pcobiplot: Computing and plotting a biplot ordination using principal...

In dave: Functions for "Data Analysis in Vegetation Ecology"

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

Example output

Loading required package: cluster
Loading required package: labdsv
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-28. For overview type 'help("mgcv-package")'.
Loading required package: MASS

Attaching package: 'labdsv'

The following object is masked from 'package:stats':

    density

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-4
Loading required package: nnet

Attaching package: 'nnet'

The following object is masked from 'package:mgcv':

    multinom

Loading required package: tree
Call:
pcobiplot.default(veg = sveg, method = "bray", y = 0.25)

dave documentation built on May 2, 2019, 1:30 p.m.