Bchron

This option writes the input file for Bayesian age modeling program Bchron (Haslett & Parnell, 2008). Bchron is an R package, which can be run in the R GUI or in RStudio. In either case, the working directory must be changed to the directory containing the Bchron input file written by Tilia, and the Bchron library must be opened. In the example below, the Bchron input file was saved to NELSON88.csv. See Modern Age Models for instructions for accessing the Export Chron Controls dialog box. 

Click the radiobutton for Bchron (*.csv) to write the Bchron input file and select the appropriate calibration curve. Two .csv files are written: one that is the Bchron input file and another that has a list of all sample depths in the data worksheet.

After the files are written, a dialog box appears with suggested Bchron commands.

This is what these commands do:

> input = read.csv('NELSON88_input.csv',header=TRUE)

  Reads the Bchron input file into array input.

> bchron = Bchronology(id=input$id,ages=input$age,ageSds=input$ageSd,positions=input$position,positionThickness=input$thickness,calCurves=input$calCurve)

   Runs Bchron. 

> plot(bchron)

  Plots a graph. 

> depths = read.csv('NELSON88_input_depths.csv',header=TRUE)

  Reads the sample depths into vector depths.

> predictAges = predict(bchron,newPositions=depths$Depth,newPositionThicknesses=depths$Thickness)

  Calculates the predicted ages for the sample depths.

> write.csv(t(summary(predictAges)),'NELSON88_input_predict_ages.csv')

  Writes the predicted sample ages to the file 'NELSON88_input_predict_ages.csv'. Note that the array is transposed.