence Plotoccurrence occurrence,EventsMCMC-method occurrence-method plot,OccurrenceEvents,missing-method
Bayesian Test for Anteriority/Posteriorityolder older,EventsMCMC,missing-method older,EventsMCMC-method older,numeric,numeric-method older-method
Compute Phasesphases phases,EventsMCMC,list-method phases,EventsMCMC,missing-method phases-method
Plot Eventsplot,MCMC,missing-method plot_events
Plot Phasesplot,PhasesMCMC,missing-method plot_phases
Read BCal Outputread_bcal read_bcal,character-method read_bcal-method
Read ChronoModel Outputread_chronomodel read_chronomodel-method read_chronomodel_events read_chronomodel_events,character-method read_chronomodel_events-method read_chronomodel_phases read_chronomodel_phases,character-method read_chronomodel_phases-method
Read OxCal Outputread_oxcal read_oxcal,character-method read_oxcal-method
Sensitivitysensitivity sensitivity,EventsMCMC-method sensitivity-method
Sort an MCMC Objectsort sort,MCMC-method sort,PhasesMCMC-method
Ordering Permutation of an MCMC Objectsort.list sort.list,MCMC-method sort.list,PhasesMCMC-method
Extract or Replace Parts of an Objectsubset [,MCMC-method [,PhasesMCMC-method
Marginal Summary Statistics for Multiple MCMC Chainssummary summary,MCMC-method summary,PhasesMCMC-method
Tempo Plotplot,CumulativeEvents,missing-method tempo tempo,EventsMCMC-method tempo-method
Transition Range Between Successive Phasestransition transition,numeric,numeric-method transition,PhasesMCMC,missing-method transition-method