some news for ape 3.0-8

[ape.git] / src / mvrs.c

diff --git a/src/mvrs.c b/src/mvrs.c
index d2aa342135a68536e407bfdeb62b3446a6f849e4..fcfdc2520ff140c02e5ad5d59c2109678f587f4d 100644 (file)
--- a/src/mvrs.c
+++ b/src/mvrs.c
@@ -1,6 +1,6 @@
-/* mvrs.c    2011-10-11 */
+/* mvrs.c    2012-04-02 */
 
-/* Copyright 2011 Andrei-Alin Popescu */
+/* Copyright 2011-2012 Andrei-Alin Popescu */
 
 /* This file is part of the R-package `ape'. */
 /* See the file ../COPYING for licensing issues. */
@@ -60,6 +60,8 @@ void mvrs(double *D, double* v,int *N, int *edge1, int *edge2, double *edge_leng
 
              if(k==i || k==j)
                {
+                 if(i!=k)R[give_index(i,j,n)]+=D[give_index(i,k,n)];
+                 if(j!=k)R[give_index(i,j,n)]+=D[give_index(j,k,n)];
                   s[give_index(i,j,n)]++;
                   //Rprintf("%i",s[give_index(i,j,n)]);
 
@@ -129,7 +131,7 @@ void mvrs(double *D, double* v,int *N, int *edge1, int *edge2, double *edge_leng
                         for (j = i + 1; j <= n; j++) {
                                 //Rprintf("S[%i]=%f, S[%i]=%f, D[%i,%i]=%f, B=%f",i,S[i],j,S[j],i,j,D[give_index(i,j,n)],B);
                                 A=S[i]+S[j]-B*D[give_index(i,j,n)];
-                                Rprintf("Q[%i,%i]=%f\n",i,j,A);
+                                //Rprintf("Q[%i,%i]=%f\n",i,j,A);
                                if (A > smallest_S) {
                                        OTU1 = i;
                                        OTU2 = j;
@@ -288,6 +290,8 @@ void mvrs(double *D, double* v,int *N, int *edge1, int *edge2, double *edge_leng
                      {
                        if(j==1 || j==i)
                        {
+                        if(i!=j)newR[give_index(1,i,n-1)]+=new_dist[give_index(i,j,n-1)];
+                        if(1!=j)newR[give_index(1,i,n-1)]+=new_dist[give_index(1,j,n-1)];
                          newS[give_index(1,i,n-1)]++;
                          continue;
                        }
@@ -318,6 +322,7 @@ void mvrs(double *D, double* v,int *N, int *edge1, int *edge2, double *edge_leng
                 {if(new_dist[give_index(1,i,n-1)]==-1)continue;
                  for(j=i+1;j<=n-1;j++)
                   {if(new_dist[give_index(1,j,n-1)]==-1)continue;
+                   if(new_dist[give_index(i,j,n-1)]==-1)continue;
                    newR[give_index(i,j,n-1)]+=(new_dist[give_index(1,i,n-1)]+new_dist[give_index(1,j,n-1)]);
                    newS[give_index(i,j,n-1)]++;
                   }
@@ -392,6 +397,3 @@ void mvrs(double *D, double* v,int *N, int *edge1, int *edge2, double *edge_leng
        edge_length[*N*2 - 5] = (D[0] + D[2] - D[1])/2;
        edge_length[*N*2 - 6] = (D[2] + D[1] - D[0])/2;
 }
-
-
-