allen_observe_frequency {ArchaeoPhases}

Observed Frequency of an Allen Set

Description

Creates a matrix of observed frequencies of a given Allen set among two or more groups of chains from the MCMC output of a Bayesian calibration.

Usage

allen_observe_frequency(x, groups, ...)

## S4 method for signature 'PhasesMCMC,missing'
allen_observe_frequency(x, set)

## S4 method for signature 'EventsMCMC,list'
allen_observe_frequency(x, groups, ...)

Arguments

x

An EventsMCMC or a PhasesMCMC object containing the output of the MCMC algorithm.

groups

A list of (named) vector of names or indexes of columns in x (see phases()).

...

Currently not used.

set

A character string representation of an Allen set.

Value

A square matrix of observed frequencies.

Author(s)

T. S. Dye, N. Frerebeau

See Also

Other Allen's intervals: allen_analyze(), allen_complement(), allen_composition(), allen_converse(), allen_illustrate(), allen_intersect(), allen_joint_concurrency(), allen_observe(), allen_relation(), allen_relation_code(), allen_union()

Examples

if (requireNamespace("ArchaeoData", quietly = TRUE)) {
  ## Load the Anglo Saxon burials dataset
  path <- system.file("oxcal/burials.csv", package = "ArchaeoData")
  burials <- read.table(path, header = TRUE, sep = ",", dec = ".",
                        check.names = FALSE)

  ## Coerce to event
  burials <- as_events(burials, calendar = CE())

  ## Dates associated with bead BE3 Amber
  be3_amber <- c(
    "UB-4836 (WG27)", "UB-5208 (ApD107)", "UB-4965 (ApD117)",
    "UB-4735 (Ber022)", "UB-4739 (Ber134/1)", "UB-4728 (MH064)",
    "UB-4729 (MH068)", "UB-4732 (MH094)", "UB-4733 (MH095)",
    "UB-4734 (MH105c)", "UB-4984 (Lec018)", "UB-4709 (EH014)",
    "UB-4707 (EH079)", "UB-4708 (EH083)", "UB-6033 (WHes113)",
    "UB-4706 (WHes118)", "UB-4705 (WHes123)", "UB-6040 (CasD053)",
    "UB-6037 (CasD134)", "UB-6472 (BuD222)", "UB-6473 (BuD250)",
    "UB-6476 (BuD339)", "UB-4963 (SPTip208)", "UB-4890 (MelSG075)",
    "UB-4887 (MelSG082)", "UB-4888 (MelSG089)", "MaDE1 & E2",
    "UB-4552 (MaDE3)", "UB-4975 (AstCli12)", "UB-4835 (ApD134)",
    "SUERC-39108 ERLK G322", "SUERC-39109 ERL G362", "SUERC-39112 ERL G405",
    "SUERC-51560 ERL G038", "SUERC-39091 (ERL G003)", "SUERC-39092 (ERL G005)",
    "SUERC-39113 (ERL G417)", "SUERC-51549 (ERL G195)", "SUERC-51552 (ERL G107)",
    "SUERC-51550 (ERL G254)"
  )

  ## Dates associated with bead BE1 Dghnt
  be1_dghnt <- c(
    "UB-4503 (Lec148)", "UB-4506 (Lec172/2)", "UB-6038 (CasD183)",
    "UB-4512 (EH091)", "UB-4501 (Lec014)", "UB-4507 (Lec187)",
    "UB-4502 (Lec138)", "UB-4042 (But1674)", "SUERC-39100 (ERL G266)"
  )

  ## Construct a list of lists
  chains <- list(
    list("BE3-Amber" = be3_amber, "BE1-Dghnt" = be1_dghnt),
    list("BE1-Dghnt" = be1_dghnt, "BE3-Amber" = be3_amber)
  )

  ## Plot
  allen_observe(x = burials, groups = chains)

  ## Observe 2x2 frequency matrix of the relation of trunk to branch
  allen_observe_frequency(burials, groups = chains, set = "oFD")
}