dpoilog: Poisson-lognormal distribution

In sads: Maximum Likelihood Models for Species Abundance Distributions

Poisson-lognormal distribution

Description

Density, distribution function, quantile function and random generation for Poisson-lognormal distribution with parameters mu and sigma.

Usage

dpoilog( x, mu, sig, log=FALSE)
ppoilog( q, mu, sig, lower.tail=TRUE, log.p=FALSE)
qpoilog( p, mu, sig, lower.tail = TRUE, log.p = FALSE)
rpoilog( n, mu, sig)

Arguments

x	vector of (non-negative integer) quantiles. Usually a vector of abundances of species in a sample.
q	vector of (non-negative integer) quantiles. Usually a vector of abundances of species in a sample.
n	number of random values to return.
p	vector of probabilities.
mu, sig	parameters of the compounding lognormal distribution (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].

Details

A compound Poisson-lognormal distribution is a Poisson probability distribution where its single parameter lambda is a random variable with lognormal distribution. The density function is

p(x) = \frac{e^{x \mu + x^2 \sigma/2} (2 \pi \sigma)^{-1/2}}{x!} \, g(y)

where

g(y) = \int_{-\infty}^\infty \, e^{-e^y} \frac{e^{(-y-\mu-x \sigma)^2}}{2 \sigma} \, dy

(Bulmer 1974 eq.5). For x = 0, 1, 2, ... .

In ecology, this distribution gives the probability that a species has an abundance of x individuals in a random sample of a fraction 'f' of the community. In the community, the species abundances are independent random variables that follow a lognormal density function, with parameters (mu + ln(f), sigma) (Engen et al. 2002).

Hence, a Poisson-lognormal distribution is a model for species abundances distributions (SAD) in a sample taken from a community under the assumptions: (a) species abundances in the community are independent identically distributed lognormal variables, (b) sampling is a Poisson process with expected value E[x]= f*n where n is the abundance in the community and f the fraction of individuals sampled, (c) individuals are sampled with replacement, or the fraction of total individuals sampled is small enough to approximate a sample with replacement. See Engen (1977) and Alonso et al. (2008) for critical evaluations.

Value

'dpoilog' gives the (log) density of the density, 'ppoilog' gives the (log) distribution function, 'qpoilog' gives the quantile function.

Author(s)

Paulo I. Prado [e-mail], Andre Chalom and Murilo Dantas Miranda

Source

These functions were built from dpoilog function from poilog package (Vidar Grøtan and Steinar Engen).

dpoilog is just a wrapper of poilog::dpoilog with an additional log argument.

ppoilog does the cumulative sum of poilog::dpoilog.

qpoilog uses modified bisection method to find numerically quantiles using ppoilog.

rpoilog selects random values from a poilog distribution. It is unrelated to the function of the same name in poilog.

References

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.

Bulmer,M. G. 1974. On Fitting the Poisson Lognormal Distribution to Species-Abundance Data. Biometrics, 30: 101-110.

Grøtan V. and Engen S. 2008. poilog: Poisson lognormal and bivariate Poisson lognormal distribution. R package version 0.4.

Engen, S. 1977. Comments on two different approaches to the analysis of species frequency data. Biometrics, 33: 205-213.

Engen, S., R. Lande, T. Walla & P. J. DeVries. 2002. Analyzing spatial structure of communities using the two-dimensional Poisson lognormal species abundance model. American Naturalist 160: 60-73.

See Also

dpois, dlnorm; dpoilog and rpoilog in poilog package; rsad for random generation, fitpoilog for maximum likelihood estimation.

sads documentation built on June 22, 2024, 12:18 p.m.