pm_chao: Chao lower bound estimator

In ampatzia/pasaR: Pangenome Statistical Analysis for R

Description

This function computes two versions of the lower bound Chao Estimator for the pangenome size.

Usage

pm_chao(Panmatrix, biased = FALSE)

Arguments

Panmatrix	Panmatrix produced by make_panmatrix functions
biased	produces a biased estimation, same as the chao() function in micropan

Details

The function prodused a biased & unbiased version of the metric along with variance and a 95 estimation of the pangenome compared to other estimators. This function is an optimized and expanded version of chao() from package micropan.

References

Chao, A. (1987). Estimating the population size for capture-recapture data with unequal catchability. Biometrics 43, 783-791. Gotelli, N.J. and Colwell, R.K., 2011. Estimating species richness. Biological diversity: frontiers in measurement and assessment, 12, pp.39-54.

Examples

## Not run: pm_chao(Panmatrix)

ampatzia/pasaR documentation built on May 12, 2019, 2:37 a.m.