niche                  package:ade4                  R Documentation

_M_e_t_h_o_d _t_o _A_n_a_l_y_s_e _a _p_a_i_r _o_f _t_a_b_l_e_s : _E_n_v_i_r_o_n_m_e_n_t_a_l _a_n_d _F_a_u_n_i_s_t_i_c _D_a_t_a

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

     performs a special multivariate analysis for ecological data.

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

     niche(dudiX, Y, scannf = TRUE, nf = 2)
     print.niche (x, ...) 
     plot.niche (x, xax = 1, yax = 2, ...)

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

   dudiX: a duality diagram providing from a function 'dudi.coa',
          'dudi.pca', ... using an array sites-variables

       Y: a data frame sites-species according to 'dudiX$tab' with no
          columns of zero

  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 object of class 'niche'

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

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

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

     Returns a list of the class 'niche' (sub-class of 'dudi')
     containing : 

    rank: an integer indicating the rank of the studied matrix

      nf: an integer indicating the number of kept axes

      RV: a numeric value indicating the RV coefficient

     eig: a numeric vector with the all eigenvalues

      lw: a data frame with the row weigths (crossed array)

     tab: a data frame with the crossed array (averaging species/sites)

      li: a data frame with the species coordinates

      l1: a data frame with the species normed scores

      co: a data frame with the variable coordinates

      c1: a data frame with the variable normed scores

      ls: a data frame with the site coordinates

      as: a data frame with the axis upon niche axis

_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., Chessel, D. and Gimaret, C. (2000) Niche separation
     in community analysis: a new method. _Ecology_, *81*, 2914-1927.

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

     data(doubs)
     dudi1 <- dudi.pca(doubs$mil, scale = TRUE, scan = FALSE, nf = 3)
     nic1 <- niche(dudi1, doubs$poi, scann = FALSE)

     par(mfrow = c(2,2))
     s.traject(dudi1$li, clab = 0)
     s.traject(nic1$ls, clab = 0)
     s.corcircle(nic1$as)
     s.arrow(nic1$c1)

     par(mfrow = c(5,6))
     for (i in 1:27) s.distri(nic1$ls, as.data.frame(doubs$poi[,i]),
         csub = 2, sub = names(doubs$poi)[i])

     par(mfrow = c(1,1))
     s.arrow(nic1$li, clab = 0.7)

     par(mfrow = c(1,1))
     data(trichometeo)
     pca1 <- dudi.pca(trichometeo$meteo, scan = FALSE)
     nic1 <- niche(pca1, log(trichometeo$fau + 1), scan = FALSE)
     plot(nic1)

     data(rpjdl)
     plot(niche(dudi.pca(rpjdl$mil, scan = FALSE), rpjdl$fau, scan = FALSE))

