Community Analysis Package
Species Filtering
Species filtering is a novel ordination method developed by Peter Henderson and
Richard Seaby of Pisces Conservation Ltd. The utility of the method is yet to be
assessed, but we believe that it has many useful features. In particular it
produces a 2 dimensional ordination of the sites that has a clear biological
interpretation in terms of the species present in each sample. Our objective was a
final result that would produce an ordination of sites with the greatest possible
discrimination of sites along axes that allowed simple ecological interpretation.
Ideally the method would work for both presence/absence and quantitative
abundance data.
The method ordinates the sites in a two dimensional space. The first dimension is
an ordination in terms of species content and the second is simply a plot of the
number of species present. The key feature is the unique way in which the sites
are ordinated along axis 1. This will be described in detail.
Imagine a sieve that allowed all the samples that did not hold a species to pass
through it, but retained those samples that contained the species. We term such a
sieve a negative filter. In contrast a filter that will only allow samples that contain a
particular species would be a positive filter. Now consider a series of species
sieves placed in line so that progressively more and more of the samples are
retained. To produce a useful ordination we need a set of rules that will determine
which species should be used as sieves and in which order the sieves should be
placed. The proposed rules are quite simple.
Species present at all sites are excluded. This is because they cannot be used
to differentiate between sites.
When two or more species have the same pattern of occurrence at the sites a
single sieve represents them all.
The order of sieves should be that which will produce the most even
distribution of sites along the axis.
Rule 3 is the key feature that will lead to a useful ordination and in practice is
more difficult to discover than you might suppose. The possible arrangement of
species filters will increase factorially with the number of species present so that
even with quite a modest species number it is impossible to consider the merits of
all possible combinations. The solution to this problem is to use a numerical
method termed annealing to seek an optimal solution. While the search for a
good solution requires considerable computation our experience suggests that
even with quite large data sets a useful ordination is created with 2 to 5 minutes.
When using a negative filter, which we recommend, the final ordination along the
first axis will tend to arrange the sites (samples) in a clear and quite particular
order. Starting from the left the sites will initially be characterised by their
presence of rare or unusual species. At the opposite end of the axis will be sites
that only hold the most frequently present species. Sites at the left end of the
ordination can be classified into two groups, those that contain both infrequent
and frequent species and sites that hold only infrequent species. Sites that hold
both will tend to have higher species richness than those that only hold rarer
forms and this immediately suggests that the second axis should simply be the
total number of species in the sample.
Annealing works by taking an initially, possibly arbitrary, arrangement of the
species and changing this arrangement in a manner that will make it more likely
that any superior order will be accepted. There are two types of change allowed.

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