levins.overlap: Levin's niche overlap index

In MicroNiche: Microbial Niche Measurements

Description

This index is a measurement of the overlap between pairs of taxa across samples. A value of 1 indicates perfect overlap, and 0 indicates no overlap.

Usage

levins.overlap(df, q = 1.65)

Arguments

df	A matrix of taxa (rows) by samples (columns) as discrete counts per sample. Col 1 must be a taxon identifier.
q	A coefficient for the LOQ, set to 1.65. Decreasing or increasing q will affect which taxa are flagged as being below the LOQ.

Details

Taxon inputs must be as discrete counts across samples, with a taxon identifier in column 1. The output is a matrix of paired taxon overlap indices. Specifically, Levin's Overlap (LO) indices of LO[1,2] are rows and LO[2,1] are columns, for taxa 1 and 2.

Levin's overlap is calculated as follows: LO[i,j] = sum(p[i]*p[j])/sum(p[i]^2) whereby p[i] is the proportion of taxon i per sample and p[j] is the proportion of taxon j per sample.

Taxa below the LOQ are flagged with an asterisk.

This function depends on reshape2 to produce a matrix of overlap comparisons.

Value

An object of class "data.frame" that gives LO[1,2] as rows and LO[2,1] as columns.

Note

NA

Author(s)

Damien Finn

References

Ludwig and Reynolds. 1988 Statistical Ecology. Wiley and Sons, Milton Australia

See Also

levins.Bn

Examples

data(df)
overlapdf <- df[48:53,]
res <- levins.overlap(overlapdf)

MicroNiche documentation built on Jan. 30, 2020, 5:08 p.m.