Theory, Examples & Exercises
Section: Ordination analysis
vegan) - extracts the value of R2 and adjusted R2 from results of ordination (and also regression). For linear constrained ordinations (RDA, tb-RDA), the adjusted R2 is calculated using Ezekiel's formula, while for unimodal constrained ordinations (CCA) the calculation is based on permutation model introduced by Peres-Neto et al. (2006).
vegan) - tests the significance of the variation in species composition explained by explanatory variables in constrained ordination (RDA, CCA), using Monte Carlo permutation test. It can test the significance of
first = TRUE);
by = “axis”), sequentially from the first to the last (this is done by using samples scores on the n-th axis as explanatory variables, while using scores of the axis 1, 2, ... n as covariables);
by = “terms”; note that this variation depends on the order of variables in which they enter the model);
by = “margin”; here the variation does not depend on the order of variables in the model).