This function runs a non-parametric phase model on 14C and non-14C ages via Gaussian Mixture density estimation
BchronDensity(
ages,
ageSds,
calCurves,
pathToCalCurves = system.file("data", package = "Bchron"),
dfs = rep(100, length(ages)),
numMix = 50,
iterations = 10000,
burn = 2000,
thin = 8,
updateAges = FALSE,
store_density = TRUE
)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, ornormal(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
- numMix
The number of mixture components in the phase model. Might need to be increased if the data set is large and the phase behaviour is very complex
- iterations
The number of iterations to run for
- burn
The number of starting iterations to discard
- thin
The step size of iterations to keep
- updateAges
Whether or not to update ages as part of the MCMC run. Default is FALSE. Changing this to TRUE will improve performance but will fit a slightly invalid model
- store_density
Whether or not to store the density and age grid. Useful for plotting the output in other packages
Value
An object of class BchronDensityRun with the following elements:
thetaThe posterior samples of the restricted ages
pPosterior samples of the mixture proportions
muValues of the means of each Gaussian mixture
calAgesThe calibrated ages from
BchronCalibrateGThe number of mixture components. Equal to numMix
age_gridA grid of ages used for the final density estimate
densityThe density estimate based on the above age grid
Details
This model places a Gaussian mixture prior distribution on the calibrated ages and so estimates the density of the overall set of radiocarbon ages. 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.
See also
Bchronology, BchronRSL, BchronDensityFast for a faster approximate version of this function
Examples
# \donttest{
# Read in some data from Sluggan Moss
data(Sluggan)
# Run the model
SlugDens <- with(
Sluggan,
BchronDensity(
ages = ages,
ageSds = ageSds,
calCurves = calCurves
)
)
#>
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# plot it
plot(SlugDens)
# }