Description Usage Arguments Details Value Note Author(s) References See Also Examples

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.

1 2 |

`dis` |
a dist object returned from |

`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, |

`maxit` |
the maximum number of iterations in the isoMDS routine |

`itr` |
number of random starts to find best result |

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.

an object of class ‘nmds’, with components:

`points` |
the coordinates of samples along axes |

`stress` |
the "goodness-of-fit" computed as stress in percent |

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 at present include principal components analysis (pca), and principal coordinates analysis (pco).

Venables and Ripley for the original isoMDS function included in the MASS package.

David W. Roberts [email protected] http://ecology.msu.montana.edu/droberts

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.

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

`isoMDS`

for the original function

`plot.nmds`

for the ‘plot’ method, the ‘plotid’
method to identify points with a mouse, the ‘points’ method to
identify points meeting a logical condition, the ‘hilight’ method
to color-code points according to a factor,
the ‘chullord’ method to add convex hulls for a factor, or the
the ‘surf’ method to add surface contours for
continuous variables.

`initMDS`

for an alternative way to automate random starts

`postMDS`

for a post-solution rescaling

`metaMDS`

for a full treatment of variations

1 2 3 4 5 6 7 |

```
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
initial value 16.413924
iter 5 value 11.979735
iter 10 value 10.865550
iter 15 value 10.472783
iter 15 value 10.465003
iter 15 value 10.460451
final value 10.460451
converged
integer(0)
```

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

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.