Bchronproxyplot) for plotting proxy data with age uncertainty. Version 3.2 includes new functions for estimating rates of relative sea level change, and a quick radiocarbon calibration function for individual dates.1. Create a directory on your hard drive called Bchron.
2. Now navigate to the R directory and find the Bchron sub-directory within. On windows this will be C:\ program files\ R\ R-XXXXX\ library\ BChron\ where XXXXX is the version number of R. On other plaforms, this directory can be found by typing .libPaths() at the R command prompt.
3. In this directory, there there should be three subdirectories called Input, Output, and CalCurve. Copy these to the Bchron directory you created in step 1.
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. Locate your Bchron directory, and select IntCal04.bch as your calibration curve and Glendalough.dat as your input file. All other options can be left as default.
4. Now choose option 2 to calibrate the radiocarbon dates.
5. Choose option 3 and 'short' to do a short 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. Follow the steps above, and now choose option 5 for event prediction.
2. Type Alnus as the name of the event.
3. 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 a non-radiocarbon date for 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.
For more information see the webpage at
Bchronmenu and