Nested Manova by Canonical Analysis

Pierre Legendre
June 2002
Département de Sciences Biologiques
Université de Montréal
This program carries out nested multivariate analysis of variance (manova) by canonical redundancy analysis, with permutation testing, using 2 or 3 factors (i.e., one main factor plus 1 or 2 nested factors). If a single factor is present, the program computes simple manova with permutation test. The response table subjected to the analysis can be a single variable or a multivariate data table. The primary interest of this program is to allow nested analysis of variance to be carried out for community composition data (species presence-absence or abundance data tables). Three choices are open with such data: The main output file “NesAnova.out” contains the results of the anova or manova. An additional output file, called “FittedSc.out”, contains a PCA of the fitted site scores for each factor in the analysis, as well as a PCA of the residuals. The permutation methods used in the program are described in the user's manual distributed with the program. The user’s manual distributed with the program contains examples that describe how the factors, main and nested, should be coded using dummy variables. The program GENERATE_X, distributed with NesAnova, has been written to automatically code into dummy variables the factors of a nested anova comprising one main factor and 1 or 2 nested factors.

Program availability

Legendre, P. & M. J. Anderson. 1999. Distance-based redundancy analysis: testing multi-species responses in multi-factorial ecological experiments. Ecological Monographs 69 (1): 1-24. Legendre, P. and E. Gallagher. 2001. Ecologically meaningful transformations for ordination of species data. Oecologia 129: 271-280. (Reprint available, © 2001 "Springer-Verlag". The original publication is available on