R: Predicted frequencies of species in octaves

octavpred-methods {sads} | R Documentation

## 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 prado@ib.usp.br, 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")

[Package sads version 0.4.2 Index]