# Analysis of community ecology data in R

David Zelený

### Others

en:rarefaction_r

Section: Diversity analysis

## Rarefaction

### R functions

• iNEXT (library 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 plot draws 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 type in the function plot applied on iNEXT object, see ?plot.iNEXT).
• estimateD (library 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).
• rarefy (library 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.
• rarecurve (library vegan) - draws rarefaction curve for each row in the data. No confidence intervals calculated.
• specaccum (library vegan) - calculates accumulation curve on the community data matrix (one curve per matrix); plot draws the result (optionally with confidence interval).