Hubbell's phi: counts of species abundances
phi(x,addnames=TRUE) unphi(freq, string="spp")
- Ecosystem vector; is coerced to class
- Boolean with default
TRUEmeaning to set the name of the $i$th element to the species with abundance $i$ if unique. Set to
FALSEto suppress this, which is useful if the species names are long
- Frequency data (eg as returned by
- Character; species name to prepend (using
NULLcan be confusing)
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
unphi() does the reverse: given the output of
phi(), it returns a corresponding
count object. Note that
species names are lost.
The code for setting the names is a dog's breakfast
S. P. Hubbell 2001. The Unified Neutral Theory of Biodiversity. Princeton University Press.
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)'