phi: Hubbell's phi

In RobinHankin/untb: Ecological Drift under the UNTB

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 ith element to the species with abundance i if unique. This can be confusing. 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 ith element is the number of species with i individuals. The name of the ith element is the species with abundance i 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,addnames=FALSE) # three singleton spp, one species with abundance 2, etc
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)'

RobinHankin/untb documentation built on Dec. 7, 2024, 6:30 p.m.