Given a correlation matrix of rows or columns this selects the variable sharing a
maximum variance with all others and declares this rank 1. Reduces the matrix
(covariances, correlations) by the contribution of the variable ranked first. Repeats
the process to derive consecutive ranks until no variance is left.
Usage
orank(veg, use, rlimit=5, y=1, x.axis=NULL, y.axis=NULL,...)
orank1(veg, use, rlimit=5, y=1, x.axis=NULL, y.axis=NULL)
## Default S3 method:
orank(veg, use, rlimit=5, y=1, x.axis=NULL, y.axis=NULL,...)
## S3 method for class 'orank'
plot(x,...)
## S3 method for class 'orank'
summary(object,...)
Arguments
veg
This is a vegetation data frame, releves are rows, species columns
use
Either "rows" or "columns"
rlimit
The maximum number of ranks to be determined
y
Transformation of species scores: x'= x exp(y)
x.axis
Horizontal axis used for plotting result in a sampling plan
y.axis
Vertical axis used for plotting result in a sampling plan
x
An object of class "orank"
...
Further variables used for printing
object
An object of class "orank"
Details
If x-axis=NULL or y-axis=NULL then a pcoa-ordination is computed
and the first two axes used for plotting
Value
An object of class "orank" with at least the following items:
use
Either "rows" or "columns"
n.ranks
The number of ranks
var.names
Names of the ranked variables
var.explained
Explained variance of the ranked variables
var.percent
Percentage of the variance explained
cum.var
Cummulative variance of ranked variables, percentage
x.axis
The same as input parameter x.axis
y.axis
The same as input parameter y.axis
Note
The present function exclusively relies on a correlation matrix, function cor.
Author(s)
Otto Wildi
References
Orloci, L. 1973. Ranking characters by a dispersion criterion.
Nature 244: 371–373.
Wildi, O. 2013. Data Analysis in Vegetation Ecology. 2nd ed. Wiley-Blackwell,
Chichester.
Examples
# Uses vegetation data frame sveg with vegetation data
# and ssit with corresponding x- and y-axes scores
x.axis=ssit$x.axis ; y.axis=ssit$y.axis
o.orank<- orank(sveg,use="rows",rlimit=5,y=0.25,x.axis,y.axis)
plot(o.orank)