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.

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)

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 |-----------> Good quality graphs
       Canoco.exe         Canodraw.exe                            Canopost.exe
 


This page was created and is maintained by Michael Palmer.
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