rlq                   package:ade4                   R Documentation

_R_L_Q _a_n_a_l_y_s_i_s

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

     RLQ analysis performs a double inertia analysis of two arrays (R
     and Q) with a link expressed by a contingency table (L). The rows
     of L correspond to the rows of R and the columns of Q correspond
     to the rows of Q. RLQ analysis is an extension of coinertia
     analysis (see as.coinertia function).

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

     rlq(dudiR, dudiL, dudiQ, scannf = TRUE, nf = 2)
     print.rlq(x, ...)
     plot.rlq(x, xax = 1, yax = 2, ...)
     summary.rlq(object, ...)
     as.coinertia (dudiRLQ, fixed="R")
     randtest.rlq(xtest,nrepet = 999, RV = TRUE, ...)

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

   dudiR: a duality diagram providing from one of the functions
          dudi.hillsmith, dudi.pca, ... 

   dudiL: a duality diagram of the function dudi.coa 

   dudiQ: a duality diagram providing from one of the functions
          dudi.hillsmith, dudi.pca, ... 

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

      nf: if scannf FALSE, an integer indicating the number of kept
          axes 

       x: an rlq object 

     xax: the column number for the x-axis

     yax: the column number for the y-axis

 dudiRLQ: an rlq object 

  object: an rlq object 

   fixed: "R" indicates that dudiR is not modified, otherwise "Q" 

      RV: a logical value indicating whether the test is based on RV or
          inertia 

   xtest: an rlq object 

  nrepet: the number of permutations 

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

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

     Returns a list of class 'dudi', sub-class 'rlq' containing: 

    call: call

    rank: rank

      nf: a numeric value indicating the number of kept axes

      RV: a numeric value, the RV coefficient

     eig: a numeric vector with all the eigenvalues

      lw: a numeric vector with the rows weigths (crossed array)

      cw: a numeric vector with the columns weigths (crossed array)

     tab: a crossed array (CA)

      li: R col = CA row: coordinates

      l1: R col = CA row: normed scores

      co: Q col = CA column: coordinates

      c1: Q col = CA column: normed scores

      lR: the row coordinates (R)

      mR: the normed row scores (R)

      lQ: the row coordinates (Q)

      mQ: the normed row scores (Q)

      aR: the axis onto co-inertia axis (R)

      aQ: the axis onto co-inertia axis (Q)

_W_A_R_N_I_N_G:

     IMPORTANT : row weights for 'dudiR' and 'dudiQ' must be taken from
     'dudiL'.

_N_o_t_e:

     'as.coinertia' transforms a 'rlq' object into a 'coinertia' object
     but user must specify which 'dudi' is fixed and not modified.

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

     Stephane Dray dray@biomserv.univ-lyon1.fr

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

     Doledec, S., Chessel, D., ter Braak, C.J.F. and Champely, S.
     (1996)  Matching species traits to environmental variables: a new
     three-table ordination method. _Environmental and Ecological
     Statistics_,  *3*, 143-166.

     Dray, S., Pettorelli, N., Chessel, D. (2002) Matching data sets
     from two different spatial samplings.  _Journal of Vegetation
     Science_, *13*, 867-874.

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

     'coinertia'

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

     data(aviurba)
        coa1 <- dudi.coa(aviurba$fau, scannf = FALSE, nf = 2)
        dudimil <- dudi.hillsmith(aviurba$mil, scannf = FALSE, nf = 2, row.w = coa1$lw)
        duditrait <- dudi.hillsmith(aviurba$traits, scannf = FALSE, nf = 2, row.w = coa1$cw)
        rlq1 <- rlq(dudimil, coa1, duditrait, scannf = FALSE, nf = 2)
        plot(rlq1)
        summary(rlq1)
        randtest.rlq(rlq1)

