Introduction
Theory, R functions & Examples
Section: Ordination analysis
rda
- this function calculates RDA if matrix of environmental variables is supplied (if not, it calculates PCA). Two types of syntax are available: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 covariablesRDA = 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.