Principal Component Analysis  PCA 
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The relationship between samples (columns) in terms of their variables cannot normally be visualised because this would require a plot with as many axes as there are variables (rows). If your study only includes 3 variables this is possible, but is quite impossible given 4 or more variables or species. PCA is a technique that may summarise the relationship between the samples in a small number of axes that can be plotted. For such a summarisation to work, there must be some degree of correlation between the descriptive variables so that the effect of a number of these variables can be combined into a single axis. For good general introductions to PCA for nonmathematicians see Kent & Coker (1992) and Legendre & Legendre (1983).
From the ordination dropdown menu CAP offers a PCA undertaken on either the correlation or variancecovariance matrix between the descriptors (the variables in the rows). Once either PCA correlation or PCA covariance is selected a PCA on the working data set is undertaken.
Output from a PCA is presented under a number of tabbed components that can each be viewed by clicking on the tab. These are described in turn below:
Principal Axis vs Variable Plot
