Appendix C:

Overview of available software

The use of any multivariate statistical method even for small datasets
requires a computer program to perform the analysis. Most of the known sta-
tistical methods are implemented in several statistical packages. In this book,
we demonstrate how to use the ordination methods with possibly the most
widely employed package, Canoco for Windows. We also show how to use
the methods not available in CANOCO (clustering, NMDS, ANOVA) with the
general package Statistica for Windows. In the next paragraph, we provide
information on obtaining a trial version of the CANOCO program, which you
can use to work through the tutorials provided in this book, using the sam-
ple datasets (see Appendix A for information on how to obtain the datasets).
We also provide an overview of other available software in tabular form and
show both the freely available as well as the commercial software. The atten-
tion is focused on the specialized software packages, targeting ecologists (or
biologists), so we do not cover general statistical packages such as S-Plus, SAS or
GENSTAT.
The Canoco for Windows program is commercial software requiring
a valid licence for its use. But we reached agreement with its distributor
(Microcomputer Power, Ithaca, NY, USA), who will provide you on request with
a trial version of the software, which will be functional for a minimum of one
month. You can use it to try the sample analyses discussed in this book, using
the data and CANOCO projects provided on our web site (see Appendix A). To
contact Dr Richard Furnas from Microcomputer Power, write to the following
E-mail address: [email protected].
Table 20-1 lists the main available packages, which can be used for some or
many parts of the multivariate analysis of ecological data, and their function-
ality is compared. We do not own all the listed programs, so the information
is often based on the data excerpted from their web pages. For most of them,
the authors or distributors reviewed and corrected the provided information.

258

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Table 20-1. Overview of the functionality, relevant to the book contents, of the most often used commercial and freely available software

ADE4 CAP Canoco DECODA ECOM MVSP NTSys-pc PATN PCORD Primer R SYN-TAX Vegan / R ViSTA
1
Distribution F C C C C C C C C C F C F F
Mac2 yes no no no no no no no no no yes yes yes yes
transf 3 yes yes yes yes yes yes yes yes yes yes yes yes no 9 ?
stand3 yes yes yes yes yes yes yes yes yes yes yes yes yes yes
PCA yes yes yes no no yes yes yes yes yes yes yes no 9 yes
RDA yes no yes no yes no no no no no yes yes no yes
CA yes yes yes yes no yes yes yes yes no yes yes yes yes
DCA no yes yes yes no yes no yes yes no no no yes no
CCA yes no yes no yes yes no no yes no yes yes yes no
perm. tests4 yes no yes no yes no no yes yes no yes no yes no
partial ord5 yes no yes no no no no no no no yes no yes no
CVA yes no yes no no no yes no no no yes yes no no
PCoA yes no yes ? no yes yes yes no no yes yes no 9 yes
NMDS no yes no yes no no yes yes yes yes no yes yes yes
Mantel test yes no no ? no no yes yes yes yes yes no yes no
clustering6 yes yes no no no yes yes yes yes yes yes yes no 9 yes
coefficients7 many few several several no many many many many few many many several many
TWINSPAN no yes no yes no no no yes yes no no no no no
regression8 yes no yes no? yes no yes yes no no yes no no 9 yes

1
F – the software is provided for free, C – commercial software;
2
yes means the program runs natively on MacIntosh platforms: where no is shown, the program can probably be executed using one of the commercial emulator programs
available from third parties; all the programs run on Microsoft Windows platform;
3
transf – basic transformations (such as log or sqrt) are provided, stand – standardizations by data columns and rows are available;
4
permutation tests refer here only to permutation testing of multivariate hypotheses in the framework of RDA/CCA ordination methods, as discussed in this book (but see also
the Mantel test further down in the table);
5
yes means that the program uses the concept of covariates (covariables);
6
here we refer to hierarchical agglomerative clustering, many packages also implement the other methods;
7
does the package provide calculation of distance (dissimilarity) or similarity coefficients in the appropriate context (such as PCoA, NMDS, clustering);
8
multiple linear regression;
9
this functionality is provided by the base R system, see Vegan details in the list at the end of this Appendix.

