Bchron: BchronDensityFast – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

BchronDensityFast

Non-parametric phase model (faster version)

Description

This function runs a non-parametric phase model on 14C and non-14C ages via Gaussian Mixture density estimation through the mclust package

Usage

BchronDensityFast(
  ages,
  ageSds,
  calCurves,
  pathToCalCurves = system.file("data", package = "Bchron"),
  dfs = rep(100, length(ages)),
  samples = 2000,
  G = 30
)

Arguments

`ages`	A vector of ages (most likely 14C)
`ageSds`	A vector of 1-sigma values for the ages given above
`calCurves`	A vector of values containing either `intcal20`, `shcal20`, `marine20`, or `normal` (older calibration curves such as intcal13 are also supported). Should be the same length the number of ages supplied. Non-standard calibration curves can be used provided they are supplied in the same format as those previously mentioned and are placed in the same directory. Normal indicates a normally-distributed (non-14C) age.
`pathToCalCurves`	File path to where the calibration curves are located. Defaults to the system directory where the 3 standard calibration curves are stored.
`dfs`	Degrees-of-freedom values for the t-distribution associated with the calibration calculation. A large value indicates Gaussian distributions assumed for the 14C ages
`samples`	Number of samples of calibrated dates required
`G`	Number of Gaussian mixture components

Details

This is a faster approximate version of BchronDensity that uses the densityMclust function to compute the Gaussian mixtures for a set of calibrated ages. The method is an approximation as it does not fit a fully Bayesian model as BchronDensity does. It is designed to be a probabilistic version of the Oxcal SUM command which takes calibrated ages and sums the probability distributions with the aim of estimating activity through age as a proxy.

Value

An object of class BchronDensityRunFast with the following components:

`out`	The output from the run of `densityMclust` with the given number of mixture components
`calAges`	The calibrated ages from the `BchronDensity` function

Examples

# Read in some data from Sluggan Moss
data(Sluggan)

# Run the model
SlugDensFast <- with(
  Sluggan,
  BchronDensityFast(
    ages = ages,
    ageSds = ageSds,
    calCurves = calCurves
  )
)

# plot it
plot(SlugDensFast)

Bchron

Radiocarbon Dating, Age-Depth Modelling, Relative Sea Level Rate Estimation, and Non-Parametric Phase Modelling

v4.7.4

GPL (>= 2)

Authors

Andrew Parnell

Initial release

2021-01-28