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

 ```1 2 3 4 5 6 7``` ```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".

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

Otto Wildi

References

Wildi, O. 2013. Data Analysis in Vegetation Ecology. 2nd ed. Wiley-Blackwell, Chichester.

Examples

 ```1 2``` ```o.pcovar<- pcovar(sveg,y=1) plot(o.pcovar,reversals=c(0,0,0,0,0,0)) ```

dave documentation built on May 29, 2017, 5:54 p.m.