en:rarefaction_r

### Table of Contents

Section: Diversity analysis

## Rarefaction

### R functions

(library`iNEXT`

`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*in*terpolation-*ext*rapolation 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`

).(library`estimateD`

`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).(library`rarefy`

`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.(library`rarecurve`

`vegan`

) - draws rarefaction curve for each row in the data. No confidence intervals are calculated.(library`specaccum`

`vegan`

) - calculates accumulation curve on the community data matrix (one curve per matrix);`plot`

draws the result (optionally with confidence interval).

### Further reading:

- Vignette about how to use iNEXT package can be found on CRAN: https://cran.r-project.org/web/packages/iNEXT/vignettes/Introduction.pdf

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