Dendrochronology software

Introduction

In collaboration with Dr. Ed Cook of Columbia University’s, Lamont-Doherty Earth Observatory, we are providing here links to some of the commonly used programs in Dendrochronology. For many years these programs have served us, and the greater tree-ring community, well by providing both basic and sophisticated tools for the inspection and analysis of tree-ring data. Consequently, the programs are continually updated and improved, reflecting our commitment to furthering tree-ring research, as well as keeping up with the latest analytical methodologies, and computing platform technologies and software. Therefore, it is wise to visit this site from time to time to check for updates and new additions.

All these programs are written in ANSI standard Fortran77 and Fortran90 with emphasis on performance rather than appearance. What this means is they do not look or operate with the typical drop and drag GUI interface that many, particularly younger students and scientists, are used to. However, do not think their seemingly primitive appearance belies their computational power and usefulness, that would be massively incorrect. Over the years these programs have been in existence they have been optimized to produce the most commonly performed operations in Dendrochronology with extreme precision and speed, and without any costly third-party interventions.

System requirements

Regrettably 2020 will be the last year we will support 32bit platforms. From now on all new programs and updates to existing programs will only come in the form of 64bit applications. We will still provide  32bit versions upon request  but they will only be archived versions lacking any post-2020 updates.

Disclaimer

All  programs, with few exceptions (ŧ), are the intellectual properties of the Tree-Ring Lab (TRL), Columbia University, and the Tree Ring Unit (TRU), University of Cambridge. However, you are free to use them and give them to others.

That being said, we (TRL and TRU) are not responsible for what you do with these programs, nor make any claim for or against results from experiments you perform with them.

We are also not responsible for training or supporting of these programs beyond that provided here on this website or contained in the program descriptions files that may or may not accompany a program. A popular destination for public software support is the International Tree-Ring Data Base Forum (ITRDBfor). More often than not a search through the forum’s archives will provide one with the answer they are looking for. If, after going to the forum you are still experiencing difficulties you may send questions to Paul Krusic [pk466@cam.ac.uk], be sure to include information about the platform you are using, the program name and version, as detailed a description of the issue as you can and, if applicable, a sample of the data/files you are experiencing difficulty with.

Programs

Downloads (last update: July, 15 2022)

To receive the latest TRL-TRU program suite click on the appropriate link below.

• Mac OSX12 Program Suite
• Windows7 Program Suite
• Mac OSX10 Program Suite

Installation notes

Immediately you will receive a compressed .zip archive that contains all the above programs, a folder with some example input files and, in some cases, a plain text file containing a brief description of the program. After decompressing the archive, and before launching a program, it is advisable to move the executable file out of the decompressed archive folder it came in to a new location/folder on you hard drive. For some reason the latest OSX operating systems will not allow you to launch a downloaded program in the folder it came in. Once removed, simply double-clicking on the program icon launches the program. Be aware that both the program and any input data you wish to use with the program must be in the same folder/directory.

Graphics program installation notes

Programs with an asterisk (*) following their name produce publication quality (eps) graphics and require a couple extra installations steps before they may be used.

Step 1. Install the appropriate X11 server and graphics libraries for your operating system.

OSX: XQuartz

Windows: CygWinX.

Step 2. Install the PLplot graphics font files.

OSX: Place the folder PLPLOT_DATA, with all its content, in your computer’s /Applications folder.

Windows: Place the folder PLPLOT_DATA, with all its content, in your computer’s C:\ directory.

Step 3. OSX 10.8 and greater

Finally, for Mac users running OSX 10.8 and greater. Before attempting to launch any of these programs move the program out of the folder it came to a new location on your hard drive. This is really important because your OS will not allow an un-certified program to run within its distribution folder. Secondly, the first time you attempt to open any of these programs your operating system will either display an ominous “access denied” message, with no further details, or ask you to relax the security embargo it automatically places on any program that did not come with an Apple Security Certificate. In both instances you must go to your computer’s System Preferences/Security Control Panel and “release” the program. Once “freed” from Apple’s embargo -clearly they don’t trust anyone to make judicious decisions for themselves, you may move and run the program anywhere on your computer as many times as you like. So long as you do not delete or replace the program with a new version that has the same name you will never have to do this again.

