nmds {labdsv}R Documentation

Nonmetric Multidimensional Scaling

Description

This function is simply a wrapper for the isoMDS function in the MASS package by Venables and Ripley. The purpose is to establish a nmds class to simplify plotting and additional graphical analysis as well as a summary.

Usage

nmds(dis,k=2,y=cmdscale(d=dis,k=k),maxit=50)
bestnmds(dis,k=2,itr=20,maxit=100)

Arguments

dis a dist object returned from dist() or a full symmetric dissimilarity or distance matrix
k the desired number of dimensions for the result
y a matrix of initial locations (objects as rows, coordinates as columns, as many columns as specified by k). If none is supplied, cmdscale is used to generate them
maxit the maximum number of iterations
itr number of random starts to find best result

Details

The nmds function simply calls the isoMDS() function of the MASS library, but converts the result from a list to an object of class "nmds." The only purpose for the function is to allow ‘plot’, ‘identify’, ‘surf’, and other additional methods to be defined for the nmds class, to simplify the analysis of the result.

The ‘bestnmds’ function runs ‘itr’ number of random initial locations and returns the best result of the set.

Value

an object of class ‘nmds’, with components:

points the coordinates of samples along axes
stress the "goodness-of-fit" computed as stress in percent

Note

nmds is included as part of the LabDSV package to provide a consistent interface and utility for vegetation ordination methods. Other analyses included with the same interface include principal components analysis (pca), principal coordinates analysis (pco), correspondence analysis (ca), canonical correspondence analysis (cca), and fuzzy set ordination (fso).

Author(s)

Venables and Ripley for the original isoMDS function

David W. Roberts droberts@montana.edu http://ecology.msu.montana.edu/labdsv for the nmds class and interface

References

Kruskal, J.B. (1964) Multidimensional scaling by optimizing goodness of fit to nonmetric hypothesis. Psychometrics 29:1-27.

Kruskal, J.B. (1964) Nonmetric multidimensional scaling: a numerical method. Psychometrics 29:115-129.

T.F. Cox and M.A.A. Cox. (1994) Multidimensional Scaling. Chapman and Hall.

See Also

isoMDS for the original function

plot.nmds for the plot method

points.nmds for a points method

plotid.nmds for a function to identify points in the graphic

surf.nmds for a function to plot contours of independent variables on top of the graphic (using the gam and interp functions to calculate the surface

jsurf.nmds for a function to plot contours of independent variables on top of the graphic (using the gam() and interp() functions to calculate the surface. Jitters the coordinates of points on the axes to avoid errors in the embedded interp function.

bestnmds for a way to automate multiple ramdom starts and save the best result

initMDS for an alternative way to automate random starts

postMDS for a post-solution rescaling

metaMDS for a full treatment of variations

Examples

    data(bryceveg)
    data(brycesite)
    dis.man <- dist(bryceveg,method="manhattan")
    demo.nmds <- nmds(dis.man,k=4)
    plot(demo.nmds)
    data(brycesit)
    points(demo.nmds,brycesite$elev>8000)
    plotid(demo.nmds)

[Package labdsv version 1.0-1 Index]