R: Predicted ranked abundance of species

radpred-methods {sads} | R Documentation

## Predicted ranked abundance of species

### Description

Creates an object of `rad-class` with the ranked abundances predicted by a species abundance distribution or 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.
`distr` | Deprecated since sads 0.2.4. See `distr` function
`S` | positive integer; number of species in the sample.
`N` | positive integer; number of individuals in the sample.

### Methods

`signature(object = "fitrad", sad = "missing", rad = "missing", coef = "missing", trunc = "missing", distr = "missing", S = "missing", N = "missing")`

  ranked abundances of species predicted from a rank-abundance model fitted with function `fitrad`.

`signature(object = "fitsad", sad = "missing", rad = "missing", coef = "missing", trunc = "missing", distr = "missing", S = "missing", N = "missing")`

  ranked abundances of species predicted from a abundance distribution model fitted with function `fitsad`.

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

  ranked abundances of species predicted from abundance distribution named by `sad` with parameters defined in `coef`.

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

  ranked abundances of species predicted from a rank-abundance distribution named by `rad` with parameters defined in `coef`.

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

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

### Note

The rank-abundance function is the inverse of the quantile function of the species abundance distribution (May 1975). `radpred` uses numeric interpolation with `approxfun` to find quantiles, instead of the slower bisection method used in many quantile functions in the package sads. Hence results from `radpred` and from the quantile functions may not match exactly.

### Author(s)

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

### References

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.

### Examples

    ## Predicted frequencies from a fitted model
    ## meta-community zero-sum multinomial for BCI data
    moths.mzsm <- fitsad(moths, "mzsm")
    moths.mzsm.r <- radpred(moths.mzsm)
    ## Rank-abundance plot with observed and predicted frequencies
    plot(rad(moths))
    lines(moths.mzsm.r)
    ## Alternative model: local zero-sum multinomial
    ## Alonso & Mckane (Ecol. Lett. 2004, table 1) give theta = 41 and m = 0.77
    moths.lzsm.r <-
      radpred( moths, sad = "volkov",
               coef =list(theta = 41, m = 0.77, J=sum(moths))
             )
    ## Adding predicted frequencies to the plot
    lines(moths.lzsm.r, col = "red")

[Package sads version 0.4.2 Index]