# 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

 1 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.

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 droberts@montana.edu

## 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

 1 2 3 4 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.