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:
ArchaeoPhases_2.0.tar.gz
ArchaeoPhases_2.0.zip(r-4.5)ArchaeoPhases_2.0.zip(r-4.4)ArchaeoPhases_2.0.zip(r-4.3)
ArchaeoPhases_2.0.tgz(r-4.4-any)ArchaeoPhases_2.0.tgz(r-4.3-any)
ArchaeoPhases_2.0.tar.gz(r-4.5-noble)ArchaeoPhases_2.0.tar.gz(r-4.4-noble)
ArchaeoPhases_2.0.tgz(r-4.4-emscripten)ArchaeoPhases_2.0.tgz(r-4.3-emscripten)
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')) |
Bug tracker:https://github.com/archaeostat/archaeophases/issues
- mcmc_events - Events
- mcmc_phases - Phases
archaeologybayesian-statisticsgeochronologymarkov-chainradiocarbon-dates
Last updated 7 months agofrom:76add93b49 (on v2.0). Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 05 2024 |
| R-4.5-win | NOTE | Nov 05 2024 |
| R-4.5-linux | NOTE | Nov 05 2024 |
| R-4.4-win | OK | Nov 05 2024 |
| R-4.4-mac | OK | Nov 05 2024 |
| R-4.3-win | OK | Nov 05 2024 |
| R-4.3-mac | OK | Nov 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
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 page | Topics |
|---|---|
| Activity Plot | activity activity,CumulativeEvents-method activity,EventsMCMC-method activity-method plot,ActivityEvents,missing-method |
| Analyze Composite Allen Relations | allen_analyze |
| Complement of an Allen Relation | allen_complement allen_complement,character-method allen_complement,matrix-method allen_complement-method |
| Composition of Allen Relations | allen_composition allen_composition,character,character-method allen_composition-method |
| Converse of an Allen Relation | allen_converse allen_converse,character-method allen_converse,matrix-method allen_converse-method |
| Illustrate Basic and Composite Allen Relations | allen_illustrate |
| Intersection of Allen Relations | allen_intersect allen_intersect,character,character-method allen_intersect-method |
| Joint Concurrence of Two or More Observed Intervals | allen_joint_concurrency allen_joint_concurrency,EventsMCMC,list-method allen_joint_concurrency-method |
| Observe the Relation Between two Phases | allen_observe allen_observe,EventsMCMC,list-method allen_observe,PhasesMCMC,missing-method allen_observe-method |
| Observed Frequency of an Allen Set | allen_observe_frequency allen_observe_frequency,EventsMCMC,list-method allen_observe_frequency,PhasesMCMC,missing-method allen_observe_frequency-method |
| Allen Relation Between Definite Intervals | allen_relation allen_relation,ANY,missing-method allen_relation,numeric,numeric-method allen_relation-method |
| The Basic Allen Relation Set | allen_relation_code allen_relation_concurrent allen_relation_distinct allen_relation_string |
| Union of Allen Relations | allen_union allen_union,character,character-method allen_union-method |
| Coerce to Coda | as_coda as_coda,MCMC-method as_coda-method |
| Coerce to Events | as_events as_events,data.frame-method as_events,matrix-method as_events-method |
| Coerce to Phases | as_phases as_phases,data.frame-method as_phases,matrix-method as_phases-method |
| Combine two MCMC Objects | bind cbind2,MCMC,MCMC-method |
| Phase Time Range | boundaries boundaries,numeric,numeric-method boundaries,PhasesMCMC,missing-method boundaries-method |
| Age-Depth Modeling | bury bury,AgeDepthModel-method bury,EventsMCMC,numeric-method bury,EventsMCMC-method bury-method plot,AgeDepthModel,missing-method predict,AgeDepthModel-method |
| Check for an Original MCMC File | check 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 Frame | as.data.frame,ActivityEvents-method as.data.frame,CumulativeEvents-method as.data.frame,OccurrenceEvents-method as.data.frame,TimeRange-method data.frame |
| Phase Duration | duration duration,numeric,numeric-method duration,PhasesMCMC,missing-method duration-method |
| Elapsed Time Scale | elapse elapse,MCMC-method elapse-method |
| Hiatus Between Two Dates | hiatus hiatus,EventsMCMC,missing-method hiatus,EventsMCMC-method hiatus,numeric,numeric-method hiatus,PhasesMCMC,missing-method hiatus-method |
| Interpolate Between Two Dates | interpolate interpolate,EventsMCMC,missing-method interpolate,numeric,numeric-method interpolate-method |
| Bayesian Credible Interval | interval_credible interval_credible,MCMC-method interval_credible-method |
| Bayesian HPD Regions | interval_hdr interval_hdr,MCMC,missing-method interval_hdr-method |
| Events | mcmc_events |
| Phases | mcmc_phases |
| The Names of an Object | names names,MCMC-method names,PhasesMCMC-method names<-,MCMC-method names<-,PhasesMCMC-method |
| Occurrence Plot | occurrence occurrence,EventsMCMC-method occurrence-method plot,OccurrenceEvents,missing-method |
| Bayesian Test for Anteriority/Posteriority | older older,EventsMCMC,missing-method older,EventsMCMC-method older,numeric,numeric-method older-method |
| Compute Phases | phases phases,EventsMCMC,list-method phases,EventsMCMC,missing-method phases-method |
| Plot Events | plot,MCMC,missing-method plot_events |
| Plot Phases | plot,PhasesMCMC,missing-method plot_phases |
| Read BCal Output | read_bcal read_bcal,character-method read_bcal-method |
| Read ChronoModel Output | read_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 Output | read_oxcal read_oxcal,character-method read_oxcal-method |
| Sensitivity | sensitivity sensitivity,EventsMCMC-method sensitivity-method |
| Sort an MCMC Object | sort sort,MCMC-method sort,PhasesMCMC-method |
| Ordering Permutation of an MCMC Object | sort.list sort.list,MCMC-method sort.list,PhasesMCMC-method |
| Extract or Replace Parts of an Object | subset [,MCMC-method [,PhasesMCMC-method |
| Marginal Summary Statistics for Multiple MCMC Chains | summary summary,MCMC-method summary,PhasesMCMC-method |
| Tempo Plot | plot,CumulativeEvents,missing-method tempo tempo,EventsMCMC-method tempo-method |
| Transition Range Between Successive Phases | transition transition,numeric,numeric-method transition,PhasesMCMC,missing-method transition-method |
