mafragh                 package:ade4                 R Documentation

_P_h_y_t_o-_E_c_o_l_o_g_i_c_a_l _S_u_r_v_e_y

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

     This data set gives environmental and spatial informations about
     species and sites.

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

     data(mafragh)

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

     'mafragh' is a list of 6 components.

     _x_y are the coordinates of 97 sites.

     _f_l_o is a data frame with 97 sites and 56 species.

     _e_s_p_n_a_m_e_s is a vector of the names of species.

     _n_e_i_g is the neighbourhood graph of the 97 sites (an object of
          class 'neig').

     _m_i_l is a data frame with 97 sites and 11 environmental variables.

     _p_a_r_t_i_t_i_o_n is a factor classifying the 97 sites in 5 classes.

     _a_r_e_a is a data frame of class 'area'

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

     Belair, G.d. and Bencheikh-Lehocine, M. (1987) Composition et
     dterminisme de la vgtation d'une plaine ctire marcageuse :
     La Mafragh (Annaba, Algrie). _Bulletin d'Ecologie_, *18*,
     393-407.

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

     data(mafragh)
     par(mfrow = c(3,2))
     s.label(mafragh$xy, inc = FALSE, neig = mafragh$neig, 
         sub = "Samples & Neighbourhood graph")
     coa1 <- dudi.coa(mafragh$flo, scan = FALSE)
     s.value(mafragh$xy, coa1$li[,1], sub = "Axis 1 - COA")
     pca1 <- dudi.pca(mafragh$xy, scan = FALSE)
     s.value(mafragh$xy, pca1$li[,1], sub = "Axis 1 - PCA")
     s.class(pca1$li, mafragh$partition, sub = "Plane 1-2 - PCA")
     s.class(coa1$li, mafragh$partition, sub = "Plane 1-2 - COA")
     s.chull(mafragh$xy, mafragh$partition, optchull = 1)
     par(mfrow=c(1,1))

     ## Not run: 
     link1 <- area2link(mafragh$area)
     neig1 <- neig(mat01 = 1*(link1>0))
     nb1 <- neig2nb(neig1)
     par(mfrow = c(2,1))
     area.plot(mafragh$area,center = mafragh$xy,clab=0.75)
     area.plot(mafragh$area,center = mafragh$xy,graph=neig1)
     if (require(maptools, quiet = TRUE) & require(spdep, quiet = TRUE)) {
         lw1 <- apply(link1,1,function(x) x[x>0])
         listw1 <- nb2listw(nb1,lw1)
         coa1 <- dudi.coa(mafragh$flo, scan = FALSE, nf = 4)
         ms1 <- multispati(coa1, listw1, scan = FALSE, nfp = 2, nfn = 0)
         summary(ms1)
         par(mfrow = c(2,2))
         barplot(coa1$eig)
         barplot(ms1$eig)
         s.corcircle(ms1$as)
         plot(coa1$li[,1], ms1$li[,1])
     }
     par(mfrow = c(1,1))
     ## End(Not run)

