Density, distribution function, quantile function and random generation for the Fisher's
log-series probability distribution with parameter `alpha`

.

1 2 3 4 |

`x` |
vector of (integer, x>0) quantiles. Usually a vector of abundances of species in a sample. |

`q` |
vector of (integer, x>0) quantiles. Usually a vector of abundances of species in a sample. |

`p` |
vector of probabilities. |

`n` |
number of random values to return. |

`N` |
sample size. Usually the total number of individuals in the sample (see details). |

`alpha` |
real positive; Fisher's alpha parameter (see details). |

`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]. |

The Fisher log-series is a limiting case of the Negative Binomial where the dispersion parameter of the negative binomial tends to zero. It was originally proposed by Fisher (1943) to relate the expected number of species in a sample from a biological community to the sample size as:

Where alpha is the single parameter of the log-series distribution, often used as a diversity index. From this relation follows that the expected number of species with x individuals in the sample is

*S(x) = alpha*X^x/x*

Where X is a function of alpha and N, that tends to one as the sample size N increases:

*X = N / (alpha+ N)*

The density function used here is derived by Alonso et al. (2008, supplementary material). In ecology, this density distribution gives the probability that a species has an abundance of x individuals in a random sample of size N of the community. In the community, the species abundances are independent random variables that follow a log-series distribution. Thus, a random sample of a log-series is also a log-series distribution.

Therefore, a log-series distribution is a model for species abundances distributions (SAD) under the assumptions that (a) species abundances in the community are independent identically distributed log-series variables, (b) sampling is a Poisson process, (c) sampling is done with replacement, or the fraction sampled is small enough to approximate a sample with replacement.

`dls`

gives the (log) of the density, `pls`

gives the (log)
distribution function, `qls`

gives the (log) the quantile function.

Invalid values for parameter `alpha`

will result in return
values `NaN`

, with a warning.

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

Alonso, D. and Ostling, A., and Etienne, R. S. 2008 The implicit assumption of symmetry and the species abundance distribution. Ecology Letters, 11: 93-105.

Fisher, R.A, Corbert, A.S. and Williams, C.B. (1943) The Relation between the number of species and the number of individuals in a random sample of an animal population. The Journal of Animal Ecology, 12(1): 42–58.

Green,J. and Plotkin, J.B. 2007 A statistical theory for sampling species abundances. Ecology Letters 10:1037–1045

Pielou, E.C. 1977. Mathematical Ecology. New York: John Wiley and Sons.

`dpois`

, `dnbinom`

, `dpoig`

.
For maximum likelihood estimation in the context of species
abundance distributions see `fitls`

, `fisherfit`

in vegan package
and `fisher`

in untb package.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ```
x <- 1:100
PDF <- dls(x=x, N=100, alpha=5)
CDF <- pls(q=x, N=100, alpha=5)
par(mfrow=c(1,2))
plot(x,CDF, ylab="Cumulative Probability", type="b",
main="Log-Series distribution, CDF")
plot(x,PDF, ylab="Probability", type="h",
main="Log-Series distribution, PDF")
par(mfrow=c(1,1))
## Fisher log-series is a discrete PDF, hence:
all.equal(pls(10,N=1000,alpha=50), sum(dls(1:10,N=1000,alpha=50))) # should be TRUE
## qls is the inverse of pls
all.equal(qls(CDF,N=100,alpha=5), x) # should be TRUE
``` |

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.