Community Analysis Package
that mould community structure.
There is a considerable literature on multivariate techniques. Useful texts for
ecologists are 
Legendre & Legendre (1998)
Digby & Kempton (1987)
Kent and Coker (1992)
This method can be used with presence absence, % cover and quantitative data.
The ability to effectively handle % cover makes the method attractive to botanists.
The Two Way INdicator SPecies ANalysis procedure (Hill 
et al.
 1975) also
produces dendrograms of the relationship between species and samples but uses
the reciprocal averaging ordination method to order the species and samples.
Thus the method is something of a hybrid between classificatory and ordination
methods. It is particularly attractive in studies where the objective is to classify
communities so that field workers can quickly assign an area to a community type
and is much favoured by botanists. This is because it identifies indicator species
characteristic of each group identified.
TWINSPAN is a useful technique when you are seeking to identify species that
can be used to characterise particular communities. It is, however, not always an
easy method to understand. A particular, oddity of the method is the concept of
 pseudospecies . Each species is divided into a number of pseudospecies which
represent the different abundance levels at which it was found.
Principal Component Analysis (PCA)
Principal Component Analysis (PCA) is the oldest and still one of the most
frequently used ordination techniques in community ecology. It is most
appropriate for full quantitative data, but can be used if abundance is classified
into a number of abundance classes. The objective of the method is to express
the relationship between the samples in a 2 or 3 dimensional space that can be
plotted and usefully visualized. This can only be achieved if many of the species
are positively or negatively correlated. Normally this will be so for a number of
reasons. First, there is the interdependence between organisms in an ecosystem
and second, because many species respond similarly to environmental variables
such as temperature and water.
General descriptions of the procedure for biologists are given
Legendre & Legendre (1998)
Digby & Kempton (1987)
Kent & Coker (1992)
The analysis is undertaken on either the between site variance covariance or
correlation matrix. If the species vary greatly in abundance you will probably need
to transform the data by taking logarithms or using a square root transformation.
Logarithmic transformations would be excellent if it were not for the fact that zeros
cannot be handled. A frequently used procedure is to add 1 to all the
observations. This can distort the output and it is probably more appropriate to
use a square root transformation.
If you undertake a PCA on the correlation matrix you will be giving all species,

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