ordcomp: Ordination to Dissimilarity Comparison

Description Usage Arguments Value Note Author(s) References Examples

View source: R/ordcomp.R

Description

Plots the distribution of pair-wise distances of all points in an ordination over the distances in the dissimilarity or distance matrix the ordination was calculated from. Prints the correlation between the two on the graph.

Usage

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ordcomp(x,dis,dim,xlab="Computed Distance",ylab="Ordination Distance",
            title="",pch=1)

Arguments

x

an ordination object from pca, pco, nmds, fso or ordiplot

dis

an object of class dist

dim

the number of dimensions in the ordination to use (default=all)

xlab

the X axis label for the graph

ylab

the Y axis label for the graph

title

a title for the plot

pch

the symbol to plot

Value

A plot is created on the current graphics device. Returns the (invisible) correlation.

Note

Ordinations are low dimensional representations of multidimensional spaces. This function attempts to portray how well the low dimensional solution approximates the full dimensional space.

Author(s)

David W. Roberts [email protected]

References

http://ecology.msu.montana.edu/labdsv/R/labs/lab9/lab9.html

Examples

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data(bryceveg) # produces a vegetation data.frame
dis.bc <- dsvdis(bryceveg,'bray/curtis') # creates a Bray/Curtis dissimilarity matrix
pco.bc <- pco(dis.bc,2) # produces a two-dimensional Principal Coordinates Ordination object
ordcomp(pco.bc,dis.bc)

Example output

Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-25. For overview type 'help("mgcv-package")'.
Loading required package: MASS
Loading required package: cluster

Attaching package: 'labdsv'

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

    density

labdsv documentation built on May 30, 2017, 12:46 a.m.