RUNNING CANOCO AND CANODRAW
(versions before 4.5)
This section is practically extinct! I am
leaving it on the web just in case you have an early version of CANOCO
installed in your laboratory, and cannot afford (or have not yet ordered) a
recent upgrade. Most of the issues discussed below are currently
irrelevant, or of merely historical interest. The bulk of this page
involves version 3.x.
For versions 4.5 and above, the documentation has improved substantially, and there is little need for an additional guide (unless you have pirated software, in which case, please report yourself to the authorities).
This section covers the DOS versions of the program (CANOCO 3.x). The newer Windows95 version is much smoother, and easier to use. If you are using it, please browse this section, and then jump to CANOCO for WINDOWS.
Please also read Data formats for input into CANOCO, DECORANA, or TWINSPAN
My coverage of CANOCO and related programs here is not meant to imply endorsement. It is merely meant to clarify some of the most frequently encountered problems in one of the most frequently used packages.
Note that CANOCO and CANODRAW have their own manuals. Because of this, I am only giving a cursory outline of the use of CANOCO and CANODRAW.
To perform Analyses on CANOCO and view graphical output, the general procedure is:
- Get data into shape: full format or reduced condensed
format, SAVED AS ASCII FILE.
- Run CANOCO and answer questions.
- Run CANODRAW.
CANOCO
creates two output files (By default, CANOCO.OUT and CANOCO.SOL), as well as a
file called CANOCO.CON which includes information on the choices you make, as
well as the files you use and create.
It is usually worthwhile to rename the CANOCO.CON file to describe the data set; for example: "OK-BIRDS.CON" for a study of Oklahoma birds. If you do not rename it, the file will be overwritten the next time you run CANOCO.
CANODRAW uses the information in the "*.con" file to plot the output.
It is also possible to edit the *.con file to slightly change the run-time parameters (e.g. to use a different data set for input), and run CANOCO again (such can be done from within the CANOCO environment in the Windows95 version).
Most important
files used or produced by CANOCO or CANODRAW
The
below are the most important kinds of files used in the CANOCO package.
There are some other kinds of files optionally used or produced. Most of
the below are ASCII files, and can therefore viewed in word processors or text
editors. I strongly recommend using a 'nonproportional'
font (such as Courier) to view these files. "Proportional"
fonts such as Times New Roman or Arial give less space for small letters (such
as i) and more for large letters (such as m), and
therefore columns do not line up nicely. ASCII files are readily imported
into spreadsheets, statistical packages, or graphics packages for further
display or analysis. Some additional processing may be necessary before
the output is ready to use; the details will depend on your package.
Most of the files below can have alternate extensions, such as
"*.txt", "*.dat", "*.prn", or anything you
like. However, I recommend adopting distinctive extensions such as the
below, in order to avoid confusion.
|
*.con |
Console
file; produced by CANOCO. It contains the instructions for
analysis. |
|
*.spe |
Species
file; produced by the user. It contains species abundance information,
species names, and sample names. |
|
*.env |
Environmental
file; produced by the user. It contains environmental variables, names
of these variables, and sample names (which should agree with those in the
species file). |
|
*.cov |
Covariables
file; produced by the user. It is identical in format to the
environmental file. Indeed, it is usually advisable for the covariables
file to be the same file as the environmental file. |
|
*.out |
Output
file; produced by CANOCO. This contains species scores, sample scores,
and depending on analyses and options chosen, various other output. In
theory, the output file is supposed to be easier to read and understand than
the solution file. |
|
*.sol |
Solution file; produced by CANOCO. This contains much the same
information as the output file, except in a more simplified form. The
solution file can be read by CANODRAW to produce graphical output. |
|
*.psc |
Postscript
file, produced by CANODRAW. A file (not ASCII!) with instructions to a
postscript printer for producing graphic images. In Canoco
for Windows, the *.psc file can be input into CANOPOST for further
editing. |
|
*.pun |
Classification
