R: Computing and plotting a biplot ordination using principal...
pcobiplot
R Documentation
Computing and plotting a biplot ordination using principal coordinates analysis
Description
Computing a principal coordinates analysis of releves (rows, see pco) and subsequently the correlations with all species (columns). Two ordinations are plotted, one for releves and an arrow-plot for species. Species are restricted to the list given in sel.sp and species names are abbreviated upon request (see make.cepnames).
Usage
pcobiplot(veg, method, y = 1, ...)
pcocoor(veg, method, y = 1)
## Default S3 method:
pcobiplot(veg,method,y=1,...)
## S3 method for class 'pcobiplot'
plot(x,...,axes=c(1,2),sel.sp=NULL,shortnames=TRUE)
Arguments
veg
This is a vegetation data frame, releves are rows, species columns
method
The method used for calculating distance. See function vegdist(), package vegan.
y
Transformation of species scores: x'= x exp(y)
...
Plot parameters axes=c(1,2), sel.sp=NULL (species selection),shortnames=TRUE for
abbreviation of species names
shortnames
A logical variable, when TRUE delivering shortnames of species (package vegan used).
axes
A vector of length two, assessing the axes used for plotting. Default is c(1,2).
x
An object of class "pcobiplot"
sel.sp
The species (column numbers) to be included in the plot of arrows
Value
An object of class "pcobiplot" with at least the following items:
nrel
The number of releves
nspe
The number of species
rpoints
Ordination scores of releves
spoints
Ordination scores of species
allspnames
The full list of species names
Note
If sel.sp is not specified a random selection of 6 species is taken
Author(s)
Otto Wildi
References
Wildi, O. 2013. Data Analysis in Vegetation Ecology. 2nd ed. Wiley-Blackwell, Chichester.
Examples
sel.sp<- c(3,11,23,31,39,46,72,77,96) # selection of species
o.pcobiplot<- pcobiplot(sveg,method="bray",y=0.25) # used pco
plot(o.pcobiplot,sel.sp=sel.sp,axes=c(1,2),shortnames=TRUE) # plot of releves, sepecies
providing 
.