How to use the modified versions of DECORANA and TWINSPAN

The files DECORANA.EXE and TWINSPAN.EXE are modified versions of these programs that can be run on any PC with an intel 486 or Pentium processor. Best performance will be obtained if you have at least 4Mb of RAM. The programs will still run on systems with less memory, as they include a virtual memory manager, but they may run slowly. These modified versions use the "strict" convergence criteria of Oksanen & Minchin (Journal of Vegetation Science 8, 447-454; 1997) for eigenanalysis, with a tolerance of 0.000005 and a maximum iteration limit of 999. In DECORANA, the bug in SMOOTH has been corrected.

Both programs require an input data file in Cornell Condensed format, containing the community data to be analysed. The layout of this file should follow the same rules as for the original versions of DECORANA and TWINSPAN. Versions from 30 July 1997 accept somewhat relaxed formats (some but not all CANOCO files), but it may be still safer to use the original strict Cornell format. Both programs also ask a series of questions about analysis options. These can either by answered interactively from the keyboard or else the programs can be instructed to read the answers from a disk file (see below).

Output files

Each program produces up to two output files. For DECORANA, they are:

For TWINSPAN, the two output files are:

You may give your own names for these files or else default or standard names will be used (see below).

Running the programs

To run DECORANA, type the following at the DOS prompt:

DECORANA datafile scoresfile printfile

where datafile is the name of the Cornell Condensed file with your community data, scoresfile is a name for the output file with ordination scores and printfile is a name for the printout file. If you omit printfile, the standard name of decorana.prt will be used (and existing decorana.prt file will be overwritten). If you also omit scoresfile, the standard name of decorana.out will be used for the ordination scores file (and any existing decorana.out will be overwritten). If you type just DECORANA with no file names at all, you will be prompted to enter the name of the input data file and standard names will be used for the two output files.

If you have answers to the questions about analysis options in a disk file, you can instruct DECORANA to read the answers from the file by typing:

DECORANA datafile scoresfile printfile < answerfile

where answerfile is the name of the disk file with the answers.

To run TWINSPAN, type the following at the DOS prompt:

TWINSPAN datafile classfile printfile

where datafile is the name of the Cornell Condensed file with your community data, classfile is a name for the output file with group memberships and printfile is a name for the printout file. If you omit printfile, the standard name of twinspan.prt will be used (and existing twinspan.prt file will be overwritten). If you also omit classfile, the standard name of twinspan.out will be used for the group membership file (and any existing twinspan.out will be overwritten). If you type just TWINSPAN with no file names at all, you will be prompted to enter the name of the input data file and standard names will be used for the two output files.

If you have answers to the questions about analysis options in a disk file, you can instruct TWINSPAN to read the answers from the file by typing:

TWINSPAN datafile classfile printfile < answerfile

where answerfile is the name of the disk file with the answers.

Source files

FORTRAN source files, DECORANA.FOR and TWINSPAN.FOR are also provided for those who wish to change the maximum dimensions and/or to install them on a non-DOS system. For that, you will need a FORTRAN 77 or FORTRAN 90 compiler. Changing the maximum dimensions is simply a matter of changing the numbers in the first PARAMETER statement in each program. The source files contain only one non-standard feature: a call to the Lahey FORTRAN 90 routine GETCL, which returns the contents of the command line. Most FORTRAN compilers will have some alternative method for doing this. Alternatively, extraction of file names from the command line can be disabled and all file names can be entered interactively.


Dr Peter R. Minchin
July 1997