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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)

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.