R: Class '"octav"' for frequencies in abundance octaves

octav-class {sads} | R Documentation

## Class `"octav"` for frequencies in abundance octaves

### Description

Data frame of frequencies of entities (usually species) in classes of logarithm of abundances at base 2 (Preston's octaves).

### Usage

    ## S4 method for signature 'octav'
    lines(x, prop=FALSE, mid=TRUE, ...)
    ## S4 method for signature 'octav'
    plot(x, prop=FALSE, x.oct=FALSE, par.axis=list(), ...)
    ## S4 method for signature 'octav'
    points(x, prop=FALSE, mid=TRUE, ...)

### Arguments

`x` | an object of class `octav`
`prop` | logical; if `TRUE` relative frequencies are returned.
`x.oct` | logical; if `TRUE` axis labels are octave numbers, if `FALSE` upper limit of abundance class are used as labels.
`mid` | logical; if `TRUE` x coordinates of abundances are set to the mid of each octave, if `FALSE` x coordinates of abundances are the values of its octave (see examples)
`par.axis` | list; further graphical parameters for the plot axes.
`...` | further parameters to be passed to `lines`, `points` or `plot` functions (except axes in `plot`, which are set by `par.axis`.

### Objects from the Class

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

### Slots

`.Data`:

  Object of class `"list"` a data frame of three vectors: octave number (integer), which is the upper limit of the class in log2; upper limit of the class in arithmetic scale (numeric); number of cases in each class (numeric).

`names`:

  Object of class `"character"`; names of the three vectors of `.Data`, `"octave"`, `"upper"`, and `"Freq"`, respectively.

`row.names`:

  Object of class `"data.frameRowLabels"`; default line names for `.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 = "octav")`: adds frequency data contained in the object as lines in an octave plot created by `plot` method.

plot

  `signature(x = "octav", y = "ANY")`: creates a histogram of frequencies of species in each octave in the object, a.k.a 'Preston plot'

points

  `signature(x = "octav")`: adds frequency data contained in the object as points in a octave plot created by `plot` method.

### Author(s)

Andre Chalom and Paulo I Prado prado@ib.usp.br

### References

Magurran, A.E. 1989. Ecological diversity and its measurement. Princenton University Press.

Preston, F.W. 1948. The commonness and rarity of species. Ecology 29: 254–283.

### See Also

`octav` to get an object of the class from a vector of abundances; `octavpred` to get an `octav` object of predicted abundances from a theoretical distribution; man page of `prestonfit` in package `vegan` for a detailed account of Preston's octaves and an alternative way to get octaves and model fitting.

### Examples

    ## Creates an octav object from an abundance vector
    birds.oc <- octav(birds)
    moths.oc <- octav(moths)

    ## default plot
    plot(birds.oc)
    ## Octave values instead of abundances at x-axis
    plot(moths.oc, x.oct=TRUE)

    ## Using line and argument prop to superpose two data sets
    ## (Fisher's et al moth data and Preston's bird data)
    ## mid=FALSE plots points at each octave value and not
    ## in the midclass (default, useful for histograms)
    plot(moths.oc, col=NULL, border=NA, prop=TRUE, x.oct=TRUE, xlab="Octave")
    lines(moths.oc, prop=TRUE,  mid=FALSE)
    lines(birds.oc, prop=TRUE, mid=FALSE, col="red")

[Package sads version 0.4.2 Index]