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

Author(s)

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]