5 // Created by SarahsWork on 12/10/13.
6 // Copyright (c) 2013 Schloss Lab. All rights reserved.
12 #include "communitytype.h"
14 /**************************************************************************************************/
16 class Pam : public CommunityTypeFinder {
19 Pam(vector<vector<int> >, vector<vector<double> >, int);
20 vector<double> calcSilhouettes(vector< vector< double> >);
21 double calcCHIndex(vector< vector< double> >);
25 map<int, int> medoid2Partition;
27 vector<vector<double> > dists;
28 vector<vector< double> > Dp; // [numSamples][2] - It contains Dp and Ep. Dp is in [numSamples][0] and Ep is in [numSamples][1]. Dp is the distance between p and the closest sample in S and Ep is the distance between p and the second closest object in S. Both are used in the build and swap phases.
36 /**************************************************************************************************/