euclidify               package:labdsv               R Documentation

_N_e_a_r_e_s_t _E_u_c_l_i_d_e_a_n _S_p_a_c_e _R_e_p_r_e_s_e_n_t_a_t_i_o_n _o_f _a _D_i_s_s_i_m_i_l_a_r_i_t_y _O_b_j_e_c_t

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

     Calculates the nearest Euclidean space representation of a 
     dissimilarity object by iterating the transitive closure of
     Pythagoras' theorem

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

     euclidify(x,upper=FALSE,diag=FALSE)

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

       x: a distance or dissimilarity object returned from 'dist', 
          'vegdist', or 'dsvdis'

   upper: a logical switch to control whether to return the lower
          triangle (upper=FALSE) or upper triangle (upper=TRUE) of the
          distance matrix

    diag: a logical switch to control whether to return the diagonal of
          the distance matrix

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

     Implements a constrained iteration of the transitive closure of
     Pythagoras' theorem, such that the squared distance between any
     two objects is less than or equal to the sum of the squared
     distances from the two objects to all possible  third objects.

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

     an object of class 'dist'

_N_o_t_e:

     Many multivariate statistical methods are designed for euclidean
     spaces, and yet the direct calculation of euclidean distance is
     often inappropriate due to problems with joint absences. 
     euclidify takes any dissimilarity matrix and converts it to the
     closest euclidean representation, generally to avoid negative
     eigenvalues in an eigenanalysis of the matrix.

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

     David W. Roberts droberts@montana.edu <URL:
     http://ecology.msu.montana.edu/droberts>

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://ecology.msu.montana.edu/labdsv/R>

_S_e_e _A_l_s_o:

     'metrify'

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

         data(bryceveg) # returns a vegetation data.frame
         dis.bc <- dsvdis(bryceveg,'bray/curtis') # calculate a Bray/Curtis
                   #     dissimilarity matrix
         dis.euc <- euclidify(dis.bc) # calculate the nearest euclidean representation 
         ## Not run: plot(dis.bc,dis.euc)

