Search
Upcoming
Syndicate
Open Source Dendrochronology? Not yet
The Aardvarchaeology blog run by Martin Rundkvist has an interesting and detailed article about one current major problem of dendrochronology, which he summarises as:
Dendrochronology has a serious organisational problem that impedes its development as a scientific discipline and tends to compromise its results. This is the problem of proprietary data. When a person or organisation has made a reference curve, then in many cases they will not publish it. They will keep it as an in-house trade secret and offer their paid services as dendrochronologists. This means that dendrochronology becomes a black box into which customers stick samples, and out of which dates come, but only the owner of the black box can evaluate the process going on inside. This is of course a deeply unscientific state of things. And regardless of the scientific issue, I am one of those who feel that if dendro reference curves are produced with public funding, then they should be published on-line as a public resource.
I can't but agree with his view, perhaps observing that this Bad Practice™ is more widespread than one usually thinks, at least in all archaeological sub-fields, not to talk about other disciplines.
The interesting news is that someone is actively working to enhance dendrochronology and make data available with common 21st century tools like the web. There is a wiki dedicated to methods, programming, equipment, measurement data and sites related to dendrochronological studies (you might know I have a strong passion for wikis), run by a Swedish company, but it's open to anyone willing to contribute.
One drawback of this initiative is that even though the guys behind the wiki have also developed two software tools for recording and analysing dendrochronology data, but this software isn't free nor open source (and it only runs on Windows, but this wouldn't be my primary concern if I had the source code). Thus, speaking of open source dendrochronology is largely misleading at this point.
The IOSA.it website is a work by the IOSA Project and is licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License. Based on a work at www.iosa.it.
Comments
Pingback
[...] is the original post: Open Source Dendrochronology? Not yet | IOSA.it This entry was posted on Tuesday, June 23rd, 2009 at 4:40 am and is filed under News, Software, [...]
Open software
There are open and free dendro software available too. Please have a look at
http://web.utk.edu/~grissino/software.htm
An other Open source project
An other Open source project for dendrochronology is:
http://cran.r-project.org/web/packages/dplR/
But I do not know much about it. It may probably be focused on other things than archeology, eg. dendroclimatology, but the needs for archaeological purposes is the basic features (correct dating of single samples towards references and synchronize collections of samples and compiling chronologies from such collections) and those functions will certainly be there too, in one or another way.
Open software or software not enough open
Corina is an open source, freely available, dendrochronology program used and developed by the Cornell Tree-Ring Laboratory.
http://dendro.cornell.edu/corina/index.php
About a year ago (or less) I tried to download the package but I did not manage to make it work. I think that it requires a database being set up for it. Neither have I been able to find documentation that gives an introduction to using the package. I suppose that the support group is not yet big enough to be able to write all that is needed. Eventually - and hopefully - this may change.
My own package, CDendro & CooRecorder, that is sort of criticized for not being free, is anyhow sold at a very low price (68 US$) to make it available to anybody interested.
open vs free (as in freedom)
Lars,
thanks for your reply. I didn't mean to be harsh. Actually, I do appreciate your work in putting data and information on the web, available for anyone, and I was glad to read your article.
Given that the IOSA project is dedicated to free and open source software (see http://www.gnu.org/philosophy/free-sw.html for a brief introduction on what is meant by “free and open source”), I found it obvious to point out that, no matter how low the price is, your packages are not “open source” in any sense (you could even charge for them anyway http://www.gnu.org/philosophy/selling.html ).
I'll try to write a brief summary about FOSS for dendrochronology and freely available data in the next few days if I have some spare time.
Transparent dendrochronology
Martin did use the term "Open source dendrochronology" (we have not used it ourself) and we have discussed it together with Martin after reading your post, and you are of course right: What we are doing is not strictly "Open source dendrochronology", as "Open source" is normally about software. "Transparent dendrochronology" may be a better term for what we are trying to do. About dendrochronology the main problem is the lack of dendrochronological data. Without reference data any dendro software - open source or not - is almost useless, and no skill helps if you do not have access to reference data or adequate wood samples to measure. So our scope is to try to make as much useful reference dendro data as possible accessible for anybody by pointing at what is already available and by making our own material open and also reusable. We also are interested in testing methods, to find out reliable statistical levels according to different methods, to find out when a dendrological match is reliable or not and things like that, although there are no articles in the wiki in that field yet. It would be fine if open source programs for dendrochronology will be written. I will very much encourage people who are interested in the field and know about programming to either join the Corina project, or start something new. I would be happy to support with information about methods etc, although I am not a programmer myself. I think we may also be aware that an institution may very well GNU license their software but still keeping all their valuable dendro data closed. So it is at least two tasks here: Software and Data. Both are important, but they do not necessarily have to be driven by the same people. Any openly published dendrochronological data will anyway be valuable for other dendrochronologists despite they may use open source software or not! And the point is that if it is published not only as average series, but "sample by sample", it will be possible for anyone to evaluate the quality of the material if it is consistent or not. So the fact that a collection of samples once may have been build with non open software, is in fact not a problem: What is really a problem is that data (measurements and references) is closed so that results can not be scrutinized by others.
Torbjörn, I couldn't have
Torbjörn,
I couldn't have summarized the whole topic better than you. I agree with you entirely.
Free circulation of data is probably the most important issue, and for this I recommend not only to embrace standard formats (universal or not, provided they're readable without being constrained to a single program), but also to follow best practices like those published the the Science Commons initiative (e.g. the Protocol for Implementing Open Access Data). By the way I was glad to find on the Corina website a reference to the Tridas effort to produce a universal data standard for the dendrochronological data.
At the very same level of data are of course methods, and when it comes to statistics we have started our (generic) collection of methods on the Quantitative Archaeology Wiki (no dendro there, though I'd like to have it). Of course dendrochronology is not just for archaeologists, but I do believe that spreading and enable people to actually learn those methods, and then test them against data, is by far the best way to make a good practice.
And it is true that there are many institutions and people who might like a GNU license but won't share their data: I like to think about free software more like a “methods” thing, but for a discipline to actually grow “open” I firmly believe the two (data and methods/software) are sort of indivisible. Personally, I started experimenting with free software, and a few years later I found out that it was of little use to share tools without sharing data. Probably the inverse is less obvious, but at least I hope that the general scientific feeling will go in the direction of promoting both, together.
So, you have my whole support for your effort in data sharing. I'll try to put together a brief page about open source software for dendrochronology on the Cybis wiki if you agree, but more than that I'm interested in statistical methods.
Thank you both for your replies, and of course also to Martin... if he didn't write "open source" I wouldn't probably have even noticed his article ;-)
Tridas and more
You are welcome to contribute to the Cybis wiki! In the future there will probably be articles on Cybis wiki about statistical issues which may also be useful at iosa wiki too, but it is still somewhere in the unknown future... We still have a huge amount of work to make our own data available in a useful way.
About the Tridas-initiative: Yes it is very welcomed. We are seeing forward to its release. The case is not that we do not have open formats yet. Indeed we have, especially the tucson-format http://www.cybis.se/wiki/index.php?title=Tucson_format is widely spread and really transparent, and free (PD i think...). It is a bit of a compromise between what is optimal to be readable for humans and for machines. You will be able to do some edits by hand if you like. But the format is unfortunately very poor when it comes to handle metadata, and complementary measurement data as well. So hopefully Tridas will become a useful tool for sharing and storing data.
Pingback
[...] Open Source Dendrochronology? Not yet | IOSA.it [...]