Setting up CDendro

Last update: Jan 17 2014
There are a few standard settings in CDendro that you might change:
Curve plotting:
Old times to the right - or old times to the left (now default and as with most diagrams in a book)?
Curves can be plotted with old times to the right or to the left. The old default setting was old times to the right, a relict from early versions of CDendro when this was the only way to plot. Today you can have the curves plotted the way you want. Change the setting as you like through the menu command Settings/Plotting window settings. See that the box "Plot curves with old times towards right" is unchecked to get the curves look as conventionally in books and journals.

Note: A few old examples within the help texts might still have old times plotted towards right!

Naming of cropped samples.
CDendro has a mechanism to crop a sample, i.e. to cut out a section of a ring width curve and show it within a new "sample window".
Note that in CDendro the ring width index is always counted from the late end of the curve!
The cropped sample in its new window is given the same name as the original but with a default extension of "_BLOCKOF" as shown above.

If you then want to save your cropped sample as e.g. a ring width file, the proposed file name will also be like "6680NY_BLOCKOF.wid"

Although "BLOCKOF" is very clear, you might find it a bit clumsy. Personally I have changed that extension from "_BLOCKOF" to just "_C" (C for cropped).

You can change this through the menu command Settings/More settings/Extension to use in file names for cropped blocks. We recommend using the more cryptical but shorter string "_C" instead of "_BLOCKOF"!

Note: The command "Uncheck members already in target collection", will uncheck also those members where a cropped version is within the target collection according to the name used.

Making the red normalized curve more visible
You might prefer to make the red normalized curves more distinct! This might be especially important for demonstrations or for pictures to be published but also for daily use. You can choose an appropriate stroke weight for these curves through the command Settings/Plotting window settings as shown above!
Display of crossdating correlation results.
If you are new to CDendro, click the button "Set small default" shown as the leftmost button in the lower part of the picture above. This will give you access to a pair of crossdating algorithms which will give you useful values for most of your crossdating problems.

When you feel more experienced, come back here and make your choise among all the other normalization methods which are available within CDendro.

If you are new to CDendro, skip this section and come back later!

Tree ring width data should best be processed by a high pass frequency filter before any correlation analysis is done on the data. In CDendro this process is named "normalization", see the section on "Dendrochronology, curve matching and mathematics".

There are a number of normalization methods available. The default "main" method since CDendro 7.7 is "Proportion of last two years growth LIMITED, P2YrsL". (The "main" method is selected with one of the radio buttons above.)

On the "Workbench" you can see the results of a correlation analysis done, e.g. with only results from that "main" method displayed:

--Rel Over  P2YrsL----**  (year) 
-year  lap   CorrC TTest 
    0  103    0.73  10.7  (1995) (as dated) 
  238  103    0.28   2.9  (1757) 
    4  103    0.28   2.9  (1991) 
   19  103    0.26   2.7  (1976) 
  .... 

Most methods are sometimes fooled to signal a match though it is false. But it is very rare that all methods are fooled at the same time! Therefore we recommend you to enable CDendro to calculate and display correlation values for more than one normalization method! With the settings as in the picture above we get:

--Rel Over   P2Yrs------  BaPi-------  C84F-------  BesIE------  MeanSF-----  GLK--  Skel- P2YrsL----**  (year) 
-year  lap   CorrC TTest  CorrC TTest  CorrC TTest  CorrC TTest  CorrC TTest    GLK   Chi2  CorrC TTest 
    0  103    0.72  10.5   0.75  11.4   0.71  10.3   0.61   7.7   0.70   9.8   0.71   26.7   0.73  10.7  (1995) (as dated) 
  238  103    0.27   2.8   0.18   1.8   0.20   2.1   0.13   1.3   0.20   2.0   0.56    2.4   0.28   2.9  (1757) 
    4  103    0.28   2.9   0.32   3.3   0.28   2.9   0.23   2.3   0.28   2.9   0.55    2.4   0.28   2.9  (1991) 
   19  103    0.27   2.8   0.30   3.2   0.26   2.8   0.21   2.1   0.26   2.7   0.56    2.9   0.26   2.7  (1976) 
  .... 

Note that the rows are here sorted according to the TTest values of the "main" method which is identified with "**"
Please also note that (since CDendro 7.7) sorting by TTest or by Correlation Coefficient can be changed by a checkbox on the Workbench of every sample window. Changing this will make the change for all currently open windows.

The "MeanSF" method is calculated from a mean of correlation coefficient values from P2Yrs, Baillie/Pilcher, Cross84 and BesIE. When the "MeanSF" method is selected as the "main" method the normalized curves shown are based on the P2Yrs method but all correlation coefficients shown in the curve display are based on mean values of the four methods.

The P2YrsL method is based on the P2Yrs method (=this years growth divided by the growth during this and the previous year) though high peaks are cut to avoid making the method fooled (i.e. the correlation calculus using the method fooled) by extremely narrow rings. This is a great advantage with this method. Anyhow we strongly recommend you to always check that the Skeleton Chi2 value is high enough. If this value is very low, your current "match" is usually false! For a treatise on this matter, see the section Fooled by narrow rings and the normalization method.

Setting up Windows to show file name extensions.
CDendro identifies the content of your data files by the file name extension of your files, e.g. a Tucson decadal .rwl file should be named like Namdo.rwl, a Heidelberg formatted collection file is named e.g. myData.fh etc.
So, to avoid problems, you should setup your Windows system to show your file name extensions! This can be done either for your whole system or for individual directories where you store tree ring data.

Warning: When you download a tree ring data file from e.g. the ITRDB database, you might be presented with an option to save the file as "Save as type: Text document" with the name swed302.rwl
But then Windows will usually save the file as "swed302.rwl.txt"!
If you then do not see the file name extension (.txt), you will see "swed302.rwl", which CDendro will not understand as a .rwl collection file as it is actually named swed302.rwl.txt!
This is a common problem not only with CDendro!

To get the file saved with the proper extension ".rwl", you should change the type from Text Document into "Save as type: All Files" before you click on the Save button!

When some button cannot be reached... About Font size setting within Windows

It might happen that some pop-up window in CDendro is too large to make it fully visible on your screen. This is because CDendro has not been tested and modified for Windows large font settings, which makes all buttons larger and all text larger.

The picture above shows a pop-up window in CDendro seen (left) with a Large font setting and (right) with Normal font setting.

If you run over this error, see that you change your Windows font setting to "Normal"!

To do this, in Settings/Control panel/Display/Appearance change the FONT SIZE to normal!

If this makes text too small and difficult to read, consider to use an external large screen. Mine is 18 inches wide with 1680 pixels in width - works fine for me!



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