dave (version 2.0)

pcovar: Plotting 6 variants of principal coordinates analysis

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)
# S3 method for default
pcovar(veg, y, ...)
# S3 method for 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".

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

Details

pco, vegdist, procrustes for the main functions used

References

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

Examples

# NOT RUN {
o.pcovar<- pcovar(sveg,y=1)
plot(o.pcovar,reversals=c(0,0,0,0,0,0))
# }