chevaine                package:ade4                R Documentation

_E_n_z_y_m_a_t_i_c _p_o_l_y_m_o_r_p_h_i_s_m _i_n _L_e_u_c_i_s_c_u_s _c_e_p_h_a_l_u_s

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

     This data set contains a list of two components: a spatial map and
     allellic profiles.

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

     data(chevaine)

_F_o_r_m_a_t:

     This data set is a list of two components:

     _t_a_b a data frame with 27 populations and 9 allellic profiles

     _c_o_o a list containing all the elements to build a spatial map

_S_o_u_r_c_e:

     Exemple du logiciel GENETIX.
      Belkhir k. et al. GENETIX, logiciel sous WindowsTM pour la
     gntique des populations.  Laboratoire Gnome, Populations,
     Interactions CNRS UMR 5000, Universit de Montpellier II,
     Montpellier (France). <URL:
     http://www.univ-montp2.fr/~genetix/genetix/genetix.htm>

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

     Guinand B., Bouvet Y. and Brohon B. (1996) Spatial aspects of
     genetic differentiation of the European chub in the Rhone River
     basin. _Journal of Fish Biology_, *49*, 714-726.

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

     data(chevaine)
     'fun.chevaine' <- function(label=TRUE) {
         opar <- par(mar = par("mar"))
             on.exit(par(opar))
             par(mar = c(0.1, 0.1, 0.1, 0.1))
         s.label(chevaine$coo$poi, xlim = c(-20,400), clab = 0, cpoi = 0)
         invisible(lapply(chevaine$coo$lac, polygon,col = "blue", type = "l", lwd = 2)) 
         invisible(lapply(chevaine$coo$riv, points, col = "blue", type = "l", lwd = 2))
         if (label){
             s.label(chevaine$coo$poi, clab = 0.75, add.p = TRUE)
             s.label(chevaine$coo$sta, add.p = TRUE, clab = 0.5)
         }
         arrows(200,100,300,100, code = 3, angle = 15, length = 0.2)
         text(250,125,"50 Km")
     }

     fun.chevaine()

     che.genet <- freq2genet(chevaine$tab)
     che.pca <- dudi.pca(che.genet$tab, center = che.genet$center, scannf = FALSE, nf = 3)

     par(mfrow = c(1,2))
     fun.chevaine(FALSE)
     s.value(chevaine$coo$sta, che.pca$li[,1], csi = 2, add.p = TRUE)
     fun.chevaine(FALSE)
     s.value(chevaine$coo$sta, che.pca$li[,2], csi = 2, add.p = TRUE)

     w = prep.fuzzy.var (che.genet$tab, che.genet$loc.blocks)
     che.fca <- dudi.fca(w, scannf = FALSE, nf = 3)

     fun.chevaine(FALSE)
     s.value(chevaine$coo$sta, che.fca$li[,1], csi = 1.5, add.p = TRUE)
     fun.chevaine(FALSE)
     s.value(chevaine$coo$sta, che.fca$li[,2], csi = 1.5, add.p = TRUE)

