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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.

http://ordination.okstate.edu/running.htm (1 of 6)11/20/2010 10:52:26 AM

It is identical in format to the environmental file.cov Indeed. the output file is supposed to be easier to read and understand than the solution file. Some additional processing may be necessary before the output is ready to use. the details will depend on your package. "*. produced by the user.txt". and run CANOCO again (such can be done from within the CANOCO environment in the Windows95 version). Environmental file. "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). *. Output file. Species file. in order to avoid confusion.env variables. There are some other kinds of files optionally used or produced.htm (2 of 6)11/20/2010 10:52:26 AM . produced by the user. Solution file. It is also possible to edit the *.out depending on analyses and options chosen. or anything you like. *. sample scores. Most of the files below can have alternate extensions. or graphics packages for further display or analysis.okstate.prn". This contains much the same information as the output *. CANODRAW uses the information in the "*.spe and sample names. produced by the user.con file to slightly change the run-time parameters (e. *. Most important files used or produced by CANOCO or CANODRAW The below are the most important kinds of files used in the CANOCO package. http://ordination. and sample names (which should agree with those in the species file).CON" for a study of Oklahoma birds. produced by CANOCO. In theory. the file will be overwritten the next time you run CANOCO.g. It contains environmental variables. I recommend adopting distinctive extensions such as the below. various other output. ASCII files are readily imported into spreadsheets. produced by CANOCO. If you do not rename it. It contains species abundance information. names of these *. and can therefore viewed in word processors or text editors.con" file to plot the output. such as "*. Covariables file. I strongly recommend using a 'nonproportional' font (such as Courier) to view these files.con Console file. produced by CANOCO. statistical packages. for example: "OK- BIRDS. and therefore columns do not line up nicely. except in a more simplified form.dat". It contains the instructions for analysis. However. and *. This contains species scores. "*. to use a different data set for input). Running CANOCO and CANODRAW It is usually worthwhile to rename the CANOCO.sol file. Most of the below are ASCII files.CON file to describe the data set. The solution file can be read by CANODRAW to produce graphical output. it is usually advisable for the covariables file to be the same file as the environmental file. species names.edu/running.

so that the *.exe Canodraw.con |-------------> Output |-->*.exe pCCA.con |-------------> Output |-->*. Classification file. Running CANOCO and CANODRAW Postscript file.sol |-------------> Graphical|-->print or *.exe CCA.sol |-------------> Graphical|-->print or *.out --->for you to read *.con |-------------> Output |-->*.out --->for you to read *. containing the programs.env|----------->|*.psc file can be input into CANOPOST for further editing. "applications"). and cannot be easily viewed. In Canoco for Windows.psc file Canodraw.it contains information on whether the species. pDCA |*.htm (3 of 6)11/20/2010 10:52:26 AM . pDCCA.sol |-------------> Graphical|-->print or *. CA.psc file http://ordination.exe Canodraw. General Flowcharts PCA. produced by TWINSPAN or CANODRAW .con |-------------> Output |-->*.cov| |*. A file (not ASCII!) with instructions to a postscript *.spe| |*. or environmental variables have been classified.pun results of the classification can be displayed as part of the ordination in CANODRAW and/or CANOPOST Executable files (or under newer parlance.psc file Canoco.out --->for you to read *.spe|----------->|*. DCA: |*. samples. These are *.exe pPCA.edu/running. the *.psc printer for producing graphic images. or RDA: |*.cov|----------->|*. pCA.env|----------->|*.spe|----------->|*.out --->for you to read *.spe -----------> |*.sol |-------------> Graphical|-->print or Canoco. produced by CANODRAW.okstate.psc file Canoco. pRDA *.exe not ASCII. DCCA.exe |*.

However. along with the sample number. CANOPOST images can be copied and pasted into other Windows applications. http://ordination. for transferring data from a spreadsheet to an ASCII file. ● There is a new facility. which are available for future editing. with the following exceptions: It requires Windows 95. and edited with a new program. MENU TREE FOR CANODRAW CANODRAW is a very flexible program.cps). ● Results from CANODRAW can be saved to a file. CANOPOST.log) is optionally produced. When you explore in CANODRAW. jot down notes on this copy. For versions before 4. The general procedure is much the same.and many of these things are not completely described in the manual. which produces graphs of higher quality. you might wish to print out a list of all your samples. Running CANOCO and CANODRAW Canoco. and (if your are performing direct gradient analysis) a list of all your environmental variables. transform. a list of all your species. optionally.htm (4 of 6)11/20/2010 10:52:26 AM . ● The new version of CANOCO can handle many more species.okstate. WCanoImp.out) is no longer produced. than the previous version. etc.so for large data sets. I strongly suggest that you photocopy the first several pages of Section 5 in the CANODRAW manual. in most cases suitable for publication. weight.0. and a much better manual. One of the most difficult parts of using CANODRAW is navigating around the menu. samples. along with the variable number. with varying success. produce canopost files (*.exe Canodraw. CANOPOST can. I am always discovering new things about it . and variables than previous versions. This will make it much easier for you when deciding which samples/species/variables to omit.edu/running.exe SUGGESTION FOR RUNNING CANOCO Before you run CANOCO. there are some memory limitations . along with the species number. ● CANODRAW can be accessed from a button within CANOCO. you still need to rely on an alternative graphics program. Windows NT or Higher (Please check the CANOCO Home page for more details) ● An output file (*. a log file (*. This will help you remember the next time around! CANOCO FOR WINDOWS Canoco for Windows has a much improved user interface. This is a printed outline of the menu tree.

cps file and/or *.spe| *.cps file and/or *.sol |-------------> Graphical|-->print or |-----------> *. pRDA *.env|----------->|*. DCA *.con |-------------> Output |-->*. pDCA *.exe PCA. rename. exe pPCA.exe Canopost.cps file and/or Canoco. Running CANOCO and CANODRAW ● *.con |-------------> Output |-->*.cov CanoImp. exe CCA. DCCA.con |-------------> Output |-->*. pDCCA. and rerun from within the CANOCO environment. env and/or *.psc file http://ordination.con |-------------> Output |-->*. pCA. CA.exe Canodraw.psc file|-----------> Good quality graphs Canodraw.env|----------->|*.spe|----------->|*.htm (5 of 6)11/20/2010 10:52:26 AM .sol |-------------> Graphical|-->print or |-----------> *.exe Canodraw.cov|----------->|*.psc file|----------- > Good quality graphs Canoco.sol |-------------> Graphical|-->print or |----------- > *.exe Canopost.con files are easier to edit.edu/running.cps file and/or *. or RDA *.spe and/or *.spe -----------> |*.okstate.psc file|----------- > Good quality graphs Canoco. copy. General Flowchart for CANOCO for Windows All techniques (optional): Data.spe|----------->|*.exe Canopost.sol |-------------> Graphical|-->print or |----------- > *. copied from spreadsheet into clipboard -----------> *.cov| |*. exe pCCA.exe |*.

okstate.exe Canodraw. To the ordination web page http://ordination. exe This page was created and is maintained by Michael Palmer. Running CANOCO and CANODRAW |-----------> Good quality graphs Canoco.htm (6 of 6)11/20/2010 10:52:26 AM .edu/running.exe Canopost.