calc_S_C: Calculate species richness for a given coverage level.

In MoBiodiv/mobr: Measurement of Biodiversity

Calculate species richness for a given coverage level.

Description

This function uses coverage-based rarefaction to compute species richness. Specifically, the metric is computed as the

Usage

calc_S_C(x, C_target = NULL, extrapolate = TRUE, interrupt = TRUE)

Arguments

x	a site by species matrix or a species abundance distribution
C_target	target coverage between 0 and 1 (default is NULL). If not provided then target coverage is computed by calc_C_target
extrapolate	logical. Defaults to TRUE in which case richness is extrapolated to sample sizes larger than observed in the dataset using the Chao1 method (Chao 1984, 1987).
interrupt	logical. Should the function throw an error when C_target exceeds the maximum recommendable coverage?

Value

numeric value which is the species richness at a specific level of coverage.

References

Chao, A. 1984. Nonparametric Estimation of the Number of Classes in a Population. Scandinavian Journal of Statistics 11:265–270.

Chao, A. 1987. Estimating the population size for capture-recapture data with unequal catchability. Biometrics, 43, 783-791.

Chao, A., and L. Jost. 2012. Coverage-based rarefaction and extrapolation: standardizing samples by completeness rather than size. Ecology 93:2533–2547.

Chao, A., N.J. Gotelli, T.C. Hsieh, E.L. Sander, K.H. Ma, R.K. Colwell, and A.M. Ellison 2014. Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies. Ecological Monographs 84:45-67.

T. C. Hsieh, K. H. Ma and Anne Chao. 2024. iNEXT: iNterpolation and EXTrapolation for species diversity. R package version 3.0.1 URL: http://chao.stat.nthu.edu.tw/wordpress/software-download/.

See Also

invChat

Examples

data(tank_comm)
# What is species richness for a coverage value of 60%?
calc_S_C(tank_comm, C_target = 0.6)

MoBiodiv/mobr documentation built on Oct. 26, 2024, 10:51 a.m.