phi: Calculating the phi Statistic on Taxon Classifications

In optpart: Optimal Partitioning of Similarity Relations

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

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.

φ = \frac{ad - bc}{√{(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

Value

A data.frame of φ values with species as rows and clusters as columns

Author(s)

David W. Roberts [e-mail]

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

data(shoshveg)
dis.bc <- dsvdis(shoshveg,'bray')
opt.5 <- optpart(5,dis.bc)
phi(shoshveg,opt.5)

optpart documentation built on March 26, 2020, 6:18 p.m.