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BESANÇON STANDARDIZED TREE-RINGS DATA CONVERTER
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Alessandro Ravotto, July 4, 2017.



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1. BACKGROUND AND PURPOSE OF THE PROGRAM
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The "Laboratoire de Chrono-Ecologie" at Besançon uses a standardization method called "corridor method". For some technical details on this method, see Lambert et al. (2005), p. 245-247, Larsson (unpublished) and - probably, but I've not read it - Lambert (2006).

This standardization method can lead to have tree-rings indexes both negative and positive. A consequence of this is that no avaiable dendro program can use this type of data for analysis,[1] neither those that can deal with several types of dendro formats.[2]

Anyway, if values are shifted so they are all above zero, they can be crossdated as if they were "pure" tree-rings widths.
Once transformed, I suppose they cannot be used for dendroclimatic analysis, but they still are useful for dendroarchaeological purposes.

This program offsets above zero all the values in a collection of "standardized Besançon series (or curves)", so it can be used as reference curve.

For what I know, actually there is only one chronology freely avaiable whose data are published in that format, and it's called "HistoricOaks-20050126".[3]
It is formed by "low altitude oaks" (below 500 m a.s.l.) from France and it is published in two diferent versions, maybe according to two variations of the standardization method.
You can download it from https://chrono-environnement.univ-fcomte.fr/spip.php?article1820&lang=fr, clicking on "Hist20050126-EBes" or on "Hist20050126-C1" files.

This is a command-line utility. No need for a Graphical User Interface for an almost "single use" program.


Footnotes:
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[1] Except, supposely, a program called "Dendron II", that was the subject of the Research diploma of G. Lambert (Lambert 2006) and is not avaiable to the public.

[2] The programs CDendro (L. A. Larsson, Cybis Elektronik & Data AB) and TRiCYCLE (Brewer et al. 2011) can perform conversions from "pure tree-rings widths" of "Besançon format" to the mosts used formats in dendrochronology, but not from this kind of standardized values.

[3] See Lambert et al. (2005). The other big contribution of French laboratories to the European dendrochronology consists in a second chronology, spanning from protohistoric to roman times. This chronology is published in "raw values" and in standardized values, the latter according to some method that produce only positive values. No need of this program in such cases.


References:
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Brewer, P. W., Murphy, D., Jansma, E. 2011, "TRiCYCLE: a universal conversion tool for digital tree-ring data", Tree-Ring Research, 67, 135-144

Lambert, G., Durost, S., Cuaz, J. 2005, "2500 years from dendrochronology back to ancient French human biotopes. Trees studied: low altitude oaks", Annual conference on Tree Ring, Climate, Archaeology and Environment (TRACE), Fribourg, 21-23 Apr. 2005. Association for Tree Ring Research (ATR), 4, 244-264.

Lambert, G. 2006, Dendrochronologie, histoire et archéologie, modélisation du temps; le logiciel Dendron II et le projet Historic Oaks. Research diploma. 2 vol. Besançon.

Larsson, L. A., unpublished,  "The Besancon corridor method", http://www.cybis.se/wiki/index.php?title=Corridor_method



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2. USAGE OF THE PROGRAM
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The program needs at least Java 1.6 installed in your machine.

Start the program by opening a Command Line console in the folder to which you have saved the program and type "java -jar DendroBesConv.jar" (without quotes, case sensitive).


Quick usage test:
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1) Download the file "Hist20050126-EBes.txt" from https://chrono-environnement.univ-fcomte.fr/spip.php?article1820&lang=fr and copy it into your User Directory.
2) Start the program
3) Type the following options: 3, 3, 4, 5, pressing 'Enter' after each selection.
4) You will have in your User Directory a "Heidelberg format" file called "BesFileConverted.fh".


Detailed usage:
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The program brings you to tree diferents steps. On Linux, each menu will be presented as a nice "new screen"; on Windows (and probably on Mac), each menu is showed below the previous one. 
The options presented by the program are quite self-explanatory, anyway:

- "Main menu"
Type "1" (without quotes) and press Enter for Help. At this moment, anyway, there is no Help inside the program.
All instructions are in this README file.
Type "2" (without quotes) and press Enter to check where is your "User directory", that has a relevant part in the process. Though I suppose you already know where it is.
Type "3" (without quotes) and press Enter to really start the program and go to "Step 1".
Type "4" (without quotes) and press Enter to exit the program.

- "Step 1: Read file"
Type "1" (without quotes) and press Enter to go back to the Main Screen.
Type "2" (without quotes) and press Enter to set the path to the file to be read.
The program can convert files with values expressed in "EBES" or in "POL1", apparently two different variations of the "Corridor standardization method".
Though all files produced by the French laboratory are "text files" (they have the ".txt" extension), the files that contain "EBES" values have a name that ends with "-EBes", while the files that contain "POL1" values ends with "-C1".
By default, the program searches for a file called "Hist20050126-EBes.txt" and located in your User Directory.
Probably the easier way is to copy the file "Hist20050126-EBes.txt" to your User Directory and let the program find it.
If you prefere to read a "EBes" file in another directory, or to read a "C1" file, you can type a new (complete) path and the corresponding filename by selecting this option. 
Type "3" (without quotes) and press Enter to read the specified "EBES" or "POL1" Besançon standardized file and go to "Step 2".

- "Step 2: Offset values"
Type "1" (without quotes) and press Enter to go back to the Main Screen.
Type "2" (without quotes) and press Enter to examine the original values of a single curve of the collection before the conversion. Look at the list printed on screen, enter a "curve number" and press Enter. Before the values, some metadata are also presented; if you can'y see them, scroll up your console.
Type "3" (without quotes) and press Enter to specify the minimum "ring width" to which each curve of the collection will be shifted to. Default value is 20. I don't believe it makes some difference for crossdating purpose.
Type "4" (without quotes) and press Enter to start conversion and go to "Step 3".

- "Step 3: Save transformed data to file"
Type "1" (without quotes) and press Enter to go back to the Main Screen.
Type "2" (without quotes) and press Enter to examine the original values of a single curve of the collection after the conversion. Look at the list printed on screen, enter a "curve number" and press Enter. Before the values, some metadata are also presented; if you can't see them, scroll up your console.
Type "3" (without quotes) and press Enter to change the type of file to which data will be saved to. At this moment, anyway, there is only one type of file avaiable (with extension ".fh", i.e. "Heidelberg format").
Type "4" (without quotes) and press Enter to change the path and the name of the new file that will be saved.
By default, the program will save in your User Directory a file called "BesFileConverted.fh".
If you prefere to change the path and the name of the file, enter a valid complete path and remember to add the extension ".fh" to the name.
Type "5" (without quotes) and press Enter to save transformed data on the disk. The file will be saved without "collection metadata", only with the usual "Headers" of each curve.

END OF README