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UNSUPPORTED SOFTWARE: USE AT OWN RISK

Converting Tabular Data for CANOCO and TWINSPAN using toccf

24-Mar-1998

The latest version of this document is at http://www2.biology.ualberta.ca/jbrzusto/ftp/trees/toccfdoc.html
Bugs and changes are listed at the end.

This program is available as an executable 32-bit DOS versions that runs on a '386 or higher, with or without a math processor, in DOS or the DOS box of Windows 3.1 or '95. You can run it from the command line, or use a front end program to help you specify parameters: krebs (for Win3.1 or '95) or potemkin (for Win'95).

Get the program:

Command line version only:
Send your web browser to: http://www2.biology.ualberta.ca/jbrzusto/ftp/trees/dos32/toccf.exe or ftp (with userid anonymous) to gause.biology.ualberta.ca and change directory to /pub/jbrzusto/trees/dos32 and then get toccf.exe (making sure to use binary mode).

If you want to run these programs in plain DOS, (ie. not within a Windows DOS box), you must also download cwsdpmi.exe and put it in the same directory, unless you are already running a DPMI server. This driver provides programs with access to extended memory.

The directory http://www2.biology.ualberta.ca/jbrzusto/ftp/trees/source.zip has ANSI-C source code and makefile, if you want to recompile the program on your machine.

Krebs/win:
Get this from http://www2.biology.ualberta.ca/jbrzusto/ftp/krebs/index.html Installation instructions are available at http://www2.biology.ualberta.ca/jbrzusto/ftp/krebs/README.TXT

Potemkin:
Get this from http://www2.biology.ualberta.ca/jbrzusto/ftp/potemkin/potzip.exe Installation instructions are available at http://www2.biology.ualberta.ca/jbrzusto/ftp/potemkin/potemkin.html This program requires Windows '95.

Put your data into a text file:

toccf works on text files. To put your data into this format, do one of the following:

export your data matrix from a spreadsheet into text or ASCII format
copy your data from the spreadsheet into the clipboard, and paste it into Notepad or Wordpad, then save the file from there
use a text editor like EDIT or NOTEPAD to create the file from scratch.

Run the program (command line version):

toccf is run from the DOS command prompt, so if you are using Windows, you must first open a DOS window, and change to the directory into which you downloaded the programs.

Here is a simple example of the command:

toccf 210 180 -fc test.txt > canotest.txt

The options mean:

210: the number of rows of data in the input file (ie. the number of lines in the file)

180: the number of columns of data in the input file (e.g. a line like "123 34 5.2" has 3 columns)

-fc: format output for CANOCO

test.txt: name of file containing your data

> canotest.txt: output Cornel condensed format to the file canotest.txt

Here is a more complicated example of the command:

toccf 210 180 -nr -nc -ft -r -t -s5F6.2 test1.txt test2.txt > twintest.txt

The options mean:
210: the number of rows in the input file, not including column names
340: the number of columns in the input files combined, not including row names
-nr: names of rows are present. The first item in each row is the name of that row.
-nc: names of columns are present. The first line in the file is a list of column names.
-ft: format output for TWINSPAN
-r: each sample is a row in the input, rather than a column
-t: the input file uses TAB characters to separate values, some of which can be blank (treated as 0). If there are blank entries in your data matrix, your file must use TABs and you must use this option for toccf
-s5F6.2: the format for output. In this example, 5 couplets are printed per line and each character value occupies 6 spaces with 2 digits after the decimal point.
test1.txt: name of first data file
test2.txt: name of second data file. Multiple input files are pasted together side by side, so that the first row in the input consists of the first row in file1 joined to the first row in file 2, and so on. This option is included because some spreadsheets can't export very wide lines as text files, so you might have to manually select consecutive groups of (for example) 100 columns, one group at a time, and export each to a separate file.
> twintest.txt: output Cornel condensed format to the file twintest.txt

Changes and Bugs:

Date reported	Date Fixed/Made	Change/Bug/Fix
	21-Oct-1997	added the -s option for specifying couplet output format

Bugs, comments, etc. to John Brzustowski junkjbrzusto@ualberta.cacaca but removing the obvious parts

There are more free programs at http://www2.biology.ualberta.ca/jbrzusto/index.html