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
Bill.Venables at csiro.au
2008-Jul-05 04:32 UTC
[R] p-value for Nonmetric Multidimentional Scaling?
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.
On Fri, 2008-07-04 at 21:14 -0700, Michael Denslow wrote:> 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?No, but the following discussion on the r-forge repository for vegan presents some ways that an analysis of this type could be done using metaMDS: http://r-forge.r-project.org/forum/forum.php?thread_id=586&forum_id=194 But read Jari's comments carefully. If your data are species, then consider whether permuting row, columns or both is appropriate when they don't preserve the row or column totals. So a question to ask yourself is, is permuting rows, columns or both going to derive the appropriate Null hypothesis for the test you have in mind? Please feel free to follow this up in the forum post I refer to. All the best, G> > 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.