ComputeM           package:GraphAlignment           R Documentation

_C_o_m_p_u_t_e _s_c_o_r_e _m_a_t_r_i_x _M

_D_e_s_c_r_i_p_t_i_o_n:

     Compute the score matrix M.

_U_s_a_g_e:

     ComputeM(A, B, R, P, linkScore, selfLinkScore, nodeScore1,
       nodeScore0, lookupLink, lookupNode, clamp=TRUE)

_A_r_g_u_m_e_n_t_s:

       A: adjacency matrix for network A

       B: adjacency matrix for network B

       R: node similarity matrix

       P: permutation vector to be used as the initial alignment (see
          InitialAlignment)

linkScore: link score matrix (see ComputeLinkParameters)

selfLinkScore: self link score matrix (see ComputeLinkParameters)

nodeScore1: node score vector (s1) (see ComputeNodeParameters)

nodeScore0: node score vector for unaligned nodes (s0) (see
          ComputeNodeParameters)

lookupLink: link bin lookup table (see GetBinNumber)

lookupNode: node bin lookup table (see GetBinNumber)

   clamp: clamp values to range when performing bin lookups

_D_e_t_a_i_l_s:

     This function computes the score Matrix M from the network
     adjacency  matrices A and B, the node similarity matrix R, an
     alignment P (given as a  permutation vector) and the node and link
     scores with their associated  binning information. The alignment P
     is either generated by the previous  iterative step, or,
     initially, by using InitialAlignment. The matrix M  is then given
     to the linear assignment solver to compute the new alignment.

_V_a_l_u_e:

     The return value is the score matrix M.

_A_u_t_h_o_r(_s):

     Joern P. Meier, Michal Kolar, Ville Mustonen, Michael Laessig, and
     Johannes Berg

_E_x_a_m_p_l_e_s:

       ex<-GenerateExample(dimA=22, dimB=22, filling=.5, covariance=.6,
         symmetric=TRUE, numOrths=10, correlated=seq(1,18))
       
       pinitial<-InitialAlignment(psize=34, r=ex$r, mode="reciprocal")
       
       lookupLink<-seq(-2,2,.5)
       linkParams<-ComputeLinkParameters(ex$a, ex$b, pinitial, lookupLink)
       
       lookupNode<-c(-.5,.5,1.5)
       nodeParams<-ComputeNodeParameters(dimA=22, dimB=22, ex$r,
         pinitial, lookupNode)
       
       ComputeM(A=ex$a, B=ex$b, R=ex$r, P=pinitial,
         linkScore=linkParams$ls,
         selfLinkScore=linkParams$ls,
         nodeScore1=nodeParams$s1, nodeScore0=nodeParams$s0,
         lookupLink=lookupLink, lookupNode=lookupNode)

