(1) A randomly chosen length of the species sequence is removed and replaced
at a randomly chosen site or (2) the order of a randomly chosen length of the
species sequence is reversed. When any such change is made a test is
undertaken to see if the new arrangement produces a more even distribution of
the sites. If it does, the new arrangement is accepted. The temperature comes
into play by allowing possibly inferior arrangements to be accepted. The higher
the temperature the more likely this is to occur. The reason for this feature is that
it tends to allow the program to find a global optimal solution and not become
trapped by a local minimum. The higher the temperature the more likely an
inferior arrangement is likely to be accepted. Annealing proceeds by a steady and
gradual reduction in temperature.
The first axis therefore consists of a series of species, which are labelled on the
output. These species are the key members of the community, whose presence
or absence can be used to distinguish between sites.
Species Filtering Setup
When species filtering is selected you are initially presented with an options
screen which can be used to tune the annealing and also select key features of
the filter options.
Iterations / temperature set
This option sets the maximum number of
rearrangements of the species filter order that will be attempted at each
Successes per Temperature Step
This option determines how many superior
arrangements in the species order will be found at each temperature before the
The higher the initial temperature the more mixing of the
species order will occur. In practice a temperature above 100 (boiling point) will
be unlikely to be useful.
Proportional decrease in T per Step
This option should be less than 1. A
value of 0.2 will result in a reduction to 20% of the initial value at each step.
Minimum shuffle size
This sets the minimum length of the species sequence
that will be rearranged. For example if it is set at 3 no sequence of less than 3
species will be moved or reversed.
For presence/absence data this should be set to 0. For
quantitative or percentage composition data it can be set to a higher number. If it
is set to say 4 then negative filters will only retain sites (samples) where the
abundance of the species exceeds 4.
This allows a switch from negative to positive filtration. Negative is
normally recommended. In negative filtration a sample is retained if the species is
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