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Nmds

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The nmds command is modelled after the nmds code written in R by Sarah Goslee, using Non-metric multidimensional scaling function using the majorization algorithm from Borg & Groenen 1997, Modern Multidimensional Scaling.



Default settings

A phylip-formatted distance matrix must be inputted for nmds to be successful.

mothur > nmds(phylip=98_sq_phylip_amazon.dist)

Options

axes

The axes parameter allows you to enter a file containing a starting configuration. By default mothur will generate a random starting configuration.

mindim

The mindim parameter allows you to select the minimum dimensions to use. Default=2

maxdim

The maxdim parameter allows you to select the maximum dimensions to use. Default=2

maxiters

The maxiters parameter allows you to select the maximum number of iters to try with each random configuration. Default=500

iters

The iters parameter allows you to select the number of random configuration to try. Default=10.

epsilon

The epsilon parameter allows you to select set an acceptable stopping point. Default=1e-12.


Revisions