Hubbell's phi

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 \(i\)th 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 \(i\)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.

References

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

Author

Robin K. S. Hankin

Note

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

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
#> [1] 3 1 1 0 1
unphi(phi(a))   #should match 'a' except for species names (which are lost)
#> spp6 spp5 spp4 spp1 spp2 spp3 
#>    5    3    2    1    1    1 

data(butterflies)
phi(butterflies,add=FALSE)
#>  [1] 10  5  6  1  2  2  0  1  1  0  0  0  0  0  0  0  0  0  1  2  1  0  0  1  0
#> [26]  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  1  0  0  0
#> [51]  0  0  2

summary(unphi(phi(butterflies)))  #should match 'summary(butterflies)'
#> Number of individuals: 376 
#> Number of species: 37 
#> Number of singletons: 10 
#> Most abundant species: spp36 (53 individuals)
#> estimated theta:  9.989579