R: Frequencies of species in octaves

octav-methods {sads} | R Documentation

## Frequencies of species in octaves

### Description

Creates an object of `octav-class` with number of species in octaves of abundances from a vector of abundances or from a fitted model.

### Usage

    octav(x, oct, preston=FALSE)

### Arguments

`x` | a numerical vector of abundances or an object of class `fitsad` or `fitrad`.
`oct` | integer vector; the octaves to tabulate abundances. Should include all abundance values in `x`.
`preston` | logical; if 'TRUE' use Preston method to count frequencies (see details), if 'FALSE' class intervals are open on the left (default in `cut`).

### Details

Preston (1948) popularized the use of histograms with logarithmic classes to depict species abundance distributions (Magurran 1989). Preston used classes at log base two, which he called ‘octaves’ as their end-points double from one class to the other. In Preston original method half of the species with abundances equal to the limits of octaves are credited to the neighboring octave. If `preston=TRUE` this non-standard method of class closure is applied. In general this makes the histogram more bell-shaped, as Preston expected (see example).

### Value

an object of class `octav`, which is a data frame with three vectors:

`octav` | integer; octave number, which is the upper limit of the class in log2.
`upper` | numeric; upper limit of the class in arithmetic scale.
`Freq` | integer or numeric; (relative) frequencies of species in each class.

### Methods

`signature(x = "numeric")`

  number of species in each octave in a vector of species abundances.

`signature(x = "fitsad")`

  number of species in each octave in the original abundance vector used to fit a model with `fitsad`.

`signature(x = "fitrad")`

  number of species in each octave in the original abundance vector used to fit a model with `fitrad`.

### Author(s)

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

### References

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

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

### See Also

`octav-class` for methods to create an octave plot; `octavpred` to get an `octav` object of predicted abundances from a theoretical distribution; `fitsad-class` and `fitrad-class` objects, from which you can also get an object of class `octav`; man page of `prestonfit` in package vegan for a detailed account of Preston's octaves and an alternative way to get octaves and fitting of species abundances distributions.

### Examples

    ## BCI tree data
    (bci.oc1 <- octav(bci, preston=TRUE))
    ## Comparing with standard class closure
    par(mfrow=c(1,2))
    plot(octav(bci), main="octav(bci, preston=FALSE)")
    plot(bci.oc1, main="octav(bci, preston=TRUE)")
    par(mfrow=c(1,1))

[Package sads version 0.4.2 Index]