calc_S_C: 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)

Value

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

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.
interrupt: logical. Should the function throw an error when C_target exceeds the maximum recommendable coverage?

References

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

Anne Chao, Nicholas J. Gotelli, T. C. Hsieh, Elizabeth L. Sander, K. H. Ma, Robert K. Colwell, and Aaron 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/.

Examples

Run this code

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