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...stB[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. min(distA[which(distA>0)]) [1] 0.02325581 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 converged So my questions are: what am I doing wrong in the first example? Why does isoMDS converge without doing anything? Is...

...mClus=%f",mTraj[i+nbId*c],mClustersCenter[j+nbClusters*c]); Rprintf("\nDistA=%d Tmp=%d",dist,tmp); tmp = mTraj[i+nbId* c] - mClustersCenter [j+nbClusters* c]; Rprintf("\nDistB=%d Tmp=%d",dist,tmp); dist += (tmp * tmp); Rprintf("\nDistC=%d Tmp=%d",dist,tmp); --- 8< ---- Herer are the stranges results it gives : XXXX mTraj=1.000000 mClus=3.000000 DistA=0 Tmp=0 DistB=0 Tmp=0 DistC=0 Tmp=1074790400 I ask on a C chat, but no one can answer me. Any idea of what wrong ? Thanks Christophe