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.

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]

Class "rad" for rank-abundance data