| 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
|
oct |
integer vector; the octaves to tabulate abundances. Should
include all abundance values in |
preston |
logical; if 'TRUE' use Preston method to count
frequencies (see details), if 'FALSE' class intervals are open on
the left (default in |
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))