westafrica               package:ade4               R Documentation

_F_r_e_s_h_w_a_t_e_r _f_i_s_h _z_o_o_g_e_o_g_r_a_p_h_y _i_n _w_e_s_t _A_f_r_i_c_a

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

     This data set contains informations about faunal similarities
     between river basins in West africa.

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

     data(westafrica)

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

     'westafrica' is a list containing the following objects : 

     _t_a_b : a data frame with absence/presence of 268 species (rows) at
          33 embouchures (columns)

     _s_p_e._n_a_m_e_s : a vector of string of characters with the name of
          species

     _s_p_e._b_i_n_a_m_e_s : a data frame with the genus and species (columns) of
          the 256 species (rows)

     _r_i_v._n_a_m_e_s : a vector of string of characters with the name of
          rivers

     _a_t_l_a_n_t_i_c : a data frame with the coordinates of a polygon that
          represents the limits of atlantic (see example)

     _r_i_v._x_y : a data frame with the coordinates of embouchures

     _l_i_n_e_s : a data frame with the coordinates of lines to complete the
          representation (see example)

     _c_a_d_r_e : a data frame with the coordinates of points used to make
          the representation (see example)   

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

     Data provided by B. Hugueny hugueny@biomserv.univ-lyon1.fr.

     Paugy, D., Traor, K. and Diouf, P.F. (1994) Faune ichtyologique
     des eaux douces d'Afrique de l'Ouest.  In _Diversit biologique
     des poissons des eaux douces et saumtres d'Afrique. Synthses
     gographiques_,  Teugels, G.G., Gugan, J.F. and Albaret, J.J.
     (Editors). Annales du Muse Royal de l'Afrique Centrale,  
     Zoologie, N 275, Tervuren, Belgique, 35-66.

     Hugueny, B. (1989) _Biogographie et structure des peuplements de
     Poissons d'eau douce de l'Afrique de l'ouest :  approches
     quantitatives_. Thse de doctorat, Universit Paris 7.

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

     Hugueny, B., and Lvque, C. (1994) Freshwater fish zoogeography
     in west Africa: faunal similarities between river basins.
     _Environmental Biology of Fishes_, *39*, 365-380.

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

     data(westafrica)

     s.label(westafrica$cadre, xlim = c(30,500), ylim = c(50,290),
         cpoi = 0, clab = 0, grid = FALSE, addax = 0)
     old.par <- par(no.readonly = TRUE)
     par(mar = c(0.1, 0.1, 0.1, 0.1))
     rect(30,0,500,290)
     polygon(westafrica$atlantic,col = "lightblue")
     points(westafrica$riv.xy, pch = 20, cex = 1.5)
     apply(westafrica$lines, 1, function(x) segments(x[1], x[2], x[3],
         x[4], lwd = 1))
     apply(westafrica$riv.xy,1, function(x) segments(x[1], x[2], x[3],
         x[4], lwd = 1))
     text(c(175,260,460,420), c(275,200,250,100), c("Senegal","Niger",
         "Niger","Volta"))
     par(srt = 270)
     text(westafrica$riv.xy$x2, westafrica$riv.xy$y2-10, 
         westafrica$riv.names, adj = 0, cex = 0.75)
     par(old.par)
     rm(old.par)

     # multivariate analysis
     afri.w <- data.frame(t(westafrica$tab))
     afri.dist <- dist.binary(afri.w,1)
     afri.pco <- dudi.pco(afri.dist, scan = FALSE, nf = 3)
     par(mfrow = c(3,1))
     barplot(afri.pco$li[,1])
     barplot(afri.pco$li[,2])
     barplot(afri.pco$li[,3])

     if (require(spdep, quiet = TRUE)){
         #multivariate spatial analysis
         afri.neig <- neig(n.line = 33)
         afri.nb <- neig2nb(afri.neig)
         afri.listw <- nb2listw(afri.nb)
         afri.ms <- multispati(afri.pco, afri.listw, scan = FALSE,
             nfposi = 6, nfnega = 0)
         par(mfrow = c(3,1))
         barplot(afri.ms$li[,1])
         barplot(afri.ms$li[,2])
         barplot(afri.ms$li[,3])

         par(mfrow = c(2,2))
         s.label(afri.ms$li, clab = 0.75, cpoi = 0, neig = afri.neig,
            cneig = 1.5)
         s.value(afri.ms$li, afri.ms$li[,3])
         s.value(afri.ms$li, afri.ms$li[,4])
         s.value(afri.ms$li, afri.ms$li[,5])
         summary(afri.ms)
     }

     par(mfrow = c(1,1))
     library(mva)
     plot(hclust(afri.dist,"ward"),h=-0.2)

