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Ecosystem diagnostics

no.of.ind.Rd

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

Usage

no.of.ind(x)
no.of.spp(x, include.extinct=FALSE)
no.of.singletons(x)
no.of.extinct(x)
maximal.abundance(x)
singletons(x)
extinct(x)
extant(x)

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 extinct 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

References

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

Author

Robin K. S. Hankin

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()

Examples

data(butterflies)
no.of.spp(butterflies)
#> [1] 37
no.of.ind(butterflies)
#> [1] 376

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

extinct(jj1 + jj2) 
#>  bugs crabs squid 
#>     0     0     0 
extinct(jj3)               #rats and cats
#> rats cats 
#>    0    0 
extant(jj3)                #bugs and crabs
#>  bugs crabs 
#>     3     3 

singletons(jj1)
#> slugs 
#>     1 
singletons(jj2)           # empty 
#> character(0)
singletons(jj1 + jj3)     # slugs
#> slugs 
#>     1