ade4 (version 1.7-5)

westafrica: Freshwater fish zoogeography in west Africa

Description

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

Usage

data(westafrica)

Format

westafrica is a list containing the following objects :

Source

Data provided by B. Hugueny . Paugy, D., Traoré, K. and Diouf, P.F. (1994) Faune ichtyologique des eaux douces d'Afrique de l'Ouest. In Diversité biologique des poissons des eaux douces et saumâtres d'Afrique. Synthèses géographiques, Teugels, G.G., Guégan, J.F. and Albaret, J.J. (Editors). Annales du Musée Royal de l'Afrique Centrale, Zoologie, 275, Tervuren, Belgique, 35--66. Hugueny, B. (1989) Biogéographie et structure des peuplements de Poissons d'eau douce de l'Afrique de l'ouest : approches quantitatives. Thèse de doctorat, Université Paris 7.

References

Hugueny, B., and Lévêque, C. (1994) Freshwater fish zoogeography in west Africa: faunal similarities between river basins. Environmental Biology of Fishes, 39, 365--380.

Examples

data(westafrica)

if(!adegraphicsLoaded()) {
  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$tab))
afri.dist <- dist.binary(afri.w,1)
afri.pco <- dudi.pco(afri.dist, scan = FALSE, nf = 3)
if(adegraphicsLoaded()) {
  G1 <- s1d.barchart(afri.pco$li[, 1:3], p1d.hori = F, plab.cex = 0)
} else {
  par(mfrow = c(3, 1))
  barplot(afri.pco$li[, 1])
  barplot(afri.pco$li[, 2])
  barplot(afri.pco$li[, 3])
}

if(requireNamespace("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)
  
  if(adegraphicsLoaded()) {
    G2 <- s1d.barchart(afri.ms$li[, 1:3], p1d.hori = F, plab.cex = 0)
    
    g31 <- s.label(afri.ms$li, plab.cex = 0.75, ppoi.cex = 0, nb = afri.nb, plot = F)
    g32 <- s.value(afri.ms$li, afri.ms$li[, 3], plot = F)
    g33 <- s.value(afri.ms$li, afri.ms$li[, 4], plot = F)
    g34 <- s.value(afri.ms$li, afri.ms$li[, 5], plot = F)
    G3 <- ADEgS(list(g31, g32, g33, g34), layout = c(2, 2))
    
  } else {
    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))
plot(hclust(afri.dist, "ward.D"), h = -0.2)