R: Geometric series distribution

dgs {sads} | R Documentation

## Geometric series distribution

### Description

Density, distribution function, quantile function and random generation for the Geometric Series distribution, with parameter `k`.

### Usage

    dgs( x, k, S, log = FALSE )
    pgs( q, k, S, lower.tail = TRUE, log.p = FALSE )
    qgs( p, k, S, lower.tail = TRUE, log.p = FALSE )
    rgs( n, k, S )

### Arguments

`x` | vector of (non-negative integer) quantiles. In the context of species abundance distributions, this is a vector of abundance ranks of species in a sample.
`n` | number of random values to return.
`k` | positive real, 0 < k < 1; geometric series coefficient; the ratio between the abundances of i-th and (i+1)-th species.
`q` | vector of (non-negative integer) quantiles. In the context of species abundance distributions, a vector of abundance ranks of species in a sample.
`p` | vector of probabilities.
`S` | positive integer 0 < S < Inf, number of elements in a collection. In the context of species abundance distributions, the number of species in a sample.
`log, log.p` | logical; if TRUE, probabilities p are given as log(p).
`lower.tail` | logical; if TRUE (default), probabilities are P[X <= x], otherwise, P[X > x].

### Details

The Geometric series distribution gives the probability (or expected proportion of occurrences) of the i-th most abundant element in a collection:

p(i) = C * k * (1-k)^(i-1)

where C is a normalization constant which makes the summation of p(i) over S equals to one:

C = 1/(1 - (1-k)^S)

where S is the number of species in the sample.

Therefore, `[dpq]gs` can be used as rank-abundance model for species ranks in a sample or biological community see `fitrad-class`.

### Value

`dgs` gives the (log) density and `pgs` gives the (log) distribution function of ranks, and `qgs` gives the corresponding quantile function.

### Note

The Geometric series is NOT the same as geometric distribution. In the context of community ecology, the first can be used as a rank-abundance model and the former as a species-abundance model. See `fitsad` and `fitrad` and vignettes of sads package.

### Author(s)

Paulo I Prado prado@ib.usp.br and Murilo Dantas Miranda.

### References

Doi, H. and Mori, T. 2012. The discovery of species-abundance distribution in an ecological community. Oikos 122: 179–182.

May, R.M. 1975. Patterns of Species Abundance and Diversity. In Cody, M.L. and Diamond, J.M. (Eds) Ecology and Evolution of Communities. Harvard University Press. pp 81–120.

### See Also

`fitgs`, `fitrad` to fit the Geometric series as a rank-abundance model.

### Examples

    x <- 1:25
    PDF <- dgs(x=x, k=0.1, S=25)
    CDF <- pgs(q=x, k=0.1, S=25)
    par(mfrow=c(1,2))
    plot(x,CDF, ylab="Cumulative Probability", type="b",
         main="Geometric series distribution, CDF")
    plot(x,PDF, ylab="Probability, log-scale", type="h",
         main="Geometric series distribution, PDF", log="y")
    par(mfrow=c(1,1))

    ## quantile is the inverse of CDF
    all.equal(qgs(CDF, k=0.1, S=25), x)

[Package sads version 0.4.2 Index]