phi

0th

Percentile

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.

See Also

preston

Aliases
  • phi
  • unphi
Examples
# NOT RUN {
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 1.7-4, License: GPL

Community examples

Looks like there are no examples yet.