Canonical Correspondence Analysis (Legendre & Legendre 1998) is correspondence analysis of a site/species matrix where each site has given values for one or more environmental variables (temperature, depth, grain size etc.). The ordination axes are linear combinations of the environmental variables. CCA is thus an example of direct gradient analysis, where the gradient in environmental variables is known a priori and the species abundances (or presence/absences) are considered to be a response to this gradient.
Each site should occupy one row in the spreadsheet. The environmental variables should enter in the first columns, followed by the abundance data (the program will ask for the number of environmental variables).
The implementation in PAST follows the eigenanalysis algorithm given in Legendre & Legendre (1998). The ordinations are given as site scores - fitted site scores are presently not available. Environmental variables are plotted as correlations with site scores. Both scalings (type 1 and 2) of Legendre & Legendre (1998) are available. Scaling 2 emphasizes relationships between species.
Missing values are supported by column average substitution.
References
Legendre, P. & L. Legendre. 1998. Numerical Ecology, 2nd English ed. Elsevier, 853 pp.