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cmds
2006 Apr 19
3
isoMDS and 0 distances
...#39;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
converged
The other approach I've tried is replacing the 0's with small numbers.
In this case isoMDS does reduce the stress values...