R help - Jul 2010 - interpretation of stress in NMDS

Among those users of Primer, stress values greater than 0.3 are
interpreted as "questionable".  Using both isoMDS and metaMDS (vegan
package), the stress values returned are much higher using my own data
and using examples provided in R Help.  For example Rstress = 8.3, and
the stressplot r2 = 0.99 indicating (to me) that the ordination is OK.
I am guessing that the "stress" values across packages are not the
same,
and googling about has not returned a satisfactory answer ... thus this
posting.  My concern being that reporting a stress value of 8 for what I
consider a satisfactory result may raise a few Primer-user's eyebrows.

 

Gregory A. Graves, Lead Scientist

Everglades REstoration COoordination and VERification (RECOVER) 

Restoration Sciences Department

South Florida Water Management District

Phones:  DESK: 561 / 682 - 2429 

                   CELL:  561 / 719 - 8157

 


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On 7/22/2010 2:21 PM, Graves, Gregory wrote:
> Among those users of Primer, stress values greater than 0.3 are
> interpreted as "questionable".  Using both isoMDS and metaMDS
(vegan
> package), the stress values returned are much higher using my own data
> and using examples provided in R Help.  For example Rstress = 8.3, and
> the stressplot r2 = 0.99 indicating (to me) that the ordination is OK.
> I am guessing that the "stress" values across packages are not
the same,
> and googling about has not returned a satisfactory answer ... thus this
> posting.  My concern being that reporting a stress value of 8 for what I
> consider a satisfactory result may raise a few Primer-user's eyebrows.
Dear Gregory,

as the help file of ?isoMDS tells us:

"stress   The final stress achieved (in percent)"

So 8.3 is in reality 0.083.

Thomas Petzoldt