between                 package:ade4                 R Documentation

_B_e_t_w_e_e_n-_C_l_a_s_s _A_n_a_l_y_s_i_s

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

     Performs a particular case of a Principal Component Analysis with
     respect to Instrumental Variables, in which there is only one
     instrumental variable, and it is a factor.

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

     between(dudi, fac, scannf = TRUE, nf = 2)
     plot.between(x, xax = 1, yax = 2, ...) 
     print.between(x, ...) 

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

    dudi: a duality diagram, object of class 'dudi' from one of the
          functions dudi.coa, dudi.pca, ...

     fac: a factor partitioning the rows of 'dudi$tab' in classes

  scannf: a logical value indicating whether the eigenvalues bar plot
          should be displayed

      nf: if scannf FALSE, a numeric value indicating the number of
          kept axes

       x: an object of class 'between'

xax, yax: the numbers of the x-axis and the y-axis

     ...: further arguments passed to or from other methods

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

     Returns a list of subclass 'between' of class 'dudi' (see 'dudi') 

     tab: a data frame class-variables, array of variables means in
          each class

      cw: a numeric vector of the column weigths

      lw: a numeric vector of the group weigths

     eig: a numeric vector with all the eigenvalues

    rank: an integer

      nf: an integer value indicating the number of kept axes

      c1: a data frame with the column normed scores

      l1: a data frame with the class normed scores

      co: a data frame  with the column coordinates

      li: a data frame with the class coordinates

    call: the origin

   ratio: the bewteen-class inertia percentage

      ls: a data frame with the row coordinates

      as: a data frame containing the projection of inertia axes onto
          between axes

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

     Daniel Chessel chessel@biomserv.univ-lyon1.fr

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

     Doldec, S. and Chessel, D. (1987) Rythmes saisonniers et
     composantes stationnelles en milieu aquatique I- Description d'un
     plan d'observations complet par projection de variables. _Acta
     Oecologica, Oecologia Generalis_, *8*, 3, 403-426.

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

     data(meaudret)
     par(mfrow = c(2,2))
     pca1 <- dudi.pca(meaudret$mil, scan = FALSE, nf = 4)
     s.class(pca1$li, meaudret$plan$sta,
         sub = "Principal Component Analysis (mil)", csub = 1.75)
     pca2 <- dudi.pca(meaudret$fau, scal = FALSE, scan = FALSE, nf = 4)
     s.class(pca2$li, meaudret$pla$sta,
         sub = "Principal Component Analysis (fau)", csub = 1.75)
     bet1 <- between(pca1, meaudret$plan$sta, scan = FALSE, nf = 2)
     bet2 <- between(pca2, meaudret$plan$sta, scan = FALSE, nf = 2)
     s.class(bet1$ls, meaudret$plan$sta,
         sub = "Between sites PCA (mil)", csub = 1.75)
     s.class(bet2$ls, meaudret$plan$sta,
         sub = "Between sites PCA (fau)", csub = 1.75)

     par(mfrow = c(1,1))
     coib <- coinertia(bet1, bet2, scann = FALSE)
     plot(coib)

