AlignedPairs         package:GraphAlignment         R Documentation

_G_e_t _a_l_i_g_n_e_d _n_o_d_e _p_a_i_r_s

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

     Create a matrix of pairs of aligned nodes from networks A and B
     using the permutation vector P, where P is in the format returned
     by AlignNetworks().

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

     AlignedPairs(A, B, P)

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

       A: adjacency matrix for network A

       B: adjacency matrix for network B

       P: permutation vector to be used as the alignment

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

     This function creates a matrix containing pairs of aligned nodes
     from networks A and B using the permutation vector P, where P is
     in the format returned by AlignNetworks.

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

     The return value is a matrix with two columns. The number of rows
     is equal to the number of aligned node pairs. Each row in the
     matrix denotes a pair of aligned nodes. In each row, the first
     element (index 1) is the label of a node in network A, and the
     second element (index 2) is the label of a node in network B.

_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)
       
       al<-AlignNetworks(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,
         bStart=.1, bEnd=30,
         maxNumSteps=50)
       
       alignedPairs<-AlignedPairs(A=ex$a, B=ex$b, al)

