levins.Bn: Levins' niche breadth index

In MicroNiche: Microbial Niche Measurements

Description

This index is a measurement of niche breadth (Bn) of a taxon weighted by the number of differing environments (R), whereby a value of 1 indicates generalist taxa that are equally abundant across environments, and 0 indicates specialist taxa that favour specific environments.

Usage

levins.Bn(df, R, sampleInfo, 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.
R	The number of different environments being compared.
sampleInfo	A categorical variable identifying which samples correspond to which environment.
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. This function also performs null model testing against a distribution of Bn generated from R random proportions permuted 999 times. This allows the user to perform significance testing and to determine a probability that the taxa Bn differs from the null Bn. The output includes each taxon's Bn, a P value of significance testing against the null model distribution, and a Benjamin-Hochberg adjusted P value to account for false discovery rate.

A plot of the null distribution with 0.05 and 0.95 quantiles highlighted as red dotted lines is also provided.

Finally, this function also calculates the limit of quantification (LOQ) to identify taxa whose niche cannot be confidently measured. A plot of log abundance x taxon rank is provided to visualise the distribution of the data, a fitted lognormal taxa rank model, and the LOQ determined based on the standard deviation of the lognormal model.

Levin's niche breadth is calculated as follows: Bn[j] = (1/R)/sum(p[i]^2) whereby R is the number of differing environments and p[i] is the proportion of taxon j in environment i.

This function depends on ggplot2 to generate a plot of the null distribution and reshape2 to identify the taxa below the LOQ.

Value

An object of class "data.frame" that gives the Bn, P value and adjusted P value for each taxon. A column noting taxa that fall below the LOQ are identified as T.

Note

The null model testing becomes increasingly robust with increasing R. If R == 2 the results should be interpreted with caution.

Author(s)

Damien Finn

References

Feinsinger et al. 1981. A simple measure of niche breadth. Ecology 62(1):27-32

See Also

levins.overlap

Examples

data(df)
sampleInfo <- c(rep("R1",10), rep("R2",10), rep("R3",10), rep("R4",10))
res <- levins.Bn(df, 4, sampleInfo)

Example output

Loading required package: ggplot2
Loading required package: reshape2
Warning message:
Use of `Z$Null.Bn` is discouraged. Use `Null.Bn` instead. 

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