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 260 Appendix C: Overview of available software

The lists of features are actual as of July 2002 and might not be fully correct. The
table is followed by footnotes explaining the meaning of individual rows. Then
we provide individual paragraphs for each of the listed programs, with con-
tact information for the distributing companies or individuals and also
additional comments, when needed. Five additional programs (CLUSTAN,
DistPCoA, NPMANOVA, PolynomialRdaCca, and RdaCca) are listed only
there, as their functionality is rather specialized. Question marks in
Table 20-1 imply that we do not know about this particular aspect of program
functionality.
There now follows the list of contact information for the individual produc-
ers of the software listed in Table 20-1. The information provided was accurate
at the time of printing.

r ADE-4, is available from server of Lyon University

<http://pbil.univ-lyon1. fr/ADE-4/>
r CANOCO for Windows, version 4.5, is distributed by Microcomputer
Power, USA, <http://www.microcomputerpower.com>
and by Scientia, Hungary <http://ramet.elte.hu/∼scientia/>
r CAP, version 2.0, is distributed by Pisces Conservation Ltd., UK
<http://www.pisces-conservation.com/>
r DECODA, version 2.05, is distributed by Anutech Pty. Ltd., Australia
<http://www.anutech.com.au/TD/DECODA WWW/welcome.html>
r ECOM, version 1.33, is distributed by Pisces Conservation Ltd., UK
<http://www.pisces-conservation.com/>
r MVSP, version 3, is distributed by Kovach Computing Services, UK
<http://www.kovcomp.co.uk/mvsp/index.html>
r NTSYSpc, version 2.1, is distributed by Exeter Software, USA
<http://www.exetersoftware.com/cat/ntsyspc.html>
r PATN is distributed by CSIRO, Australia
<http://www.cse.csiro.au/CDG/PATN/>
r PCORD, version 4, is distributed by MjM Software, USA
<http://www.pcord.com>
r PRIMER, version 5, is distributed by Primer-E Ltd., UK
<http://www.primer-e.com>
r The R package, version 4, is available from Philippe Casgrain web site
<http://www.fas.umontreal.ca/BIOL/casgrain/en/labo/R/v4/>.
Please, note that this software’s name can be confused with the more
general statistical package R, which is a non-commercial version of the S /
S-Plus system (see also the Vegan package below).
r SYN-TAX, version 2000, is available from Scientia, Hungary
<http://ramet.elte.hu/∼scientia/>

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 Appendix C: Overview of available software 261

r Vegan, version 1.5.2, is an add-on package for the R statistical system

(<http://cran.r-project.org/>).
Vegan package is available from Jari Oksanen,
<http://cc.oulu.fi/∼jarioksa/softhelp/vegan.html>
r ViSTA, version 6.4, is available from Prof. Forrest Young web site
<http://forrest.psych.unc.edu/research/>
r CLUSTAN, version 5.0, is a package specialized in clustering and it
provides almost every known algorithm of hierarchical agglomerative
clustering (in addition to other methods such as K-means clustering) and
calculation of many coefficients of (dis)similarity. It is available from the
Clustan company, UK <http://www.clustan.com>
r DistPCoA is a simple program calculating principal coordinates analysis
(PCoA) with optional correction for negative eigenvalues; it is also able to
calculate the starting matrix of distances, using one of several available
distance measures. It is available from P. Legendre’s web site, at
<http://www.fas.umontreal.ca/biol/casgrain/en/labo/distpcoa.html>
r NPMANOVA is a program written by M.J. Anderson, and it calculates
a non-parametric multivariate ANOVA, based on a selected kind of
distance (dissimilarity) measure. It supports the two-way balanced
ANOVA designs only. It is available, together with other programs, at
<http://www.stat.auckland.ac.nz/∼mja/Programs.htm>
r PolynomialRdaCca is a simple program calculating both polynomial
and linear versions of redundancy analysis or canonical correspondence
analysis. It is available from P. Legendre’s web site, at
<http://www.fas.umontreal.ca/biol/casgrain/en/labo/plrdacca.html>
r RdaCca is a simple program calculating redundancy analysis or canonical
correspondence analysis. It is available from P. Legendre’s web site, at
<http://www.fas.umontreal.ca/biol/casgrain/en/labo/rdacca.html>

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