avijons                 package:ade4                 R Documentation

_B_i_r_d _s_p_e_c_i_e_s _d_i_s_t_r_i_b_u_t_i_o_n

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

     This data set contains informations about spatial distribution of
     bird species in a zone surrounding the river Rhne near Lyon
     (France).

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

     data(avijons)

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

     'avijons' is a list with the following objects :

     _x_y : a data frame with the coordinates of the sites

     _a_r_e_a : an object of class 'area'

     _f_a_u : a data frame with the abundance of 64 bird species in 91
          sites

     _s_p_e._n_a_m_e_s._f_r : a vector of strings of character with the species
          names in french

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

     Bournaud, M., Amoros, C., Chessel, D., Coulet, M., Doledec, S.,
     Michelot, J.L., Pautou, G., Rostan, J.C., Tachet, H. and
     Thioulouse, J. (1990)  _Peuplements d'oiseaux et proprits des
     cocomplexes de la plaine du Rhne : descripteurs de
     fonctionnement global et gestion des berges._ Rapport programme
     S.R.E.T.I.E., Ministre de l'Environnement CORA et URA CNRS 367,
     Univ. Lyon I.

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

     Thioulouse, J., Chessel, D. and Champely, S. (1995) Multivariate
     analysis of spatial patterns: a unified approach to local and
     global structures. _Environmental and Ecological Statistics_, *2*,
     1-14.

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

     data(avijons)
     w1=dudi.coa(avijons$fau,scannf=FALSE)$li
     area.plot(avijons$area,center=avijons$xy,val=w1[,1],clab=0.75,sub="CA Axis 1",csub=3)
     ## Not run: 
     data(avijons)
     if (require(pixmap,quiet=TRUE)) {
         pnm.eau <- read.pnm(system.file("pictures/avijonseau.pnm",
             package = "ade4"))
         pnm.rou <- read.pnm(system.file("pictures/avijonsrou.pnm",
             package = "ade4"))
         pnm.veg <- read.pnm(system.file("pictures/avijonsveg.pnm",
             package = "ade4"))
         pnm.vil <- read.pnm(system.file("pictures/avijonsvil.pnm",
             package = "ade4"))
         jons.coa <- dudi.coa(avijons$fau, scan = FALSE, nf = 4)
         par(mfcol = c(3,2))
         s.value(avijons$xy, jons.coa$li[,1], pixmap = pnm.rou, inclu = FALSE,
         grid = FALSE, addax = FALSE, cleg = 0, sub = "F1+ROADS", csub = 3)
         s.value(avijons$xy, jons.coa$li[,1], pixmap = pnm.veg, inclu = FALSE,
         grid = FALSE, addax = FALSE, cleg = 0, sub = "F1+TREES", csub = 3)
         s.value(avijons$xy, jons.coa$li[,1], pixmap = pnm.eau, inclu = FALSE,
         grid = FALSE, addax = FALSE, cleg = 0, sub = "F1+WATER", csub = 3)
         s.value(avijons$xy, jons.coa$li[,2], pixmap = pnm.rou, inclu = FALSE,
         grid = FALSE, addax = FALSE, cleg = 0, sub = "F2+ROADS", csub = 3)
         s.value(avijons$xy, jons.coa$li[,2], pixmap = pnm.veg, inclu = FALSE,
         grid = FALSE, addax = FALSE, cleg = 0, sub = "F2+TREES", csub = 3)
         s.value(avijons$xy, jons.coa$li[,2], pixmap = pnm.eau, inclu = FALSE,
         grid = FALSE, addax = FALSE, cleg = 0, sub = "F2+WATER", csub = 3)
     par(mfrow=c(1,1))}

     if (require(maptools, quiet = TRUE) & require(spdep, quiet = TRUE) 
             & require( pixmap, quiet = TRUE) ) {
         link1 <- area2link(avijons$area)
         lw1 <- apply(link1,1,function(x) x[x>0])
         neig1 <- neig(mat01=1*(link1>0))
         nb1 <- neig2nb(neig1)
         listw1 <- nb2listw(nb1,lw1)
         jons.ms <- multispati(jons.coa, listw1, scan = FALSE, nfp = 3,
          nfn = 2)
         summary(jons.ms)
         par(mfrow = c(2,2))
         barplot(jons.coa$eig)
         barplot(jons.ms$eig)
         s.corcircle(jons.ms$as)
         plot(jons.coa$li[,1], jons.ms$li[,1])

         par(mfcol=c(3,2))
         s.value(avijons$xy, jons.ms$li[,1], pixmap = pnm.rou, inclu = FALSE,
         grid = FALSE, addax = FALSE, cleg = 0, sub = "F1+ROADS", csub = 3)
         s.value(avijons$xy, jons.ms$li[,1], pixmap = pnm.veg, inclu = FALSE,
         grid = FALSE, addax = FALSE, cleg = 0, sub = "F1+TREES", csub = 3)
         s.value(avijons$xy, jons.ms$li[,1], pixmap = pnm.eau, inclu = FALSE,
         grid = FALSE, addax = FALSE, cleg = 0, sub = "F1+WATER", csub = 3)
         s.value(avijons$xy, jons.ms$li[,2], pixmap = pnm.rou, inclu = FALSE,
         grid = FALSE, addax = FALSE, cleg = 0, sub = "F2+ROADS", csub = 3)
         s.value(avijons$xy, jons.ms$li[,2], pixmap = pnm.veg, inclu = FALSE,
         grid = FALSE, addax = FALSE, cleg = 0, sub = "F2+TREES", csub = 3)
         s.value(avijons$xy, jons.ms$li[,2], pixmap = pnm.eau, inclu = FALSE,
         grid = FALSE, addax = FALSE, cleg = 0, sub = "F2+WATER", csub = 3)
     par(mfrow=c(1,1))
     }## End(Not run)

