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The unified neutral theory of biodiversity: the untb package

The untb package provides R-centric functionality for working with Hubbell’s unified neutral theory of biogeography and biodiversity. A vignette is provided in the package. The canonical reference is Hubbell 2001; to cite the package in publications please use Hankin 2007.

Installation

You can install the released version of the untb package from CRAN with:

# install.packages("untb")  # uncomment this to install the package
library("untb")
set.seed(0)

The untb package in use

The package has two main classes, count and census. A count object is a named integer vector, with names being species and entries being respective counts. Thus:

x <- count(c(cats=9,pigs=3,dogs=2,rats=1,hogs=1,bats=1))
x
#> cats pigs dogs rats hogs bats 
#>    9    3    2    1    1    1
summary(x)
#> Number of individuals: 17 
#> Number of species: 6 
#> Number of singletons: 3 
#> Most abundant species: cats (9 individuals)
#> estimated theta:  2.861392

Above, we see 9 cats, 3 pigs, and so on. Function summary() gives further information. A census object is an unordered factor with entries being the species of each individual:

as.census(x)
#>  [1] cats cats cats cats cats cats cats cats cats pigs pigs pigs dogs dogs rats
#> [16] hogs bats
#> Levels: cats pigs dogs rats hogs bats

The package includes example datasets:

data(sahfos)
summary(sahfos)
#> Number of individuals: 460182 
#> Number of species: 54 
#> Number of singletons: 10 
#> Most abundant species: Echinodermata larvae (247200 individuals)
#> estimated theta:  4.649568

We can give a visual summary of a dataset in two ways:

plot(sahfos)

plot(preston(sahfos))

The package also includes the ability to generate random neutral assemblages:

summary(rand.neutral(1000,10))
#> Number of individuals: 1000 
#> Number of species: 47 
#> Number of singletons: 8 
#> Most abundant species: 2 (330 individuals)
#> estimated theta:  10.09543
summary(rand.neutral(1000,10))
#> Number of individuals: 1000 
#> Number of species: 52 
#> Number of singletons: 16 
#> Most abundant species: 4 (117 individuals)
#> estimated theta:  11.50422

References

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

  • R. K. S. Hankin, 2007. “Introducing untb, an R package for simulating ecological drift under the unified nuetral theory of biodiversity”, Journal of Statistical Software 22(12)