MicroNiche (version 1.0.0)

feinsingers.PS: Feinsinger's proportional similarity index

Description

This index is a measurement of proportional similarity (PS) of a taxon in relation to an environmental parameter, such as pH or temperature. A value of 0 indicates an inverse relationship between taxon abundance and the environmental parameter, whilst 1 indicates a positive relationship between taxon abundance and the environmental parameter. A value of 0.5 indicates no relationship.

Usage

feinsingers.PS(df, R, sampleInfo, envInfo, 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.

envInfo

A quantitative variable of some environmental parameter measured per sample.

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.

Value

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

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 PS generated from R random proportions permuted 999 times. This allows the user to perform significance testing and to determine a probability that the taxa PS differs from the null PS. The output includes each taxon's PS, 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.

Feinsinger's PS is calculated as follows: PS[j] = 1 - 0.5*sum(|p[i] - r[i]|) whereby p[i] is the proportion of taxon j in environment i and r[i] is the proportion of the environmental parameter in i.

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

References

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

See Also

proportional.overlap

Examples

# NOT RUN {
data(df)
sampleInfo <- c(rep("R1",10), rep("R2",10), rep("R3",10), rep("R4",10))
pH.grad <- c(2.1, 2.2, 2, 1.9, 2.1, 1.8, 1.9, 2, 2.1, 1.9, 3.5, 3.6, 3.5, 
             3.4, 3.6, 3.5, 3.5, 3.4, 3.7, 3.4, 6.6, 6.5, 6.4, 6.8, 7, 6.6, 
             6.8, 6.9, 7, 7.1, 8, 8.2, 7.9, 8.1, 7.8, 7.9, 8.3, 8.2, 8.1, 7.9) 
res <- feinsingers.PS(df, 4, sampleInfo, pH.grad)
# }