file, produced by TWINSPAN or CANODRAW - it contains information on whether
the species, samples, or environmental variables have been classified, so
that the results of the classification can be displayed as part of the
ordination in CANODRAW and/or CANOPOST |
|
*.exe |
Executable
files (or under newer parlance, "applications"), containing the
programs. These are not ASCII, and cannot be easily viewed. |
General Flowcharts
PCA, CA, DCA:
|*.out --->for you to read
*.spe -----------> |*.sol |-------------> Graphical|-->print or
Canoco.exe |*.con |-------------> Output |-->*.psc file
Canodraw.exe
CCA, DCCA, or RDA:
|*.out --->for you to read
*.spe|----------->|*.sol |-------------> Graphical|-->print or
*.env|----------->|*.con |-------------> Output |-->*.psc file
Canoco.exe Canodraw.exe
pPCA, pCA, pDCA
|*.out --->for you to read
*.spe|----------->|*.sol |-------------> Graphical|-->print or
*.cov|----------->|*.con |-------------> Output |-->*.psc file
Canoco.exe Canodraw.exe
pCCA, pDCCA,
pRDA
*.spe| |*.out --->for you to read
*.env|----------->|*.sol |-------------> Graphical|-->print or
*.cov| |*.con |-------------> Output |-->*.psc file
Canoco.exe Canodraw.exe
SUGGESTION FOR
RUNNING CANOCO
Before
you run CANOCO, you might wish to print out a list of all your samples, along
with the sample number, a list of all your species, along with the species
number, and (if your are performing direct gradient analysis) a list of all
your environmental variables, along with the variable number. This will make it
much easier for you when deciding which samples/species/variables to omit,
weight, transform, etc.
MENU TREE FOR
CANODRAW
CANODRAW
is a very flexible program. I am always discovering new things about it - and
many of these things are not completely described in the manual. One of the
most difficult parts of using CANODRAW is navigating around the menu. I
strongly suggest that you photocopy the first several pages of Section 5 in the
CANODRAW manual. This is a printed outline of the menu tree. When you explore
in CANODRAW, jot down notes on this copy. This will help you remember the next
time around!
CANOCO
FOR WINDOWS
Canoco
for Windows has a much improved user interface, and a much better manual, than
the previous version. The general procedure is much the same, with the
following exceptions: It requires Windows 95, Windows NT or Higher (Please
check the CANOCO Home page for more
details)
- An output file (*.out) is no longer produced.
However, a log file (*.log) is optionally produced.
- There is a new facility, WCanoImp,
for transferring data from a spreadsheet to an ASCII file.
- CANODRAW can be accessed from a button within CANOCO.
- The new version of CANOCO can handle many more species,
samples, and variables than previous versions. For versions before
4.0, there are some memory limitations - so
for large data sets, you still need to rely on an alternative graphics
program.
- Results from CANODRAW can be saved to a file, and
edited with a new program, CANOPOST, which produces graphs of higher
quality, in most cases suitable for publication. CANOPOST can,
optionally, produce canopost files (*.cps),
which are available for future editing. CANOPOST images can be
copied and pasted into other Windows applications, with varying success.
- *.con files are easier to edit, rename, copy, and rerun
from within the CANOCO environment.
General Flowchart
for CANOCO for Windows
All techniques
(optional):
Data, copied from spreadsheet into clipboard -----------> *.spe and/or *.env and/or *.covCanoImp.exe
PCA, CA, DCA
*.spe -----------> |*.sol
|-------------> Graphical|-->print or |----------->
*.cps file and/or
Canoco.exe |*.con
|-------------> Output |-->*.psc file|-----------> Good
quality graphs
Canodraw.exe
Canopost.exe
CCA, DCCA, or RDA
*.spe|----------->|*.sol |-------------> Graphical|-->print or |-----------> *.cps file and/or*.env|----------->|*.con |-------------> Output |-->*.psc file|-----------> Good quality graphs
Canoco.exe Canodraw.exe Canopost.exe
pPCA, pCA, pDCA
*.spe|----------->|*.sol |-------------> Graphical|-->print or |-----------> *.cps file and/or*.cov|----------->|*.con |-------------> Output |-->*.psc file|-----------> Good quality graphs
Canoco.exe Canodraw.exe Canopost.exe
pCCA, pDCCA,
pRDA
*.spe|
*.env|----------->|*.sol |-------------> Graphical|-->print or |-----------> *.cps file and/or
*.cov| |*.con |-------------> Output |-->*.psc file |-----------> Good quality graphs
Canoco.exe Canodraw.exe Canopost.exe
This
page was created and is maintained by Michael
Palmer.
To the ordination web page