pcovar: Plotting 6 variants of principal coordinates analysis

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

Description

Plotting 6 ordinations using euclidean distance, manhattan distance, chord distance, Canberra distance, Bray-Curtis distance (vegdist) and correlation as distance respectively. Transformation of scores can be adjusted according to x'= x exp(y). All ordinations (pco) superimposed to PCA solution (pca) by procrustes analysis.

Usage

pcovar(veg, y, ...)
pcoatest(veg, y=1)

## Default S3 method:
pcovar(veg, y, ...)
## S3 method for class 'pcovar'
plot(x,...,reversals=c(0,0,0,0,0,0))

Arguments

veg	A vegetation data frame, releves are rows, species columns
y	Transformation of species scores: x'= x exp(y)
...	Additional plot paramteters, see par.
reversals	Vector reversals=c(0,0,0,0,0,0). When set to 1 the corresponding plot is mirrored vertically.
x	An object of class "pcovar".

Details

pco, vegdist, procrustes for the main functions used

Value

An object of class "pcovar" with at least the following items:

nrel	The number of releves
nspec	The number of species
y	Transformation of species scores: x'= x exp(y)
euclidpca	PCA coordinates, euclid used, adjusted by procrustes analysis
euclidpco	PCO coordinates, euclid used, adjusted by procrustes analysis
manhpco	PCO coordinates, manhattan used, adjusted by procrustes analysis
manhpca	PCA coordinates, manhattan used, adjusted by procrustes analysis
cordpco	PCO coordinates, chord distance used, adjusted by procrustes analysis
cordpca	PCA coordinates, chord distance used, adjusted by procrustes analysis
canpco	PCO coordinates, canberra dist. used, adjusted by procrustes analysis
canpca	PCA coordinates, canberry dist. used, adjusted by procrustes analysis
bpco	PCO coordinates, Bray-Curtis dist. used, adjusted by procrustes analysis
bpca	PCA coordinates, Bray-Curtis dist. used, adjusted by procrustes analysis
corpco	PCO coord., correlation as dist. used, adjusted by procrustes analysis
corpca	PCA coord., correlation as dist. used, adjusted by procrustes analysis

Note

This function serves primarily instructional purposes

Author(s)

Otto Wildi

References

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

Examples

o.pcovar<- pcovar(sveg,y=1)
plot(o.pcovar,reversals=c(0,0,0,0,0,0))

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