Introduction to CAP

CAP (Community Analysis Package) is a Windows program that offers a range of analytical techniques commonly used by researchers in fields such as biology, geology, palaeontology, archaeology and the social sciences. CAP is also tested to work on Apple machines using a PC emulator.

Programs to carry out many of these techniques have long been available, but, they are often difficult to use 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 professionals.

CAP is particularly useful for 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 many scientific disciplines the samples, which are normally collected from set localities and may be called, for example, quadrats, individuals or stations, form the columns. The variables for each sample are the rows, and may comprise for example the numbers of each species or other taxon observed, a score in a test, the frequency of a particular type of object or a chemical concentration.

Throughout this Help system, we have often referred to the contents of the rows as species, for the sake of simplicity, but it should be borne in mind that they may comprise other definitions.

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 have been recorded for a number of samples. However, two other Pisces programs, Ecom and Fuzzy Grouping, are designed for this type of data.

The methods on offer in CAP include both ordination methods such as Principal Component Analysis (PCA) and Reciprocal Averaging (RA), and classification methods such as Discriminant Analysis and TWINSPAN, 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 in a tabbed notebook style. The program will run on Apple machines with PC emulation software.

CAP uses the same data structure as Species Diversity and Richness IV which calculates a wide range of diversity and species richness measures. Together with Ecom and Fuzzy Grouping, the programs offer a very extensive range of methods for the analysis of ecological communities and multivariate relationships in general.

CAP 6 introduces the ability to run R code directly from with the program. There have been many other smaller improvements in the program.

CAP 6.0 was developed and produced by Richard Seaby, Peter Henderson and Robin Somes, and was released in August 2019.

List of methods offered by CAP

Improvements implemented in CAP 5.0 (2014)

Improvements implemented in older versions of CAP