A tip from Wayne Hamilton:
Sometimes I create ring width files in Excel and then decide to analyse them in CDendro.
Because CDendro expects to open a .wid file, it is necessary to
convert the Excel file to Example.wid. I do this by copying a column of ring width data from Excel to Notepad.
[The top of the column should be the youngest ring.]
Then I "Save As" the Notepad file as Example.wid and select "All Files" as the type, placing the new file into the appropriate folder.
A comment by Lars-Åke:
My version of Notepad has no "All Files" alternative, so then I have to save as "Text document"
(i.e. the file is saved as Example.wid.txt) and then remove the .txt extension from the file name afterwards.
(See also tip below on handling file name extensions in Windows.)
Question: I've been going through the training sessions but find that I am having
problems downloading the pola014.rwl file .. It automatically saves as a
html through the 'save as' function and if I copy and paste into notepad I
can only do it as a txt file, which when changed to Answer:
If you are farther on and are seeing the actual data on your screen:
(i.e. you have clicked the file name in the list mentioned above)
Another solution:
You can do that already from Wordpad if you use the Save-As command again.
One way is like this: (best way!!!)
When you see the LIST of various files (at the ITRDB), right-click on the file you want to store.
In the pop-up menu choose Save Target As
In the Save-As pop-up menu change SAVE AS TYPE from Text document to ALL FILES
This will save the file with its original extension and not the added .txt extension.
Select from the top-bar menu File/Save As
See that Save as type is set to Text file (.txt)
Save it by clicking the Save button.
You then have to change the file name from pola014_rwl.txt into pola014.rwl using your Windows Explorer.
When you see the data on you screen, select the whole text (e.g. press Ctrl-A)
then do a copy to the clip-board (Ctrl-C)
Then go into the Notepad editor (Programs/Accessories) and paste the text into it (Ctrl-V).
Use the menu-command File/Save As and select Save-As-type to Text document
If there is an alternative "All files", then select that!!!! (no such alternative in my version of Notepad)
If there was no All-files-alternative, you have to afterwards remove the .txt extention.
Then you can see the filename in the list as pola014.rwl.txt
Right-click on it, and select Rename and remove the .txt extension.
You will then probably get a warning - just ignore it and then exit the Save-As dialog box through the Cancel button.
Question: I have created my collections as .fil files. When and why should I have them stored in .rwl files?
The .fil file format allows me to collect a number of different coordinate (or ring width) files and relate them to each other with their offsets after crossdating. When finding errors I can easily change the inner content of a coordinate file without affecting its membership in the collection. I can backup my whole datastructure on a CD to keep in an archive. So why should I use .rwl files?
Answer: The answer is "communication" both with other projects of yours and communication with collegues and for publishing in the ITRDB.
When you open a .fil collection with 50 member files, the program looks up all these files. If you have changed the beginning of any file, that file will not be crossdated correctly to the rest of the collection. If files have been moved to another directory (that can certainly happen after two years) the collection will not open as expected.
If you move the collection to another directory, you need to have all your coordinate files placed around it as before to be able to open the collection.
On the other hand, if you Write the collection as decadal file that file will be a self-contained entity. All tree ring data is within it. You can send it anywhere, you can copy it, you can do what you like. Data will not get lost. And still you can manipulate the members. Though you do not have the coordinate information and images available for update. But that is usually not necessary during a later stage of a project or when a reference is being "just used".
As a bonus, opening a .rwl file is much faster than opening a .fil file, which matters for big collections
especially when you only want to create a mean value of the collection.
Example: The command "Test towards rest of collection" takes 27 seconds to run on my machine for a 50 member-collection
with .pos and .wid -files. When run with the members in one single .rwl file it takes only 4 seconds!
March 14 2005
Question: I have not been able to find a good way to get the reports to print out so that the columns are lined up. I can right click on the report and it will print correctly (which is very convenient) but it will only print the portion of the report that is visible and the part that is not visible is not printed.
Answer:
Reports in a collection's report frame:
Use the menu command: Collections/Save collection report As (.txt or .htm) to store the
report in a separate file. This can be edited or printed from MS Word.
You can also use a Copy-text/Paste-text operation if you first paste into the Notepad program or a source code text editor like Lugaru's Epsilon. If then copied from that program and pasted into e.g. Wordpad or MS Word using a Courier typeface, the result looks fine.
Correlation reports created from the "Workbench" of a sample:
Select the text, copy it (Ctrl-C) and Paste (Ctrl-V) it into e.g. the MS Word editor.
See that a font with fixed width is selected, e.g. Courier.
To select ALL text: Click to the left on the top line of the report.
Scroll down to the end of the report. Press the shift-key and hold it down and
click after the end of the last line. The whole report text then lights up, i.e. it is selected!
Press Ctrl-C to copy it!
March 14 2005
Here is a bit of correspondence with a new CDendro user who asked how to print the documentation. He wanted to take it with as "light reading" on a journey.
Question: I am attempting to print off the help files but I am experiencing extreme difficulty in getting the information onto an A4 sheet size ..... the text and graphs are off page to the right and even when I change the margins the text remains the same. ... Any suggestions please.
