octavpred: Predicted frequencies of species in octaves

In sads: Maximum Likelihood Models for Species Abundance Distributions

Predicted frequencies of species in octaves

Description

Creates an object of octav-class with the frequencies of species in octaves of abundances predicted by a species abundance distribution or by a rank-abundance distribution.

Arguments

object	an object of class fitrad or fitrad; fitted model of rank-abundance or species abundances distributions. Alternatively a numeric vector abundances of species.
sad, rad	character; root name of sad or rad distribution to calculate expected percentiles. See fitsad and fitrad for available distributions.
coef	named list of numeric values; parameter values of the distribution given in sad or rad. Parameters should be named as in the corresponding density function, and in the same order.
trunc	non-negative integer, trunc > min(x); truncation point if fitted distribution is truncated.
oct	integer vector; the octaves to tabulate abundances, see octav. If not provided, the octavpred method will generate an educated guess.
S	positive integer; number of species in the sample.
N	positive integer; number of individuals in the sample.
preston	logical. Should Preston original method be used? See octav.

Methods

signature(object = "fitrad", sad = "missing", rad = "missing", coef = "missing", trunc = "missing", oct = "ANY", S = "missing", N = "missing")

number of species in each octave predicted from a rank-abundance model fitted with function fitrad.

signature(object = "fitsad", sad = "missing", rad = "missing", coef = "missing", trunc = "missing", oct = "ANY", S = "missing", N = "missing")

number of species in each octave predicted from an abundance distribution model fitted with function fitsad.

signature(object = "missing", sad = "character", rad = "missing", coef = "list", trunc = "ANY", oct = "ANY", S = "numeric", N = "numeric")

number of species in each octave predicted from an abundance distribution named by sad with parameters defined in coef.

signature(object = "numeric", sad = "character", rad = "missing", coef = "list", trunc = "ANY", oct = "ANY", S = "missing", N = "missing")

same as previous method, but with S and N taken from a vector of abundances given by object.

signature(object = "missing", sad = "missing", rad = "character", coef = "list", trunc = "ANY", oct = "ANY", S = "numeric", N = "numeric")

number of species in each octave predicted from an rank-abundance distribution named by rad with parameters defined in coef.

signature(object = "numeric", sad = "missing", rad = "character", coef = "list", trunc = "ANY", oct = "ANY", S = "missing", N = "missing")

same as previous method, but with S and N taken from a vector of abundances given by object.

Author(s)

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

See Also

octav and octav-class for generic function and methods to create an octave plot and details on abundance octaves; fitsad-class and fitrad-class objects, from which you can also get an object of class octav with observed and predicted values; man page of prestonfit in package vegan for a detailed account of Preston's octaves and an alternative way to get octaves and fitting of species abundances distributions.

Examples

## Predicted frequencies from a fitted model
## meta-community zero-sum multinomial for BCI data
bci.mzsm <- fitsad(bci, "mzsm")
bci.mzsm.oc <- octavpred(bci.mzsm)
## Preston plot with observed and predicted frequencies
plot(octav(bci))
lines(bci.mzsm.oc)
## Alternative model: local zero-sum multinomial
## Alonso & Mckane (Ecol. Lett. 2004, table 1) give theta = 44 and m = 0.15
bci.lzsm.oc <- octavpred( bci, sad = "volkov", coef =list(theta = 44, m = 0.15, J=sum(bci)) )
## Adding predicted frequencies to the plot
lines(bci.lzsm.oc, col = "red")

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