Clam

This option writes the input file for the age modeling program Clam (Blaauw, 2010). Clam 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 Clam input file written by Tilia, and the Clam library must be opened. In the example below, the Clam 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 Clam (*.csv) to write the Clam input file. For Clam, the calibratin curve is included in the R command line (see below). Two .csv files are written: one that is the clam input file and another that has a list of all sample depths in the data worksheet.

 

In the Save As dialog box, the Clam input file must saved in the Clam Cores folder in a subfolder with the same name as the file name. In this example, the file NELSON88.csv was saved in the clam\Cores\NELSON88 folder. The NELSON88 subfolder was created as a New Folder in the Save As dialog box.

This R command line will run the Clam model:

> clam("NELSON88",type=4,cc=1,revaxes=TRUE,revd=FALSE,revyr=FALSE,depths.file=TRUE)

 

Explanation of parameters:

type=4   Smooth spline

cc=1  Selects IntCal20 calibration curve. 

revaxes=TRUE,revd=FALSE,revyr=FALSE  Plots the age-depth graph with age on the Y axis and depth on the X axis.

depths.file=TRUE  Reads the depths file to create an age estimate for every sample depth.

 

In this example, the age-depth controls encompassed the proxy depths. If proxy depths must be extrapolated beyond the age-depth controls, then the parameter dmin or dmax should be entered. For example, if the maximum proxy depth of 1520 cm is greater than the maximum age-control depth, then parameter dmax=1520 should be entered.

 

See the instructions for Clam for more options and explanation.

 

Below is the graph for this age model.