A3 Software for multivariate analysis

There are several specialized program packages available for multivari-ate analyses, of which I mention PC-Ord, CANOCO and SYN-TAX2000 (Gilliam & Saunders 2003). I consider my own program package MULVA-5 (Wildi & Orloci 1996) partly outdated as many of the ordination and classification methods used these days are missing. However, I implemented operations presented in this book into MULVA using FORTRAN code:

• Computing within- and between- similarity of releve groups in Section 4.6.

• Ordering synoptic tables (Section 6.6).

• Computing directed spatial dependence (Section 7.3.3).

• Implementing a simple Bayes probability model (Section 8.2).

• A means to extract rate of change of different order (Figure 9.2).

• Smoothing Markov series (Section 9.3).

• Deriving synthetic time series via space-for-time substitution (Section 9.4.1).

The space-time model of succession in the Swiss National Park (Section 10.3) is a standalone FORTRAN program as complexity exceeds flexibility of multipurpose programs. Packages for dynamic modelling exist, such as STELLA and SIMILÉ, generating flow charts as shown in Figure 10.1 upon input of differential equations and providing a flexible graphical output.

In many computer programs the default options used are hidden in program descriptions or parameter lists; this is one of the flaws of R procedures. It is good practice to compare output from different programs to avoid misunderstanding; I did so when preparing examples, using PC-Ord in parallel with other programs.

The number of methods available in the R computing environment is growing quickly and the VEGAN package (Dixon 2003) offers many methods previously available only in specialized program packages. I used R procedures for constrained ordination in Section 7.5 and also to check other ordinations processed in MULVA. In view of the rapidly growing specific functions the computing environment R offers, this may soon become the dominating platform for data analysis in vegetation ecology. Rumours confirm detailed instructions to be underway.

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