octav-methods {sads}R Documentation

Frequencies of species in octaves


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


octav(x, oct, preston=FALSE)



a numerical vector of abundances or an object of class fitsad or fitrad.


integer vector; the octaves to tabulate abundances. Should include all abundance values in x.


logical; if 'TRUE' use Preston method to count frequencies (see details), if 'FALSE' class intervals are open on the left (default in cut).


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).


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


integer; octave number, which is the upper limit of the class in log2.


numeric; upper limit of the class in arithmetic scale.


integer or numeric; (relative) frequencies of species in each class.


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.


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


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.


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

[Package sads version 0.4.2 Index]