Excerpt from my reply (later somewhat edited):
The help text is available either at my site or if installed in your machine at
C:\Program Files\Cybis\dendro\index.htm
You can read the text on your screen directly through your normal browser.
You can open the help text from CDendro - in that case CDendro opens your standard browser.
To get the widest possible printout it is best to right-click an item (chapter) in the left column
to open it in a separate new window.
As you have found out Internet Explorer is not good at printing the content of a web site.
So the result is not too good.... But there is a solution which I think you should try - it works!
Use the Mozilla Firefox browser! You can download it for free from: http://www.mozilla.org
In Firefox printing is available from the top menu through the commands File/Print preview and File/Print. The result is very readable though the page breaks occure where they are... Anyhow it works and all text is actually printed!
Firefox has another browsing function which I do like heavily:
Many sites on the net are made with very small fonts - I do have problem to read the text.
In Firefox you can click the "Ctrl +" key to make the text instantly bigger without changing any
other settings. And make it smaller with "Ctrl -".
Best use the control key in combination with the + and - keys to the very right of your keyboard.
Plotting sideways.
I get tired in my right arm and shoulder by moving my hand backwards and forwards with the mouse during a long time.
I have found that it makes much less strain to me when I move my right hand SIDEWAYS.
So when measuring a long dendro sample I find best to have the "measuring line" oriented horizontally on the screen.
Use optical mouse.
An optical mouse works much better than a mechanical one with a ball rolling on your table. An
optical mouse gives you a lot of comfort!
Arrow keys to scroll.
To make scrolling the picture without using the mouse, you can use the arrow keys!
Click with a keyboard key instead of using the mouse button.
I also get tired in my right hand by clicking with the left mouse button on that many new coordinates.
The command Settings/Key binding gives you a way of defining which keyboard key
to be used as a synonym of the left button mouse key. I prefer to use the
right shift key for this as it sits near the arrow keys on my keyboard.
So I position the cursor with the mouse in my right hand, and click
the coordinates on the keyboard with my left hand and I can quickly scroll using the arrow keys.
Right-click to enter group mode
The right button of the mouse is bound to the button for switching recording modes i.e. from/to group recording.
See the section "A trick for dendro data" in the CooRecorder help text. By right-clicking on the mouse you can quickly
shift recording mode to change the starting point for your next sequence of coordinate points.
CDendro
Standard deviations
When you click on the button "Create mean value sample"
both a ring width mean value curve and a normalized mean value curve are created.
Also the standard deviations are calculated and displayed when there is no other active reference
(which normally is shown together with your sample curve).
If there is another reference you can click in the checkbox "ShowStdDev" to see the
standard deviation curves laying on each side of both mean value curves.
Decadal files:
CDendro can read decadal files with the "-999" flag for missing ring data. According to Henri D. Grissino-Mayer, this is not an established standard, but it is nevertheless used by Dr. Schweingruber's laboratory. In this case CDendro will handle the correlation analysis as if the missing data are there, but the algorithm does not "punish" the lack of data for these years.
The correlation value for this sample towards the reference curve is 0.71.
You can replace an old measument with a new one even if it comes from another directory (2) and you will still keep the correct sorting order which makes CDendro see which members come from the same stem.
When you copy a sample (member) from a collection into the target collection, you will get a warning message if that will overwrite an already existing member in the target collection. This is an easy way to replace an erroneous measurement serie already stored in a big .rwl-file with a new measument serie from a .pos-file.
Note: The member list above is written with quite a big size font. If you prefer to have it with a smaller font size giving you more members visible on the screen, use the menu command Settings/More Settings and uncheck the box "Use big fontsize for collection members".
The test towards rest of collection gives a list of how well each member of a collection matches towards the rest of the collection. When some members actually consist of several radii like NMG01A, NM01B then you will get misleading results if NMG01B is included in the rest when we calculate how well NMG01A matches to the rest.
When "Sum by stem" is checked, all radii of the same stem will be excluded from what is considered as "the rest" of the collection. "Sum by stem" is now checked by default when a collection is opened.
NMGE4B 55 -5 0.70 6.7 49 -5 0.70 6.7 49 1995 ...
NMGE5A 54 -9 0.66 5.7 44 -9 0.66 5.7 44 1995 ...
NMGE5B 38 8 0.52 3.6 37 8 0.52 3.6 37 1995 ...
NMGE6A 40 2 0.52 3.7 39 2 0.52 3.7 39 1995 ...
Mean corr. of first column when overlap >= 40 (54 samples): 0.50
Standard deviation intervall 0.33 - 0.68
The report ends with statistics on how well each member matches towards the reference used.
In the example above a collection based on Norway spruce (PCAB) from Nämdö has been compared towards a reference
solely based on Scots pine (PISY) also from Nämdö.
The report shows a high probability that an individual spruce sample
will match towards the Scots pine curve with a correlation coefficient in the range 0.33-0.68
When the same calculation is done for living trees of Spruce and Scots pine from Dalarna in Sweden (Axelson) the range is only 0.21-0.36. When based also on timber from old houses, the range is as low as 0.11-0.31