Running CANOCO and CANODRAW

RUNNING CANOCO AND CANODRAW

(versions before 4.5)

This section is almost 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 version 4.5, 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:

1. Get data into shape: full format or reduced condensed format, SAVED AS ASCII FILE.
2. Run CANOCO and answer questions.
3. 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.

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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.
Species file; produced by the user. It contains species abundance information, species names,
*.spe
and sample names.
Environmental file; produced by the user. It contains environmental variables, names of these
*.env
variables, and sample names (which should agree with those in the species file).
Covariables file; produced by the user. It is identical in format to the environmental file.
*.cov Indeed, it is usually advisable for the covariables file to be the same file as the environmental
file.
Output file; produced by CANOCO. This contains species scores, sample scores, and
*.out 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.
Solution file; produced by CANOCO. This contains much the same information as the output
*.sol file, except in a more simplified form. The solution file can be read by CANODRAW to
produce graphical output.

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Postscript file, produced by CANODRAW. A file (not ASCII!) with instructions to a postscript
*.psc printer for producing graphic images. In Canoco for Windows, the *.psc file can be input into
CANOPOST for further editing.
Classification file, produced by TWINSPAN or CANODRAW - it contains information on
whether the species, samples, or environmental variables have been classified, so that the
*.pun
results of the classification can be displayed as part of the ordination in CANODRAW and/or
CANOPOST
Executable files (or under newer parlance, "applications"), containing the programs. These are
*.exe
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

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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.

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● *.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 *.cov

CanoImp.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

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|-----------> Good quality graphs

Canoco.exe Canodraw.exe Canopost.
exe

This page was created and is maintained by Michael Palmer.

To the ordination web page

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