phi

From untb v1.7-2 by Robin K S Hankin

Hubbell's phi

Hubbell's phi: counts of species abundances

Keywords: math

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 $i$th element to the species with abundance $i$ 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 $i$th element is the number of species with $i$ individuals. The name of the $i$th 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

References

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

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)'

Documentation reproduced from package untb, version 1.7-2, License: GPL

Community examples

Looks like there are no examples yet.

phi