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Section: Diversity analysis


R functions

  • iNEXT (library iNEXT) calculates abundance- and incidence-based rarefaction of species on the number of individuals (or sites) or on sample coverage (a measure of completeness). The name stems from interpolation-extrapolation since the function allows both interpolation (aka rarefaction) and extrapolation of the curve (extrapolation works up to two times of the maximum number of individuals or samples). Function plot draws the rarefaction curves (optionally with confidence intervals) for any combination of a number of individuals (or samples) vs the number of species vs sample coverage (modified by the argument type in the function plot applied on iNEXT object, see ?plot.iNEXT).
  • estimateD (library iNEXT) - rarifies the number of species per common number of individuals or sites or per common level of coverage (completeness). It works for species richness (q = 0) as well as for Shannon diversity (q = 1) and Simpson diversity(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 are calculated.
  • specaccum (library vegan) - calculates accumulation curve on the community data matrix (one curve per matrix); plot draws the result (optionally with confidence interval).

Further reading:

en/rarefaction_r.txt · Last modified: 2023/05/21 23:05 by David Zelený

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