kdisteuclid               package:ade4               R Documentation

_a _w_a_y _t_o _o_b_t_a_i_n _E_u_c_l_i_d_e_a_n _d_i_s_t_a_n_c_e _m_a_t_r_i_c_e_s

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

     a way to obtain Euclidean distance matrices

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

     kdisteuclid(obj, method = c("lingoes", "cailliez", "quasi"))

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

     obj: an object of class 'kdist' 

  method: a method to convert a distance matrix in a Euclidean one 

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

     returns an object of class 'kdist' with all distances Euclidean.

_N_o_t_e:

     according to the program DistPCoa of P. Legendre and M.J. Anderson
      <URL:
     http://www.fas.umontreal.ca/BIOL/Casgrain/en/labo/distpcoa.html>

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

     Daniel Chessel chessel@biomserv.univ-lyon1.fr

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

     Gower, J.C. and Legendre, P. (1986) Metric and Euclidean
     properties of dissimilarity coefficients. _Journal of
     Classification_,  *3*, 5-48.

     Cailliez, F. (1983) The analytical solution of the additive
     constant problem. _Psychometrika_,  *48*, 305-310.

     Lingoes, J.C. (1971) Somme boundary conditions for a monotone
     analysis of symmetric matrices. _Psychometrika_, *36*, 195-203.

     Legendre, P. and Anderson, M.J. (1999) Distance-based redundancy
     analysis: testing multispecies responses in multifactorial
     ecological experiments. _Ecological Monographs_, *69*, 1-24.

     Legendre, P., and L. Legendre. (1998) Numerical ecology, 2nd
     English edition edition. Elsevier Science BV, Amsterdam.

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

     w <- c(0.8,0.8,0.377350269,0.8,0.377350269,0.377350269) # see ref.
     w <- kdist(w)
     w1 <- c(kdisteuclid(kdist(w), "lingoes"), kdisteuclid(kdist(w), "cailliez"),
         kdisteuclid(kdist(w), "quasi"))
     print(w, print = TRUE)
     print(w1, print = TRUE)

     data(eurodist)
     par(mfrow = c(1, 3))
     eu1 <- kdist(eurodist) # an object of class 'dist'
     plot(data.frame(unclass(c(eu1, kdisteuclid(eu1, "quasi")))), asp = 1)
     title(main = "Quasi") ; abline(0,1)
     plot(data.frame(unclass(c(eu1, kdisteuclid(eu1, "lingoes")))), asp = 1)
     title(main = "Lingoes") ; abline(0,1)
     plot(data.frame(unclass(c(eu1, kdisteuclid(eu1, "cailliez")))), asp = 1)
     title(main = "Cailliez") ; abline(0,1)