If simply going to System Preferences/Security Control Panel and releasing the program from embargo does not work, here is the ultimate solution. If you are not already familiar with UNIX, then before attempting this you may wish to read up on some basic UNIX commands like “cd” “ls” and “pwd” etc…

1. Open the program “Terminal” in /Applications/Utilities.
2. Navigate to the folder where you placed the program using the “cd” command.
3. Enter the following:

xattr -d com.apple.quarantine <filename>

where <filename> is the complete name (case sensitive) of the program you want to liberate.

Example :> xattr -d com.apple.quarantine ARSTAN_49v1a_AWE.app

More information on installing graphics programs and changing the quarantine attribute on OSX10.14 and greater executable files can be found in the help files included with each distribution.

A help webpage for circumventing Apple’s quarantine protocol is found here: https://www.lifewire.com/fix-developer-cannot-be-verified-error-5183898

Input/output files

Remember, in order to run properly the executable program file and any input file(s) must be in the same directory. In addition, all input files must be plain text files <filename.txt>, properly formatted, and encoded with the appropriate end of line (EOL) characters. The latter is very important. Mac’s and PC’s use different conventions for marking in a file where the characters in each line end. Harking back to the days of typewriting when progressing down a page was a two-step process, one to advance the paper and a second to move the carriage, the EOL character in a Windows text file is a CarriageReturn followed by a LineFeed (CRLF). OSX Mac and UNIX text files use a different convention, a single LineFeed (LF). What all this means is, if one attempts to provide a Windows created text file to a Mac program, the program will not know how to find the end of any lines in the file and will either hang-up, crash, or even worse, appear to run successfully but produce spurious results.

All Mac programs only accept input files with UNIX EOL characters; a single LineFeed (LF). All Windows programs only accept text files with Dos EOL characters; a Carriage-Return/Line-Feed (CRLF). So, how do you find out what the text encoding is of a file? Well, on OSX and Windows computers with UNIX base systems or emulators there are two built-in EOL conversion programs; dos2unix and unix2dos. If you are not comfortable using the terminal interface on your computer to access these programs, then there are a number of free text editing programs like Notepad++ (for Windows) and TextWrangler (for Mac) that provide EOL conversion and much, much more. We have also noticed that the most recent version of MSWord can change the EOL characters of text files, just be careful to save the changed file as Plain Text when converted. If it feels like I have gone on way to far on this topic it because the vast majority of help requests we receive stem from this confusion. Besides, having a decent text editor, and learning how to use it well, is a helpful skill to have for anyone involved in quantitative studies.

How to cite and attribute

All programs, with the exception of one, are written by Dr. Ed Cook (TRL-LDEO-CU) and myself (PJK-TRU-UC). The program Cofecha was written by the late Richard Holmes (LTRR-UA).

The proper citation for program ARSTAN (including version number) is:

Cook, E.R., Krusic, P.J., Peters, K., Holmes, R.L., 2017. Program ARSTAN (version?), Autoregressive tree–ring standardization program. Tree–Ring Laboratory of Lamont–Doherty Earth Observatory.

The proper citation for the use of autoregressive modelling in tree-ring standardization, the principal advantage of the ARSTAN methodology is:

Cook, E. R. (1985). A Time Series Analysis Approach to Tree Ring Standardization. PhD thesis, The University of Arizona.

The proper citation for program SigFree (including version number) is:

Cook, E.R., Krusic, P.J., Peters, K., Melvin, T., 2017. Program Signal Free (version?), RCS Signal Free tree–ring standardization program. Tree–Ring Laboratory of Lamont–Doherty Earth Observatory.

The proper citation for the Signal Free Methodology is:

Melvin, T., Briffa, K,R., 2008. A ”signal-free” approach to dendroclimatic standardisation. Dendrochronologia 26 (2008) 71–86,

^ŧThe proper citation for program COFECHA is:

Holmes, R.L. 1983. Computer-assisted quality control in tree-ring dating and measurement. Tree-Ring Bulletin 43: 69-78.

^ŧThe proper citation for program DPL is:

Holmes, R.L. 1983. Dendrochronology Program Library, Laboratory of Tree-Ring Research, University of Arizona, Tucson, AZ USA.

To cite any other program downloaded from this site you may use the URL of this webpage.