6
Community Analysis Package
2
Introduction
CAP
 (Community Analysis Package) is a Windows  program that offers a range
of analytical techniques commonly used by community ecologists. Researchers in
other fields such as palaeontology, archaeology and the social sciences also use
many of these methods. Programs to carry out many of these techniques have
long been available, but, they are often difficult to use as they were written for
main frame computers or PCs using DOS and they frequently have little or limited
graphical output. 
CAP
 has been designed for ease of use on PCs running under
Windows . Data can be organised using standard Windows programs such as
Excel and the output from 
CAP
 is displayed, exported and printed using standard
Windows techniques. This results in a program that is easily used by both
students and professional ecologists. It is particularly useful for ecological
teaching because it allows students to quickly enter data, try different
transformations and explore a range of methods within a familiar Windows
setting.
The input data set is arranged as a two dimensional array. In ecology it is usual
for the samples, which are normally collected from set localities and may be
called, for example, quadrates or stations, to form the columns. The variables for
each sample are the rows and usually comprise the numbers of each species or
other taxon observed. 
CAP
 does not include multivariate methods which seek to
understand the relationship between two sets of data as occurs when both
physical and biological data has been recorded for a number of samples.
However, two other Pisces programs, 
Ecom
103
 and 
Fuzzy Grouping
105
, are
designed for this type of data.
The methods on offer in CAP include both ordination methods such as Principal
Components Analysis (
PCA
53
) and Reciprocal Averaging (
RA
67
) and
classification methods such as 
TWINSPAN
70
 plus a wide range of clustering
procedures. Taken together they provide a powerful suite of methods with which
to explore, compare and analyse community structure. For all methods 
CAP
offers high quality graphical and tabulated output which is organised into tabbed
notebooks. The program will run on Apple machines with PC emulation software.
CAP
 uses the same data structure as 
Species Diversity and Richness II
103
 which
calculates a wide range of diversity and species richness measures. Together
with 
Ecom
103
 and 
Fuzzy Grouping
105
, the programs offer a very extensive range
of methods for the analysis of ecological communities.
To help users to understand how to use 
CAP,
 the instructions are written from an
ecological viewpoint. We generally refer to columns as samples or quadrates and
rows as species. This is the way an ecological data set should be organised to
study both the relationship and similarity between samples and the pattern of
association between species. Techniques such as PCA can be used on any data
set of observations for each of which there are a number of variables.
CAP 3.0 was released in June 2004.
CAP 3.0 was developed and produced by Richard Seaby, Peter Henderson, John
Prendergast and Robin Somes.
Copyright 2004, PISCES CONSERVATION LTD





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