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#__________________ Function MdsDiss __________________
# Mds of a dissimilarity matrix
################################################################
MdsDiss<-function(MatDissimil,ndim=2,metric=TRUE,ties="primary",itmax=5000,eps=1e-06){
#library(smacof)
# Metric Mds of MatDissimil data
res<-smacofSym(MatDissimil,ndim=ndim,type="interval",verbose=FALSE,itmax=itmax,eps=eps)
Config<-scale(res$conf,center=TRUE,scale=FALSE)
# Rotation of the solution
W<- Config%*%t(Config)
bid<-svd(W)
Config<-bid$u[,1:ndim]%*%sqrt(diag(bid$d[1:ndim]))
if (metric==FALSE){
# Non netric Mds of MatDissimil data using metric initialisation
res<-smacofSym(MatDissimil,ndim=ndim,type="ordinal",ties=ties,init=Config,verbose=FALSE,itmax=itmax,eps=eps)
Config<-scale(res$conf,center=TRUE,scale=FALSE)
# Rotation of the solution
W<- Config%*%t(Config)
bid<-svd(W)
bid$d[1:ndim]/sum(bid$d)
Config<-bid$u[,1:ndim]%*%sqrt(diag(bid$d[1:ndim]))
}
# Percentage of inertia
Percent<-bid$d/sum(bid$d)
#Kruskal Stress
Stress<-sqrt(sum((res$dhat-res$confdist)^2)/sum(res$confdist^2))
res<-list(Config=Config,Percent=Percent,Stress=Stress)
return(res)
}
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