Bchron-package {Bchron} | R Documentation |
Runs MCMC and predictive distributions for the monotonic piece-wise linear compound Poisson Gamma process. Before a run of the Bchron model can commence, the file structures must be in the correct format. Included in the package is an example set of data from Glendalough, Ireland. All other cores must be in a similar format for the routines to work.
Package: | Bchron |
Type: | Package |
Version: | 2.0 |
Date: | 2008-04-28 |
License: | GPL (version 2 or later) |
Installation instructions for basic and first time users:
1. Type library(Bchron)
2. Now create a directory on your C drive called Bchron (it needs to be directly on the c drive).
3. Within this directory, create three more called Input, Output and CalCurve.
4. Now navigate to C:\ program files\ R\ R-XXXXX\ library\ BChron\ Data. In here there should be a file called Rdata.zip
5. Double click on it and move the files Glendalough.dat, GlendaloughEventDepthsAlnus.txt and Glendaloughddepths.txt to the input directory.
6. Move the IntCal04.bch file to the CalCurve directory.
Everything is now set up.
Example full model run (with Glendalough.dat):
1. At the command prompt in R, type library(Bchron)
2. Type Bchronmenu() and choose option 1.
3. If you've followed the steps above you should not need to change the default path, you just need to tell it that the file name is Glendalough.
4. Now choose option 2 to calibrate the radiocarbon dates.
5. Choose option 3 and short to do a run of the Bchron model.
6. Choose option 4 to run the prediction stage and create a plot of the data.
Once a satisfactory short run has been obtained, a long run should be undertaken. The long run will take much longer than the short run, but will only be required once.
Example event prediction stage (with GlendaloughEventDepthsAlnus.txt)
1. Type Bchronmenu() and choose Option 1.
2. Enter the data as instructed
3. Assuming a run of the Bchron model has already been done (as above) and that the file GlendaloughEventDepthsAlnus.txt is in the input directory, choose option 5
6. Check the output directory for GlendaloughEventAgesAlnus.txt which will contain 95% HDR age intervals for the depths of interest.
Other cores can be created in a spirit similar to that found in the Glendalough.dat file. This example input file has 5 radiocarbon dates (and the top of the core). The columns are tab delimited and represent the lab code of the sample, the radiocarbon age, the sample standard error, the depth (in cm) at which it was found, the thickness of the sample in cm. If the thickness is unknown, zero is acceptable. The next two columns contain the probabilities of being an outlier. The first probability identifies censored outliers as proposed by Christen (1994), the second indicates the probability an outlier is ignored completely by the Bchron model. The final column indicates whether this date is a radiocarbon date (type 1), a uniformly distributed date (type 2), or a normally distributed date (type 3). For uniform dates, the standard deviation value is taken to be the distance to the upper and lower limits. Type 3 dates are permitted to be outliers, with probabilities as given. Type 2 dates are not allowed to be outliers; the outlier probabilities for these dates are ignored.
Andrew Parnell <Andrew.Parnell@tcd.ie>
Haslett and Parnell (2008), A simple monotone process with application to radiocarbon-dated depth chronologies. Applied Statistics 57 (5), 1–20.
Christen, J. A. (1994). Summarizing a set of radiocarbon determinations: A robust approach. Applied Statistics 43 (3), 489 – 503.
## See Bchronmenu()