Ecosystem diagnostics

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Description

Ecosystem diagnostics such as species count, individual count, number of singletons, etc

Usage

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Arguments

x

Ecosystem vector; is coerced to class count

include.extinct

In function no.of.spp(), Boolean argument with TRUE meaning to include extinct species (ie species with an abundance of zero), and default FALSE meaning to return the number of extant species

Details

  • Function no.of.spp() returns the number of species in an ecosystem object, treating exctinct species in line with argument include.extinct

  • Function no.of.ind() returns the number of individuals

  • Function no.of.singletons() returns the number of singletons

  • Function no.of.extinct() returns the number of extinct species

  • Function maximal.abundance() returns the abundance of the most abundant species

  • Function singletons() returns a count object containing only the singletons: each abundance is one

  • Function extinct() returns a count object containing only the extinct species: each abundance is zero

  • Function extant() returns a count object containing only the extant species: each abundance is greater than zero

Note

It is sometimes useful to include species with an abundance of zero when, for example, taking a single row of the Saunders dataframe.

The default for include.extinct is FALSE because this is required for (eg) optimal.theta()

Author(s)

Robin K. S. Hankin

References

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

Examples

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data(butterflies)
no.of.spp(butterflies)
no.of.ind(butterflies)

jj1 <- count(c(dogs=7,pigs=3,crabs=1,slugs=1))
jj2 <- count(c(squid=0,octopus=0,nautilus=0))
jj3 <- count(c(bugs=3,rats=1,crabs=0,fish=0))

extinct(jj1 + jj2) 
extinct(jj3)               #cats 'n' fish
extant(jj3)                #bugs and rats

singletons(jj1)
singletons(jj2)           # empty 
singletons(jj1 + jj3)     # crabs, rats and slugs

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