Analysis of community ecology data in R

Theory R functions Examples Exercise

• RsquareAdj (library 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).
• anova.cca (library 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
  • the global model (default setting), i.e. all variables included in the analysis;
  • only the first constrained axis (adding argument first = TRUE);
  • individual axes (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);
  • individual terms (explanatory variables) added sequentially in the order in which they appear in the formula or data frame (by = “terms”; note that this variation depends on the order of variables in which they enter the model);
  • variation explained by individual explanatory variables after removing variation of all other variables in the model (by = “margin”; here the variation does not depend on the order of variables in the model).