[R] isoMDS and 0 distances
tyler.smith at mail.mcgill.ca
Wed Apr 19 04:06:56 CEST 2006
I'm trying to do a non-metric multidimensional scaling using isoMDS.
However, I have some '0' distances in my data, and I'm not sure how to
deal with them. I'd rather not drop rows from the original data, as I am
comparing several datasets (morphology and molecular data) for the same
individuals, and it's interesting to see how much morphological
variation can be associated with an identical genotype.
I've tried replacing the 0's with NA, but the isoMDS appears to stop on
the first iteration and the stress does not improve:
distA # A dist object with 13695 elements, 4 of which == 0
cmdsA <- cmdscale(distA, k=2)
distB <- distA
distB[which(distB==0)] <- NA
isoA <- isoMDS(distB, cmdsA)
initial value 21.835691
final value 21.835691
The other approach I've tried is replacing the 0's with small numbers.
In this case isoMDS does reduce the stress values.
distC <- distA
distC[which(distC==0)] <- 0.001
isoC <- isoMDS(distC)
initial value 21.682854
iter 5 value 16.862093
iter 10 value 16.451800
final value 16.339224
So my questions are: what am I doing wrong in the first example? Why
does isoMDS converge without doing anything? Is replacing the 0's with
small numbers an appropriate alternative?
Thanks for your time,
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