Community Analysis Package
Two way indicator species analysis TWINSPAN
TWINSPAN is somewhat complex divisive clustering method originally devised by
 for vegetation analysis but quite suitable for animal communities as well.
An interesting feature of TWINSPAN is that it forms what are termed
pseudospecies. These are separate variables for the different levels of
abundance of a species. Samples are ordinated using reciprocal averaging (RA).
A dichotomy is then made using the RA centroid line to divide the samples into
two groups (negative and positive). This dichotomy is then refined using an
iterative procedure. The clusters of samples obtained are then ordered so that
similar clusters are near each other. This procedure continues in a hierarchical
fashion to subdivide the groups until the minimum group size initially selected by
the user is obtained. Species are then classified using the sample (quadrate)
classification. In the original output a table is then produced showing species by 
site (quadrate or sample) relationships.
Once the TWINSPAN option is selected from the drop down menus you will be
presented with the Setup for TWINSPAN window in which options can be
selected. If no changes are made prior to clicking on OK then the default settings
will be used. For many vegetational studies the defaults are appropriate.
Site summary
Species summary
Dendrogram samples
Dendrogram species
Setup window   TWINSPAN
The setup window is divided into four panels, which will be described in turn
Cut levels
. This determines the abundance levels in the working data at which a
species is divided into pseudospecies. A maximum of 9 cut levels can be defined.
The default state is for 5 cut levels set at 0, 2, 5, 10 and 20. The radio box is set
to % coverage as these are suitable values if the original data comprises
percentage vegetation cover in quadrates. Select frequency if the original data
are expressed in terms of relative frequency (maximum value 1). Select Pres/Abs
if the working data are simply presence   absence (comprises 1s and 0s). To
select your own cut levels select custom and type in values in the line of text
boxes arranged along the panel. The cut levels must be arranged from smallest
to largest moving from left to right. The program ignores blank boxes.
. Three options are available. Maximum number of indicators per division
defines the maximum number of indicator species that can be found per division.
Maximum level of divisions defines the number of subdivisions of the groups that
can be undertaken. The maximum is 9. Minimum group size per division gives the
minimum number of samples (quadrates) in each group. Once a group size has
reached this minimum level no further subdivisions are undertaken.
. Each box in this panel gives the relative weighting given to each
pseudospecies cut level. The default is all 1s indicating that all pseudospecies are
given equal weighting.
Indicator levels
. Defines which pseudospecies cut levels can act as indicators.
The default is all, to deselect a level uncheck a box.
Output from TWINSPAN is presented under a number of tabbed components that

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