82
Community Analysis Package
17
Similarity measures
Choose the similarity measure you wish to calculate from the Similarity drop down
menu. The calculations will appear on the Similarity tab at the bottom of the
program window. For ease of use, the program will highlight sites with similarity
above a certain level. You can set this level by entering the number in the 
Set
Threshold Of
 box at the bottom of the page.
The similarity measures used.
These are simple measures of either the extent to which two habitats have
species in common (Q analysis) or species have habitats in common (R analysis
). Binary similarity coefficients use presence absence data; following the
introduction of computers more complex quantitative coefficients became
practicable. Both groups of indices can be further divided to those which take
account of the absence from both communities (double zero methods) and those
which do not. In most ecological applications it is unwise to use double zero
methods as they assign a high level of similarity to localities which both lack many
species; a problem which becomes particularly acute in habitats which have a
potentially extremely large species list such as the marine benthos. A good
account of similarity and distance measures is given in Legendre & Legendre
(1983). Because of division by zero problems for some data sets not all measures
can be calculated. When a division by zero error would occur 
CAP
 gives an index
of  99.
For measures of similarity between samples based on species presence absence
the observations can be summarised in a simple frequency table:
Sam
Species Present
Sample 2
Species Present
a
Species  Absent
c
where the number of species present in both samples is a, the number of species
present in sample 1 but missing from sample 2 is b, the number of species
missing in sample 1 but present in sample 2 is c and the number of species
missing from both samples is d. The total number of species, N, is therefore
a+b+c+d.
Binary   double zeros
Simple matching
83
Rogers_Tanimoto
83
S3
84
S4
84
S5
85
S6
85
Binary   no double zeros
Jaccards
86
Sorensen
86
S9
86
S10
87
Russel & Rao
87
Kulczynski
88
S13
88
Ochiai
89
Qualitative
Copyright 2004, PISCES CONSERVATION LTD





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