Description Usage Arguments Objects from the Class Slots Extends Methods Author(s) References See Also Examples
Data frame of frequencies of entities (usually species) in classes of logarithm of abundances at base 2 (Preston's octaves).
1 2 3 4 5 6 |
x |
an object of class |
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 |
Objects can be created by calls of the form new("octav", ...)
,
but most often by a call to octav
or octavpred.
.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
.
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.
signature(x = "octav")
: adds frequency data
contained in the object as lines in an octave plot created by plot
method.
signature(x = "octav", y = "ANY")
: creates a
histogram of frequencies of species in each octave in the object, a.k.a 'Preston plot'
signature(x = "octav")
: adds frequency data
contained in the object as points in a octave plot created by plot
method.
Andre Chalom and Paulo I Prado prado@ib.usp.br
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.
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ## 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")
|
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