Post-Processing of the Markov Chain Simulated by 'ChronoModel', 'Oxcal' or 'BCal'

Documentation for package ‘ArchaeoPhases’ version 1.8

Help Pages

AgeDepth	age depth curve Compute the age-depth curve from the output of mcmc algorithm of ages and the known depth of each dated samples.
allen_analyze	Analyze composite relations
allen_basic_relation_set	The basic Allen relation set
allen_basic_relation_strings	Allen basic relation set as strings
allen_composition	Composition of two Allen relations
allen_concurrent_relations	Allen concurrent relation set
allen_create_concurrent_vector	Create a result vector identifying concurrent relations
allen_create_distinct_endpoint_vector	Create a result vector for relations with distinct endpoints
allen_create_result_vector	Create a named result vector
allen_ensure_set_vector	Ensure an Allen set is represented as a vector of single character strings
allen_illustrate	Illustrate basic and composite relations
allen_is_result_vector	Test whether an object is a result vector
allen_is_set_string	Test if an object is a set string
allen_is_set_vector	Test if an object is a set vector
allen_joint_concurrency	Joint concurrence of two or more observed intervals
allen_lattice_x	Nokel lattice x coordinates
allen_lattice_y	Nokel lattice y coordinates
allen_observe	Observe the relation between two phases, each representing an interval of time
allen_observe_frequency	Observed frequency of an Allen set
allen_plot	Make a single plot of a Nökel lattice.
allen_proportion_result	Calculate the proportion of each relation in a result vector
allen_relate_intervals	Relate two or more observed intervals
allen_relation	Allen relation of two definite intervals
allen_set_to_vector	Convert an Allen relation set to a named vector
allen_six_value_set	Allen relation set for intervals with distinct endpoints.
allen_string_to_set	Convert a string containing Allen relation codes to a relation set
allen_string_to_vector	Convert a string containing Allen relation codes to a result vector
allen_union	Union of two Allen relation sets.
allen_update_result	Update a result vector
analyze_allen_relations	Data for an analytic graphic
app_ArchaeoPhases	Run ArchaeoPhases shiny apps
ArchaeoPhases	ArchaeoPhases: Post-Processing of the Markov Chain Simulated by 'Chronomodel', 'OxCal', or 'BCal'.
coda.mcmc	Create an 'mcmc.list' object for 'coda' users
composition_lookup_table	Construct an Allen composition lookup table
CreateMinMaxGroup	Construct the minimum and maximum for a group of events (phase)
CredibleInterval	Bayesian credible interval
credible_interval	Bayesian credible interval
DatesHiatus	Test for the existence of a hiatus between two parameters
dates_hiatus	Test for the existence of a hiatus between two MCMC chains.
estimate_range	Estimate ranges from two or more calibrations
Events	Events
illustrate_allen_relations	Data for an illustrative graphic
ImportCSV	Importing a CSV file
ImportCSV.BCal	Importing a BCal csv file
is.url	Check if string is a URL
MarginalPlot	Plot a marginal posterior density
MarginalProba	Bayesian test for anteriority / posteriority between two parameters
MarginalStatistics	Marginal summary statistics
marginal_plot	Plot a marginal posterior density
marginal_statistics	Marginal summary statistics
MultiCredibleInterval	Bayesian credible interval for a series of dates
MultiDatesPlot	Plot of credible intervals or HPD regions of a series of events
MultiHPD	Bayesian HPD regions for a series of MCMC chains
MultiMarginalPlot	Marginal posterior densities of several events
MultiPhasePlot	Several phase density plots
MultiPhasesGap	Gap or hiatus between a succession of groups (for groups in temporal order constraint)
MultiPhasesTransition	Transition range for a succession of groups (for groups in temporal order constraint)
MultiPhaseTimeRange	Phase time range for multiple groups
MultiSuccessionPlot	Successive Phases Density Plots (for phases in temporal order constraint)
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
multi_hpd	Bayesian HPD regions for a series of MCMC chains
multi_marginal_plot	Marginal posterior densities of several events
multi_marginal_statistics	Marginal summary statistics for multiple MCMC chains
new_archaeophases_mcmc	Constructor for 'archaeophases_mcmc' object
new_archaeophases_plot	Constructor for 'archaeophases_plot' object
OccurrencePlot	Plot occurrences
occurrence_plot	Plot occurrences
original_file	Check for an original mcmc file
original_file.archaeophases_mcmc	Check for an original mcmc file
original_file.archaeophases_plot	Check for an original 'archaeophases_plot' file
oxc	oxc
PhaseDurationPlot	Plot the duration of a group
PhasePlot	Plot the characteristics of a group of events
Phases	Phases
PhasesGap	Gap or hiatus between two successive phases (for phases in temporal order constraint)
PhaseStatistics	Summary statistics of a phase
PhasesTransition	Transition range between two successive phases (for phases in temporal order constraint)
phases_gap	Gap or hiatus between two successive phases (for phases in temporal order constraint)
PhaseTimeRange	Phase time range
phase_statistics	Summary statistics of a phase
plot.archaeophases_plot	Recreate a graphical plot
read_bcal	Read MCMC output from BCal
read_chronomodel	Read MCMC output from ChronoModel
read_oxcal	Read MCMC output from OxCal
reproduce	Reproduce an MCMC data frame
reproduce.archaeophases_mcmc	Reproduce an MCMC data frame
reproduce.archaeophases_plot	Reproduce an ArchaeoPhases plot
SuccessionPlot	Density plots of two successive groups (for groups in temporal order constraint)
TempoActivityPlot	Plot the derivative of the tempo plot Bayesian estimate
TempoPlot	Tempo plot
tempo_activity_plot	Plot the derivative of the tempo plot Bayesian estimate
tempo_plot	Tempo plot
undated_sample	Predictive distribution of date
valid_url	Check if a resource can be located