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

In sads: Maximum Likelihood Models for Species Abundance Distributions

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 [e-mail] 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 or from an histogram; 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)

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