Theory, R functions & Examples
Section: Diversity analysis
iNEXT) calculates abundance- and incidence-based rarefaction of species on number of individals (or sites) or on sample coverage (a measure of completeness). The name stems from interpolation-extrapolation, since the function allows both inter- and extrapolation of the rarefaction curve (extrapolation works up to 2 times of max number of individuals or samples). Function
plotdraws the rarefaction curves (optionally with confidence intervals) for any combination of number of individuals (or samples) x number of species x sample coverage (modified by the argument
typein the function
iNEXT) - rarifies number of species per common number of individuals or sites, or per common level of coverage (completeness). Does not work only for species richness (q = 0), but also for Shannon and Simpson diversity, respectively (q = 1 and q = 2).
vegan) - calculates abundance-based rarefaction. Applies on sample x species matrix (cells must be genuine abundances, i.e. counts of individuals) or vector of abundances.
vegan) - draws rarefaction curve for each row in the data. No confidence intervals calculated.
vegan) - calculates accumulation curve on the community data matrix (one curve per matrix);
plotdraws the result (optionally with confidence interval).