Analysis of community ecology data in R

David Zelený

Others

en:rda_cca_r

Section: Ordination analysis

RDA, tb-RDA, CCA & db-RDA (constrained ordination)

R functions

• 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.