phi {untb}R Documentation

Hubbell's phi

Description

Hubbell's phi: counts of species abundances

Usage

phi(x,addnames=TRUE)
unphi(freq, string="spp")

Arguments

x

Ecosystem vector; is coerced to class count

addnames

Boolean with default TRUE meaning to set the name of the iith element to the species with abundance ii if unique. Set to FALSE to suppress this, which is useful if the species names are long

freq

Frequency data (eg as returned by phi())

string

Character; species name to prepend (using NULL can be confusing)

Details

Function phi() coerces its argument to a count object and by default returns a named vector whose iith element is the number of species with ii individuals. The name of the iith element is the species with abundance ii if unique and empty otherwise. Function phi() is used by theta.prob().

Function unphi() does the reverse: given the output of phi(), it returns a corresponding count object. Note that species names are lost.

Note

The code for setting the names is a dog's breakfast

Author(s)

Robin K. S. Hankin

References

S. P. Hubbell 2001. “The Unified Neutral Theory of Biodiversity”. Princeton University Press.

See Also

preston

Examples


jj <- c(rep("oak",5) ,rep("ash",2),rep("elm",3),"pine","tea","yew")
a <- as.count(jj)

phi(a)
unphi(phi(a))   #should match 'a' except for species names (which are lost)

data(butterflies)
phi(butterflies,add=FALSE)

summary(unphi(phi(butterflies)))  #should match 'summary(butterflies)'


[Package untb version 1.7-7 Index]