Analysis of community ecology data in R

Theory R functions Examples

• varpart (library vegan) - variation partitioning (using RDA, CCA or db-RDA) among up to four matrices of environmental variables. The first argument (Y) is the 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 permutations specifies the number of permutations used to calculate adjusted R² in CCA).
• plot.varpart (library 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 showvarparts below, e.g. to add the labels for individual (groups of) variables (argument Xnames), or colours of the fractions (argument bg). Consult ?plot.varpart for more details.
• showvarparts (library vegan) - draws schema of Venn's diagram with codes of individual fractions.