man casvd


CASVD(1)						 CASVD(1)

NAME
       casvd  -	 orthogonal  correspondence analysis via singular
       value decomposition

SYNOPSIS
       casvd [options]
       Options:
       [-i input-file] [-o root-of-output-files] [-s scaling]

DESCRIPTION
       casvd  performs	correspondence	analysis  using	 singular
       value  decomposition. Correspondence analysis is a popular
       ordination method in community ecology, in  particular  in
       vegetation  science.  Singular  value decomposition is the
       most stable algorithm for correspondence analysis.   Casvd
       mimics  Canoco  in input and output, so that it can accept
       most of the files types accepted by Canoco and it produces
       files  similar to Canoco so that these can be further pro-
       cessed with the same tools.

       The development of casvd was  motivated	by  the	 reported
       instability  in	ordination  results  of Canoco.	 However,
       Canoco implements several other types of ordination analy-
       ses,  whereas  only  ordinary  correspondence  analysis is
       available in casvd.

       Canoco version 3.15 and later are free of the  instability
       problems reported originally.

       Casvd  uses  meschach  library  to  perform singular value
       decomposition.

   OPTIONS
       -i     Input data file name. Prompted if not given.

       -o     Root name for output data	 files.	 Type  extensions
	      similar  to  Canoco will be added to the root name.
	      The extensions used are .sol for the solution file,
	      .out  for the textual output file, and .con for the
	      file containing the instructions used. The  default
	      root name is casvd.

	      The .con file contains the command log which can be
	      used by Canoco to repeat the analysis with the same
	      options.	 Casvd	cannot	use  this file, but it is
	      provided for the compatibility  with  Canoco.   The
	      .out  file  contains  analysis history, and is nor-
	      mally fairly useless. However, casvd  reports  here
	      all eigenvalues, with some statistics that can help
	      in detecting cases with potential instability (i.e.
	      successive  eigenvalues  of similar magnitude). The
	      proper results are given in  the	.sol  file.  This
	      file is read by graphics programs such as CanoDraw.

version 2.4	     Ecological applications			1

CASVD(1)						 CASVD(1)

       -s     Scaling of ordination scores. Meaning similar as in
	      Canoco:

	      1	 (default)  Site scores are weighted mean species
	      scores.

	      2 Species scores are weighted mean site scores.

	      3 Symmetric scaling.

	      -1, -2, -3 As above, but in addition use ter  Braak
	      scaling,	assumed	 to  approximate  Hill	rescaling
	      (though  the  latter  is	a  non-linear  rescaling,
	      unlike performed with these options).

BUGS
       The  current  version  cannot  detect and handle data sets
       which have duplicate entries for	 some  species.	 This  is
       corrected  now,	but  the new version is not released yet.
       Please report new bugs to jari.oksanen@helsinki.fi.

AUTHOR
       Jari Oksanen (jari.oksanen@helsinki.fi). Current	 informa-
       tion can be found through http://www.helsinki.fi/~jhoksane

REFERENCE
       Oksanen, J. & Minchin, P. R. (1997) Instability of ordina-
       tion  results  under changes in input data order: explana-
       tions and remedies.   Journal  of  Vegetation  Science  8,
       447-454.

SEE ALSO
       See   the  local documentation (if available) for Canoco ,
       CanoDraw and meschach.

version 2.4	     Ecological applications			2


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