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

This vignette uses data available through the ArchaeoData package which is available in a separate repository. ArchaeoData provides MCMC outputs from ChronoModel, OxCal and BCal.

## Install data package
install.packages("ArchaeoData", repos = "https://archaeostat.r-universe.dev")

## Load package
library(ArchaeoPhases)

ChronoModel

Two different files are generated by ChronoModel: Chain_all_Events.csv that contains the MCMC samples of each event created in the modeling, and Chain_all_Phases.csv that contains all the MCMC samples of the minimum and the maximum of each group of dates if at least one group is created.

## Construct the path to the data
path_events <- file.path("chronomodel", "ksarakil", "Chain_all_Events.csv")
output_events <- system.file(path_events, package = "ArchaeoData")

## Read events from ChronoModel
chrono_events <- read_chronomodel_events(output_events)

## Plot events
plot(chrono_events)

plot of chunk read-chronomodel-events

## Construct the path to the data
path_phases <- file.path("chronomodel", "ksarakil", "Chain_all_Phases.csv")
output_phases <- system.file(path_phases, package = "ArchaeoData")

## Read phases from ChronoModel
chrono_phases <- read_chronomodel_phases(output_phases)

## Plot phases
plot(chrono_phases)

plot of chunk read-chronomodel-phases

Oxcal

Oxcal generates a CSV file containing the MCMC samples of all parameters (dates, start and end of phases).

## Construct the path to the data
path_oxcal <- file.path("oxcal", "ksarakil", "MCMC_Sample.csv")
output_oxcal <- system.file(path_oxcal, package = "ArchaeoData")

## Read OxCal MCMC samples
oxcal_mcmc <- read_oxcal(output_oxcal)

## Plot events
plot(oxcal_mcmc)

plot of chunk read-oxcal

The phase boundaries cannot be extracted automatically from Oxcal output. Use as_phases() to get the phase boundaries:

## Get phases boundaries from OxCal
oxcal_phases <- phases(
  x = oxcal_mcmc,
  groups = list(IUP = c(2, 4), Ahmarian = c(5, 18),
                UP = c(19, 23), EPI = c(24, 26))
)

## Plot phase boundaries
plot(oxcal_phases)

plot of chunk oxcal-phases

BCal

BCal generates a CSV file containing the MCMC samples of all parameters (dates, start and end of groups).

## Construct the path to the data
path_bcal <- file.path("bcal", "fishpond.csv")
output_bcal <- system.file(path_bcal, package = "ArchaeoData")

## Read BCal MCMC samples
bcal_mcmc <- read_bcal(output_bcal)

The group boundaries cannot be extracted automatically from BCal output. Use as_phases() to get the group boundaries:

## Get groups boundaries from BCal
bcal_phases <- phases(
  x = bcal_mcmc,
  groups = list(`Layer II` = c(6, 1), `Layer III` = c(9, 7))
)

## Plot group boundaries
plot(bcal_phases)

plot of chunk bcal-phases

ArchaeoStat/ArchaeoPhases documentation built on Jan. 19, 2025, 2:33 p.m.