Message-ID: <49E615CD.1040908@ua.ac.be>
Date: 2009-04-15T17:13:49Z
From: Dieter Vanderelst
Subject: Kruskal's MDS results
In-Reply-To: <481243.45020.qm@web33101.mail.mud.yahoo.com>
Hi Michael,
Thanks for the reply.
I understand that the stress is a measure of how good the algorithm managed to represent the ordinal distances between items. And I also see why it's dependent on the number of dimensions.
I was hoping someone could tell me exactly what the formula for the percentual stress is. To me it's not clear how this metric is calculated.
Regards,
Dieter
Michael Denslow wrote:
> Hi Dieter,
>
> I'll take a shot at this. As I understand it, the stress is telling
> you how the ordination distances compare with original
> dissimilarities that you calculated.
>
> It is a measure how well your ordination has done in representing the
> relationship of your sites. Note that the stress will differ
> depending on how many dimensions are used. I believe the default is k
> = 2 in isoMDS.
>
> Hope this helps, Michael
>
>
>> Dear List,
>>
>> I'm trying to interpret the results of the Kruskal's Non-metric
>> Multidimensional Scaling algorithm (isoMDS, MASS package).
>>
>> The 'goodness of fit' is reported as "The final stress achieved (in
>> percent)".
>>
>> What does this mean exactly? I've tried to google for an answer but
>> I've not come up with a definitive answer.
>>
>> Regards, Dieter
>>
>>
>> -- Dieter Vanderelst PhD Student
>>
>> Active Perception Lab University of Antwerp
>> http://batbits.webnode.com/
>>
>> Postal Address: Prinsstraat 13 B-2000 Antwerp Belgium
>
> Michael Denslow
>
> Graduate Student I.W. Carpenter Jr. Herbarium [BOON] Department of
> Biology Appalachian State University Boone, North Carolina U.S.A.
>
> -- AND --
>
> Communications Manager Southeast Regional Network of Expertise and
> Collections sernec.org
>
>
>