optpart (version 3.0-3)

phi: Calculating the phi Statistic on Taxon Classifications

Description

Calculates the \(phi\) statistic on a classified table of taxa

Usage

phi(comm,clustering,minplt=10,p.adjust=FALSE)

Arguments

comm

a data.frame with samples as rows and attributes as columns

clustering

a vector of integers or an object of class ‘clustering’, ‘partition’, or ‘partana’

minplt

the minimum number of samples a species must occur in to be included in the calculation

p.adjust

switch to control adjusting probabilities for simultaneous inference by Hochberg correction

Value

A data.frame of \(\phi\) values with species as rows and clusters as columns

Details

\(phi\) is a statistic of agreement between two vectors. In this case the function calculates the distribution of each species within clusters of a partition, calculates the \(phi\) statistic for each species in each cluster.

$$\phi = \frac{ad - bc}{\sqrt{(a+b)\times(c+d)\times(a+c)\times(b+c)}}$$

where:

a	sample is in specified type and species is present
b	sample is not in group and species is present
c	sample is in type but species is not present
d	sample is not in type and species is not present

References

Tichy, L. and M. Chytry. 2006. Statistical determination of diagnostic species for site groups of unequal size. Journal of Vegetation Science 17:809-818.

Examples

# NOT RUN {
data(shoshveg)
dis.bc <- dsvdis(shoshveg,'bray')
opt.5 <- optpart(5,dis.bc)
phi(shoshveg,opt.5)
# }