Re: [R] p-value for Nonmetric Multidimentional Scaling?

From: <Bill.Venables_at_csiro.au>
Date: Sat, 05 Jul 2008 14:32:57 +1000

You need to ask yourself a number of questions, e.g.

What is the hypothesis you wish to test? What is the test statistic you wish to use to test it? How can I get some information on where my value of that statistic sits with respect to its null hypothesis distribution?

p-values do not exist independently of hypothesis tests.

(It would also be a coutresy to the list to give your name and affiliation, as the posting guide suggests.)

Bill Venables
CSIRO Laboratories
PO Box 120, Cleveland, 4163
AUSTRALIA

Office Phone (email preferred): +61 7 3826 7251
Fax (if absolutely necessary):  +61 7 3826 7304
Mobile:                         +61 4 8819 4402
Home Phone:                     +61 7 3286 7700
mailto:Bill.Venables_at_csiro.au
http://www.cmis.csiro.au/bill.venables/

-----Original Message-----
From: r-help-bounces_at_r-project.org [mailto:r-help-bounces_at_r-project.org] On Behalf Of Michael Denslow
Sent: Saturday, 5 July 2008 2:14 PM
To: r-help_at_r-project.org
Subject: [R] p-value for Nonmetric Multidimentional Scaling?

Dear R-helpers,

I am running metaMDS in the vegan package, which uses isoMDS in MASS, to perform Nonmetric Multidimentional Scaling (NMDS).

I have seen some authors report a p-value for the NMDS ordination based on randomization of the dataset. As I understand it this is meant to compare the stress in your dataset to multiple runs of randomized data. I do not see a way to perform such a test in vegan or MASS.

So my questions are:
Is this necessary? and Does R have a function to do this?

Thanks in advance for your help,
Michael



R-help_at_r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

R-help_at_r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Sat 05 Jul 2008 - 04:37:45 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Sat 05 Jul 2008 - 05:31:04 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.

list of date sections of archive