pcobiplot {dave} 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

Otto Wildi

### References

Wildi, O. 2017. Data Analysis in Vegetation Ecology. 3rd ed. CABI, Oxfordshire, Boston.

### 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


[Package dave version 2.0 Index]