From: Ross Clement <R.P.Clement_at_westminster.ac.uk>

Date: Mon 06 Jun 2005 - 23:28:29 EST

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Mon Jun 06 19:25:05 2005

Date: Mon 06 Jun 2005 - 23:28:29 EST

(i) What is the exact stress measure used? The text in the help file

says:

This chooses a k-dimensional (default k = 2) configuration to minimize the stress, the square root of the ratio of the sum of squared differences between the input distances and those of the configuration to the sum of configuration distances squared. However, the input distances are allowed a monotonic transformation.

I presume that this is Stress-1 from Kruskal's 1964 paper "Multidimensional scaling by optimising goodness of fit to nonmetric hypothesis". (I haven't got a copy of this paper but have Borg and Groenen's book which references it). However, I'm not 100% sure given the text description in the help file, and note that isoMDS() quotes stress as a percentage.

As a preparation for using MDS I wrote some MDS code using iterative majorisation. While I'm sure that isoMDS() produces much better results, I would still like to do a like-for-like comparison. If I use a straight correlation measure between the original and recreated distances, then isoMDS() is considerably (typically about 0.05) better than my program, but I'd like to have the proper stress comparison.

(ii) I write most of my code in C. I haven't been able to pin down

exactly what the status of linking C to R is. At present I do the
following:

if ( experiment == MDS )

{

writeDistData( "temp.csv" );

system( "R --no-save < rEuclidean.R >> /dev/null" );
reread( "temp.points" );

}

else if ( experiment == PCA )

{

writeRawData( "temp.csv" );

system( "R --no-save < rEuclidean.pca.R >> /dev/null" );
reread( "temp.scores" );

}

with appropriate R commands in the .R files.

This was easy to write, seems to work fine, and doesn't seem too slow. But, I'd still like to ask if there is a tidier way of achieving the same effect.

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Mon Jun 06 19:25:05 2005

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