GetTD {scellpam}

GetTD

Description

Function that takes a PAM classification (as returned by ApplyPAM) and the dissimilarity matrix and returns the value of the TD function (sum of dissimilarities between each point and its closest medoid, divided by the number of points). This function is mainly for debugging/internal use.

Usage

GetTD(L, dissim_file)

Arguments

L

A list of two numeric vectors, L["med","clasif"], as returned by ApplyPAM (please, consult the help of ApplyPAM for details)

dissim_file

A string with the name of the binary file that contains the symmetric matrix of dissimilarities. Such matrix should have been generated by CalcAndWriteDissimilarityMatrix.

Value

TD The value of the TD function.

Examples

# Synthetic problem: 10 random seeds with coordinates in [0..20]
# to which random values in [-0.1..0.1] are added
M<-matrix(0,100,500)
rownames(M)<-paste0("rn",c(1:100))
for (i in (1:10))
{
 p<-20*runif(500)
 Rf <- matrix(0.2*(runif(5000)-0.5),nrow=10)
 for (k in (1:10))
 {
  M[10*(i-1)+k,]=p+Rf[k,]
 }
}
tmpfile1=paste0(tempdir(),"/pamtest.bin")
tmpdisfile1=paste0(tempdir(),"/pamDL2.bin")
JWriteBin(M,tmpfile1,dtype="float",dmtype="full")
CalcAndWriteDissimilarityMatrix(tmpfile1,tmpdisfile1,distype="L2",restype="float",nthreads=0)
L <- ApplyPAM(tmpdisfile1,10,init_method="BUILD")
# Final value of sum of distances to closest medoid
GetTD(L,tmpdisfile1)