Theory, Examples & Exercises
Section: Ordination analysis
vegan) - variation partitioning (using RDA, CCA or db-RDA) among up to four matrices of environmental variables. First argument (
Y) is dependent variable, usually the matrix of species composition (the function calculates RDA, or, if
chisquare = TRUE, CCA), but could be also only a single variable (in that case it calculates linear regression) or distance matrix (applying db-RDA using the function
capscale). Further arguments (up to four) are (groups of) explanatory variables. The function uses either formula interface (with ~, see examples) or matrices. The interpretation should be based on adjusted R2, although raw R2 is also reported (for CCA, adjusted R2 is calculated by permutation method of Peres-Neto et al. 2006 and may slightly vary between re-analyses of the same data; the argument
permutationsspecifies the number of permutations used to calculate adjusted R2 in CCA).
vegan) - draws Venn's diagram with fractions of explained variation. In default setting it doesn't show negative values of explained variation (argument
cutoff = 0). The function can use arguments of
showvarpartsbelow, e.g. to add the labels for individual (groups of) variables (
Xnames), or colors of the fractions (
?plot.varpartfor more details.
vegan) - draws schema of Venn's diagram with codes of individual fractions.