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ArchaeoPhases

Tools for the post-processing of the Markov Chain simulated by any software used for the construction of archeological chronologies

ArchaeoPhases provides functions for the statistical analysis of archaeological dates and groups of dates. It is based on the post-processing of the Markov Chains whose stationary distribution is the posterior distribution of a series of dates. Such MCMC output can be simulated by different applications as for instance ChronoModel, Oxcal, or BCal. The only requirement is to have a CSV file containing a sample from the posterior distribution.

If this is your first time using 'ArchaeoPhases', take a moment to read the vignettes we wrote about the main functions. If you have any questions, feel free to contact us (anne.philippe@univ-nantes.fr).

ArchaeoPhases is currently developed by Anne Philippe member of the Laboratoire de mathématiques Jean Leray, Université de Nantes, France, and by Thomas S. Dye, University of Hawai`i, in Honolulu.

If you find bugs or want to suggest new features please visit ArchaeoPhases GitHub issues or contact us directly (anne.philippe@univ-nantes.fr).

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Version

Install

install.packages('ArchaeoPhases')

Monthly Downloads

701

Version

1.8

License

GPL-3

Maintainer

Anne Philippe

Last Published

June 21st, 2022

Functions in ArchaeoPhases (1.8)

CreateMinMaxGroup

Construct the minimum and maximum for a group of events (phase)

Bayesian test for anteriority / posteriority between two parameters

Plot a marginal posterior density

MultiPhaseTimeRange

Phase time range for multiple groups

age depth curve Compute the age-depth curve from the output of mcmc algorithm of ages and the known depth of each dated samples.

ArchaeoPhases: Post-Processing of the Markov Chain Simulated by 'Chronomodel', 'OxCal', or 'BCal'.

Gap or hiatus between a succession of groups (for groups in temporal order constraint)

Plot of credible intervals or HPD regions of a series of events

Bayesian HPD regions for a series of MCMC chains

MultiSuccessionPlot

Successive Phases Density Plots (for phases in temporal order constraint)

MultiPhasesTransition

Transition range for a succession of groups (for groups in temporal order constraint)

Phase time range

TempoActivityPlot

Plot the derivative of the tempo plot Bayesian estimate

MultiCredibleInterval

Bayesian credible interval for a series of dates

Density plots of two successive groups (for groups in temporal order constraint)

MarginalStatistics

Marginal summary statistics

allen_basic_relation_set

The basic Allen relation set

allen_basic_relation_strings

Allen basic relation set as strings

CredibleInterval

Bayesian credible interval

Plot occurrences

MultiMarginalPlot

Marginal posterior densities of several events

Several phase density plots

allen_concurrent_relations

Allen concurrent relation set

allen_composition

Composition of two Allen relations

Importing a BCal csv file

Gap or hiatus between two successive phases (for phases in temporal order constraint)

PhasesTransition

Transition range between two successive phases (for phases in temporal order constraint)

allen_illustrate

Illustrate basic and composite relations

PhaseDurationPlot

Plot the duration of a group

allen_create_result_vector

Create a named result vector

allen_lattice_y

Nokel lattice y coordinates

Observe the relation between two phases, each representing an interval of time

Plot a marginal posterior density

multi_marginal_statistics

Marginal summary statistics for multiple MCMC chains

new_archaeophases_mcmc

Constructor for archaeophases_mcmc object

marginal_statistics

Marginal summary statistics

allen_lattice_x

Nokel lattice x coordinates

allen_joint_concurrency

Joint concurrence of two or more observed intervals

allen_is_result_vector

Test whether an object is a result vector

reproduce.archaeophases_mcmc

Reproduce an MCMC data frame

Reproduce an MCMC data frame

allen_is_set_vector

Test if an object is a set vector

allen_ensure_set_vector

Ensure an Allen set is represented as a vector of single character strings

allen_is_set_string

Test if an object is a set string

composition_lookup_table

Construct an Allen composition lookup table

allen_string_to_vector

Convert a string containing Allen relation codes to a result vector

Union of two Allen relation sets.

allen_create_distinct_endpoint_vector

Create a result vector for relations with distinct endpoints

allen_create_concurrent_vector

Create a result vector identifying concurrent relations

allen_six_value_set

Allen relation set for intervals with distinct endpoints.

Plot the characteristics of a group of events

Importing a CSV file

original_file.archaeophases_mcmc

Check for an original mcmc file

Check for an original mcmc file

credible_interval

Bayesian credible interval

allen_update_result

Update a result vector

original_file.archaeophases_plot

Check for an original archaeophases_plot file

analyze_allen_relations

Data for an analytic graphic

Check if a resource can be located

Test for the existence of a hiatus between two MCMC chains.

allen_set_to_vector

Convert an Allen relation set to a named vector

Allen relation of two definite intervals

plot.archaeophases_plot

Recreate a graphical plot

Estimate ranges from two or more calibrations

illustrate_allen_relations

Data for an illustrative graphic

allen_string_to_set

Convert a string containing Allen relation codes to a relation set

PhaseStatistics

Summary statistics of a phase

Read MCMC output from BCal

Predictive distribution of date

Bayesian HPD regions for a series of MCMC chains

multi_marginal_plot

Marginal posterior densities of several events

read_chronomodel

Read MCMC output from ChronoModel

multi_credible_interval

Bayesian credible interval for a series of dates

multi_dates_plot

Plot of credible intervals or HPD regions of a series of events

Check if string is a URL

reproduce.archaeophases_plot

Reproduce an ArchaeoPhases plot

Read MCMC output from OxCal

Analyze composite relations

tempo_activity_plot

Plot the derivative of the tempo plot Bayesian estimate

allen_proportion_result

Calculate the proportion of each relation in a result vector

allen_observe_frequency

Observed frequency of an Allen set

app_ArchaeoPhases

Run ArchaeoPhases shiny apps

new_archaeophases_plot

Constructor for archaeophases_plot object

Make a single plot of a N<U+00F6>kel lattice.

allen_relate_intervals

Relate two or more observed intervals

occurrence_plot

Plot occurrences

Create an mcmc.list object for coda users

phase_statistics

Summary statistics of a phase

Gap or hiatus between two successive phases (for phases in temporal order constraint)

Test for the existence of a hiatus between two parameters