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

## Documentation for package ‘ArchaeoPhases’ version 1.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
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
ImportCSV | Importing a CSV file
ImportCSV.BCal | Importing a BCal csv file
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
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.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