Bchron (version 3.2)

BchronMCMC: Run the Bchron

Description

Runs the compound Poisson-Gamma model for radiocarbon and non-radiocarbon dates

Usage

BchronMCMC(Bchrondata, iterations = 1e+05, burnin = 10000, thinby = 8, howmany = 2000, defaults = FALSE, testrun = FALSE)

Arguments

Bchrondata

A Bchron data object with fields for the the input and output files, the name of the core being used, the details of the calibration curve, and details of the model run required. See Bchronload and

iterations

Number of MCMC iterations required. Default is 100,000.

burnin

Number of discarded burn-in iterations. Default is 10,000.

thinby

Step size of iterations to thin out. Default is to take every 8th iteration.

howmany

Number of iterations before R reports back and updates the screen. Default is 2000.

defaults

If TRUE, runs BchronMCMC without any warnings and overwrites previous runs. If FALSE (default) will prompt user before continuing.

testrun

if TRUE, tries a very short run to test that BchronMCMC works.

Value

• Creates a parameter output file (corenamepars.txt) in the output directory containing outlier estimates, parameter values, and other details required. This information can be turned into chronology samples by calling Bchronpredict.

Details

The Bchron MCMC function fits a compound Poisson-Gamma distribution to the increments between the dated levels. This involves a stochastic linear interpolation where the age gaps are Gamma(2,beta) distributed, and the depth gaps are Exponential(lambda). Radiocarbon and non-radiocarbon dates (including outliers) are updated within the function also by MCMC.

References

Haslett and Parnell (2008, JRSSC, 57:399-418) and Parnell et al (2008, QSR, 27(19-20):1872-1885)

See Also

See Bchronmenu for examples.

Examples

# For the example data, the following should run (when the files are placed in the default directory in windows; c:/Bchron)
# myrun <- Bchronload("Glendalough")
# Bchroncalibrate(myrun)
# BchronMCMC(myrun)
# Bchronpredict(myrun)
# Bchronplot(myrun)