Analysis of community ecology data in R

Theory R functions Examples Exercise

• rda - this function calculates RDA if matrix of environmental variables is supplied (if not, it calculates PCA). Two types of syntax are available:
  • matrix syntax - RDA = rda (Y, X, W), where Y is the response matrix (species composition), X is the explanatory matrix (environmental factors) and W is the matrix of covariables
  • formula syntax - RDA = rda (Y ~ var1 + factorA + var2*var3 + Condition (var4), data = XW) - as explanatory are used: quantitative variable var1, categorical variable factorA, interaction term between var2 and var3, whereas var4 is used as covariable and hence partialled out.
• cca - this function calculates CCA if matrix of environmental variables is supplied (if not, it calculates CA).
• RsquareAdj - in case of CCA, it extracts only the value of R², while values of adjusted R² are not available (these need to be calculated by permutations and it is not available in R yet).
• anova.cca - tests the significance of the variation in species composition explained by explanatory variables, using Monte Carlo permutation test.