casvd - orthogonal correspondence analysis via singular
[-i input-file] [-o root-of-output-files] [-s scaling]
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
-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
-s Scaling of ordination scores. Meaning similar as in
1 (default) Site scores are weighted mean species
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).
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 email@example.com.
Jari Oksanen (firstname.lastname@example.org). Current informa-
tion can be found through http://www.helsinki.fi/~jhoksane
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,
See the local documentation (if available) for Canoco ,
CanoDraw and meschach.
version 2.4 Ecological applications 2
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