R: Class '"rad"' for rank-abundance data

rad-class {sads} | R Documentation

## Class `"rad"` for rank-abundance data

### Description

Data frame of ranked abundances of species

### Usage

    ## S4 method for signature 'rad'
    lines(x, prop=FALSE, ...)
    ## S4 method for signature 'rad'
    plot(x, prop=FALSE, ...)
    ## S4 method for signature 'rad'
    points(x, prop=FALSE, ...)

### Arguments

`x` | an object of class `rad`
`prop` | logical; if `TRUE` relative abundances are returned.
`...` | further parameters to be passed to `lines`, `points` or `plot` functions.

### Objects from the Class

Objects can be created by calls of the form `new("rad", ...)`, but most often by a call to `rad` or `radpred`.

### Slots

`.Data`:

  Object of class `"list"`; a data frame of two vectors: abundance rank of each species (integer), from most abundant (rank=1) to the least abundant (rank=length(rank)); abundance of each species (numeric)

`names`:

  Object of class `"character"`; names of the two vectors of `.Data`, `"rank"` and `"abund"`, respectively.

`row.names`:

  Object of class `"data.frameRowLabels"`; default line names for `.Data`; integer indexes from 1 to `nrow(.Data)`.

`.S3Class`:

  Object of class `"character"`; indicates inheritance from S3 class `data.frame`.

### Extends

Class `"data.frame"`, directly. Class `"list"`, by class "data.frame", distance 2. Class `"oldClass"`, by class "data.frame", distance 2. Class `"vector"`, by class "data.frame", distance 3.

### Methods

lines

  `signature(x = "rad")`: adds rank-abundance data contained in the object as lines in rank-abundance plots created by `plot` method.

plot

  `signature(x = "rad", y = "ANY")`: creates a rank-abundance plot from data in the object.

points

  `signature(x = "rad")`: adds rank-abundance data contained in the object as points in rank-abundance plots created by `plot` method.

pprad

  `signature(x = "rad", rad = "character", coef = "list")`: percentile-percentile plot, see `pprad`.

qqrad

  `signature(x = "rad", rad = "character", coef = "list", trunc = "ANY")`: quantile-quantile plot, see `qqrad`.

### Author(s)

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

### References

Whittaker, R. H. 1965, Dominance and Diversity in Land Plant Communities. Science, 147: 250–260.

### See Also

`rad` to get an object of the class from a vector of abundances; `radpred` to get a `rad-class` object of predicted abundances from a theoretical distribution, `qqrad` for quantile-quantile plots from a `rad-class` object, and `pprad` for percentile-percentile plots.

### Examples

    ## Creates a rad object from a vector of abundances
    birds.rad <- rad(birds)

    ## Rank-abundance plot
    plot(birds.rad)

    ## Same, with non-default graphical parameters
    plot(birds.rad, pch=19, xlab="Abundance rank of species")

    ## Adding points from another data set
    points(rad(okland), pch=19)

[Package sads version 0.4.2 Index]